diff --git a/README.md b/README.md
index 91d48e5e50e9899cfa1270ff2c5522ed1e40ed4f..966b03ca726183d87db8f3ce6599949094a40ccf 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,7 @@ Install CIFTools `npm install ciftools -g`
cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+ cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
**GraphQL schemas**
diff --git a/data/cif-core.csv b/data/cif-core.csv
deleted file mode 100644
index 25ce0320c9e0e7c60a833309094d6a27814b7a4c..0000000000000000000000000000000000000000
--- a/data/cif-core.csv
+++ /dev/null
@@ -1,60 +0,0 @@
-audit.block_doi
-
-database_code.depnum_ccdc_archive
-
-chemical.name_systematic
-chemical.name_common
-chemical.melting_point
-
-chemical_formula.moiety
-chemical_formula.sum
-chemical_formula.weight
-
-atom_type.symbol
-atom_type.description
-
-atom_type_scat.dispersion_real
-atom_type_scat.dispersion_imag
-atom_type_scat.source
-
-space_group.crystal_system
-space_group.name_H-M_full
-space_group_symop.operation_xyz
-
-cell.length_a
-cell.length_b
-cell.length_c
-cell.angle_alpha
-cell.angle_beta
-cell.angle_gamma
-cell.volume
-cell.formula_units_Z
-
-atom_site.label
-atom_site.type_symbol
-atom_site.fract_x
-atom_site.fract_y
-atom_site.fract_z
-atom_site.U_iso_or_equiv
-atom_site.adp_type
-atom_site.occupancy
-atom_site.calc_flag
-atom_site.refinement_flags
-atom_site.disorder_assembly
-atom_site.disorder_group
-
-atom_site.site_symmetry_multiplicity
-
-atom_site_aniso.label
-atom_site_aniso.U_11
-atom_site_aniso.U_22
-atom_site_aniso.U_33
-atom_site_aniso.U_23
-atom_site_aniso.U_13
-atom_site_aniso.U_12
-
-geom_bond.atom_site_label_1
-geom_bond.atom_site_label_2
-geom_bond.distance
-geom_bond.site_symmetry_2
-geom_bond.publ_flag
\ No newline at end of file
diff --git a/data/rcsb-graphql/codegen.yml b/data/rcsb-graphql/codegen.yml
index d470dd1734e115746ca3d64fd343534388165706..726a47193be3b15ac8085a40842d210863f722c0 100644
--- a/data/rcsb-graphql/codegen.yml
+++ b/data/rcsb-graphql/codegen.yml
@@ -1,7 +1,7 @@
-schema: http://data-beta.rcsb.org/graphql
+schema: https://data-beta.rcsb.org/graphql
documents: './src/mol-model-props/rcsb/graphql/symmetry.gql.ts'
generates:
- './src/mol-model-props/rcsb/graphql/types.d.ts':
+ './src/mol-model-props/rcsb/graphql/types.ts':
plugins:
- add: '/* eslint-disable */'
- time
diff --git a/package-lock.json b/package-lock.json
index 68aca65ce3021d1fc472ecb3836f900f775eb067..5cd5ce9e9f5b8b0c6b8e3a51e9cbd0b25dd54a4d 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 094894bad700aceefd16acaa1e26d35d6a78add6..a376d66ec660ecd0a6d414d448da20af92c989c0 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "0.5.0-dev.1",
+ "version": "0.5.1",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -72,9 +72,9 @@
"@graphql-codegen/typescript-graphql-request": "^1.12.2",
"@graphql-codegen/typescript-operations": "^1.12.2",
"@types/cors": "^2.8.6",
- "@typescript-eslint/eslint-plugin": "^2.19.2",
- "@typescript-eslint/eslint-plugin-tslint": "^2.19.2",
- "@typescript-eslint/parser": "^2.19.2",
+ "@typescript-eslint/eslint-plugin": "^2.20.0",
+ "@typescript-eslint/eslint-plugin-tslint": "^2.20.0",
+ "@typescript-eslint/parser": "^2.20.0",
"benchmark": "^2.1.4",
"circular-dependency-plugin": "^5.2.0",
"concurrently": "^5.1.0",
@@ -82,7 +82,7 @@
"css-loader": "^3.4.2",
"eslint": "^6.8.0",
"extra-watch-webpack-plugin": "^1.0.3",
- "file-loader": "^5.0.2",
+ "file-loader": "^5.1.0",
"fs-extra": "^8.1.0",
"http-server": "^0.12.1",
"jest": "^25.1.0",
@@ -95,20 +95,20 @@
"sass-loader": "^8.0.2",
"simple-git": "^1.131.0",
"style-loader": "^1.1.3",
- "ts-jest": "^25.2.0",
- "typescript": "^3.7.5",
- "webpack": "^4.41.5",
- "webpack-cli": "^3.3.10"
+ "ts-jest": "^25.2.1",
+ "typescript": "^3.8.2",
+ "webpack": "^4.41.6",
+ "webpack-cli": "^3.3.11"
},
"dependencies": {
"@types/argparse": "^1.0.38",
"@types/benchmark": "^1.0.31",
"@types/compression": "1.7.0",
"@types/express": "^4.17.2",
- "@types/jest": "^25.1.2",
- "@types/node": "^13.7.0",
+ "@types/jest": "^25.1.3",
+ "@types/node": "^13.7.4",
"@types/node-fetch": "^2.5.4",
- "@types/react": "^16.9.19",
+ "@types/react": "^16.9.22",
"@types/react-dom": "^16.9.5",
"@types/swagger-ui-dist": "3.0.5",
"argparse": "^1.0.10",
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index 3f8f15056b1e12358d4562042e570cdb8c45aa3b..79c65460b2a7fb765db156c3f5e0804b2feeb805 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -63,7 +63,7 @@ class BasicWrapper {
return parsed
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.CustomModelProperties, { properties: [StripedResidues.propertyProvider.descriptor.name] }, { ref: 'props', state: { isGhost: false } })
+ .apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [StripedResidues.propertyProvider.descriptor.name], properties: {} }, { ref: 'props', state: { isGhost: false } })
.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
}
diff --git a/src/apps/chem-comp-bond/create-table.ts b/src/apps/chem-comp-bond/create-table.ts
index 84091a6d6fc1fe54c9d80585a8a78b80c9a46681..1e26c4935c4e44adf886ccfaee13c736e08ff9f4 100644
--- a/src/apps/chem-comp-bond/create-table.ts
+++ b/src/apps/chem-comp-bond/create-table.ts
@@ -144,9 +144,9 @@ async function createBonds() {
const comp_id: string[] = []
const atom_id_1: string[] = []
const atom_id_2: string[] = []
- const value_order: string[] = []
- const pdbx_aromatic_flag: string[] = []
- const pdbx_stereo_config: string[] = []
+ const value_order: typeof mmCIF_chemCompBond_schema['value_order']['T'][] = []
+ const pdbx_aromatic_flag: typeof mmCIF_chemCompBond_schema['pdbx_aromatic_flag']['T'][] = []
+ const pdbx_stereo_config: typeof mmCIF_chemCompBond_schema['pdbx_stereo_config']['T'][] = []
const molstar_protonation_variant: string[] = []
function addBonds(compId: string, ccb: CCB, protonationVariant: boolean) {
diff --git a/src/apps/state-docs/pd-to-md.ts b/src/apps/state-docs/pd-to-md.ts
index 578753df00e954937af3058c043e397aff650d43..f0df30519f9e4e18dfd3cd60509d6b45baf244f0 100644
--- a/src/apps/state-docs/pd-to-md.ts
+++ b/src/apps/state-docs/pd-to-md.ts
@@ -22,6 +22,7 @@ function paramInfo(param: PD.Any, offset: number): string {
case 'color-list': return `One of ${oToS(param.options)}`;
case 'vec3': return `3D vector [x, y, z]`;
case 'file': return `JavaScript File Handle`;
+ case 'file-list': return `JavaScript FileList Handle`;
case 'select': return `One of ${oToS(param.options)}`;
case 'text': return 'String';
case 'interval': return `Interval [min, max]`;
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 980d525551d478941f88f7101e3158e94f55df51..507ef7a19c151e9e7dfbb02c55540c4fbcfd25b5 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -16,6 +16,8 @@ import { openCif, downloadCif } from './helpers';
import { Vec3 } from '../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
import { Sequence } from '../../mol-model/sequence';
+import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
async function downloadFromPdb(pdb: string) {
@@ -50,8 +52,10 @@ export function residueLabel(model: Model, rI: number) {
export function printSecStructure(model: Model) {
console.log('\nSecondary Structure\n=============');
const { residues } = model.atomicHierarchy;
- const { key, elements } = model.properties.secondaryStructure;
+ const secondaryStructure = ModelSecondaryStructure.Provider.get(model);
+ if (!secondaryStructure) return
+ const { key, elements } = secondaryStructure
const count = residues._rowCount;
let rI = 0;
while (rI < count) {
@@ -148,7 +152,7 @@ export function printRings(structure: Structure) {
export function printUnits(structure: Structure) {
console.log('\nUnits\n=============');
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
for (const unit of structure.units) {
l.unit = unit;
@@ -179,7 +183,8 @@ export function printUnits(structure: Structure) {
export function printSymmetryInfo(model: Model) {
console.log('\nSymmetry Info\n=============');
- const { symmetry } = model;
+ const symmetry = ModelSymmetry.Provider.get(model)
+ if (!symmetry) return
const { size, anglesInRadians } = symmetry.spacegroup.cell;
console.log(`Spacegroup: ${symmetry.spacegroup.name} size: ${Vec3.toString(size)} angles: ${Vec3.toString(anglesInRadians)}`);
console.log(`Assembly names: ${symmetry.assemblies.map(a => a.id).join(', ')}`);
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 352bd8a7ea68b7739d38bedbfb660f3438ae5a9d..bae20822d53b91a0b15532b84b2d34809b01da64 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -11,7 +11,7 @@ import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Ingredient, CellPacking, Cell } from './data';
import { getFromPdb, getFromCellPackDB } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../../../mol-model/structure';
-import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF, MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../../../mol-model-formats/structure/pdb';
import { Mat4, Vec3, Quat } from '../../../../mol-math/linear-algebra';
import { SymmetryOperator } from '../../../../mol-math/geometry';
@@ -28,11 +28,10 @@ import { compile } from '../../../../mol-script/runtime/query/compiler';
import { UniformColorThemeProvider } from '../../../../mol-theme/color/uniform';
import { ThemeRegistryContext } from '../../../../mol-theme/theme';
import { ColorTheme } from '../../../../mol-theme/color';
-import { _parse_mmCif } from '../../../../mol-model-formats/structure/mmcif/parser';
-import { ModelFormat } from '../../../../mol-model-formats/structure/format';
import { CifCategory, CifField } from '../../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { Column } from '../../../../mol-data/db';
+import { createModels } from '../../../../mol-model-formats/structure/basic/parser';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`
@@ -124,7 +123,10 @@ function getAssembly(transforms: Mat4[], structure: Structure) {
}
function getCifCurve(name: string, transforms: Mat4[], model: Model) {
- const d = model.sourceData.data.atom_site
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('mmcif source data needed')
+
+ const { db } = model.sourceData.data
+ const d = db.atom_site
const n = d._rowCount
const rowCount = n * transforms.length
@@ -201,8 +203,8 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
}
const categories = {
- entity: CifCategory.ofTable('entity', model.sourceData.data.entity),
- chem_comp: CifCategory.ofTable('chem_comp', model.sourceData.data.chem_comp),
+ entity: CifCategory.ofTable('entity', db.entity),
+ chem_comp: CifCategory.ofTable('chem_comp', db.chem_comp),
atom_site: CifCategory.ofFields('atom_site', _atom_site)
}
@@ -217,8 +219,8 @@ async function getCurve(name: string, transforms: Mat4[], model: Model) {
const cif = getCifCurve(name, transforms, model)
const curveModelTask = Task.create('Curve Model', async ctx => {
- const format = ModelFormat.mmCIF(cif)
- const models = await _parse_mmCif(format, ctx)
+ const format = MmcifFormat.fromFrame(cif)
+ const models = await createModels(format.data.db, format, ctx)
return models[0]
})
diff --git a/src/examples/proteopedia-wrapper/coloring.ts b/src/examples/proteopedia-wrapper/coloring.ts
index b694129e1dcc3e088dfd65416fa023472f361056..0f7bc4b3a5f423f5ccabcdb4f5cb38ca521508fb 100644
--- a/src/examples/proteopedia-wrapper/coloring.ts
+++ b/src/examples/proteopedia-wrapper/coloring.ts
@@ -54,7 +54,7 @@ export function createProteopediaCustomTheme(colors: number[]) {
const colors = props.colors, colorCount = colors.length, defaultColor = colors[0].color;
if (ctx.structure) {
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(ctx.structure)
const { models } = ctx.structure
const asymIdSerialMap = new Map<string, number>()
for (let i = 0, il = models.length; i < il; ++i) {
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index d376596d3157a6b9bda160bf5bb9346443dc69ae..8611b4ba02d43c5e12770e9935159e4a7520e08f 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -9,6 +9,7 @@ import { BuiltInStructureRepresentationsName } from '../../mol-repr/structure/re
import { BuiltInColorThemeName } from '../../mol-theme/color';
import { AminoAcidNames } from '../../mol-model/structure/model/types';
import { PluginContext } from '../../mol-plugin/context';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
export interface ModelInfo {
hetResidues: { name: string, indices: ResidueIndex[] }[],
@@ -72,10 +73,11 @@ export namespace ModelInfo {
}
const preferredAssemblyId = await pref;
+ const symmetry = ModelSymmetry.Provider.get(model)
return {
hetResidues: hetResidues,
- assemblies: model.symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })),
+ assemblies: symmetry ? symmetry.assemblies.map(a => ({ id: a.id, details: a.details, isPreferred: a.id === preferredAssemblyId })) : [],
preferredAssemblyId
};
}
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index c83e4d66bb6546817600de648eb6428de0efd004..7254ea8b8727546c2c030bd517a0879cec262d2d 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -94,7 +94,7 @@ class MolStarProteopediaWrapper {
const model = this.state.build().to(StateElements.Model);
const s = model
- .apply(StateTransforms.Model.CustomModelProperties, { properties: [EvolutionaryConservation.propertyProvider.descriptor.name] }, { ref: StateElements.ModelProps, state: { isGhost: false } })
+ .apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [EvolutionaryConservation.propertyProvider.descriptor.name], properties: {} }, { ref: StateElements.ModelProps, state: { isGhost: false } })
.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: StateElements.Assembly });
s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: StateElements.Sequence });
diff --git a/src/mol-canvas3d/camera.ts b/src/mol-canvas3d/camera.ts
index dc64ccf73d9b178d0cca0bd5a9af3fdcc042a537..37ac7d866989e92b87663c2b3466a63313ab4b76 100644
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -264,12 +264,13 @@ function updatePers(camera: Camera) {
function updateClip(camera: Camera) {
const { radiusNear, radiusFar, mode, fog, clipFar } = camera.state
- const cDist = Vec3.distance(camera.position, camera.target)
- let near = cDist - radiusNear
- let far = cDist + (clipFar ? radiusNear : radiusFar)
+ const normalizedFar = clipFar ? radiusNear : radiusFar
+ const cameraDistance = Vec3.distance(camera.position, camera.target)
+ let near = cameraDistance - radiusNear
+ let far = cameraDistance + normalizedFar
const fogNearFactor = -(50 - fog) / 50
- let fogNear = cDist - (radiusNear * fogNearFactor)
+ let fogNear = cameraDistance - (normalizedFar * fogNearFactor)
let fogFar = far
if (mode === 'perspective') {
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index cf08c02c979b3ad50860a19b98679de956b62b31..a00217f4b7b7aed0e509e252a7fd5ffcd6483c66 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
import { BehaviorSubject, Subscription } from 'rxjs';
@@ -37,7 +38,7 @@ import { isDebugMode } from '../mol-util/debug';
export const Canvas3DParams = {
cameraMode: PD.Select('perspective', [['perspective', 'Perspective'], ['orthographic', 'Orthographic']]),
- cameraFog: PD.Numeric(50, { min: 1, max: 100, step: 1 }),
+ cameraFog: PD.Numeric(50, { min: 0, max: 100, step: 1 }),
cameraClipFar: PD.Boolean(true),
cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
transparentBackground: PD.Boolean(false),
@@ -56,30 +57,33 @@ export { Canvas3D }
interface Canvas3D {
readonly webgl: WebGLContext,
- add: (repr: Representation.Any) => Promise<void>
- remove: (repr: Representation.Any) => Promise<void>
- update: (repr?: Representation.Any, keepBoundingSphere?: boolean) => void
- clear: () => void
-
- // draw: (force?: boolean) => void
- requestDraw: (force?: boolean) => void
- animate: () => void
- identify: (x: number, y: number) => PickingId | undefined
- mark: (loci: Representation.Loci, action: MarkerAction) => void
- getLoci: (pickingId: PickingId) => Representation.Loci
+ add(repr: Representation.Any): void
+ remove(repr: Representation.Any): void
+ /**
+ * This function must be called if animate() is not set up so that add/remove actions take place.
+ */
+ commit(isSynchronous?: boolean): void
+ update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
+ clear(): void
+
+ requestDraw(force?: boolean): void
+ animate(): void
+ identify(x: number, y: number): PickingId | undefined
+ mark(loci: Representation.Loci, action: MarkerAction): void
+ getLoci(pickingId: PickingId): Representation.Loci
readonly didDraw: BehaviorSubject<now.Timestamp>
readonly reprCount: BehaviorSubject<number>
- handleResize: () => void
+ handleResize(): void
/** Focuses camera on scene's bounding sphere, centered and zoomed. */
- resetCamera: () => void
+ requestCameraReset(durationMs?: number): void
readonly camera: Camera
readonly boundingSphere: Readonly<Sphere3D>
- downloadScreenshot: () => void
- getPixelData: (variant: GraphicsRenderVariant) => PixelData
- setProps: (props: Partial<Canvas3DProps>) => void
- getImagePass: () => ImagePass
+ downloadScreenshot(): void
+ getPixelData(variant: GraphicsRenderVariant): PixelData
+ setProps(props: Partial<Canvas3DProps>): void
+ getImagePass(): ImagePass
/** Returns a copy of the current Canvas3D instance props */
readonly props: Readonly<Canvas3DProps>
@@ -87,7 +91,7 @@ interface Canvas3D {
readonly stats: RendererStats
readonly interaction: Canvas3dInteractionHelper['events']
- dispose: () => void
+ dispose(): void
}
const requestAnimationFrame = typeof window !== 'undefined' ? window.requestAnimationFrame : (f: (time: number) => void) => setImmediate(()=>f(Date.now()))
@@ -186,6 +190,7 @@ namespace Canvas3D {
let drawPending = false
let cameraResetRequested = false
+ let nextCameraResetDuration: number | undefined = void 0
function getLoci(pickingId: PickingId) {
let loci: Loci = EmptyLoci
@@ -220,7 +225,7 @@ namespace Canvas3D {
}
function render(force: boolean) {
- if (scene.isCommiting || webgl.isContextLost) return false
+ if (webgl.isContextLost) return false
let didRender = false
controls.update(currentTime)
@@ -262,7 +267,9 @@ namespace Canvas3D {
function animate() {
currentTime = now();
+ commit();
camera.transition.tick(currentTime);
+
draw(false);
if (!camera.transition.inTransition && !webgl.isContextLost) {
interactionHelper.tick(currentTime);
@@ -274,22 +281,35 @@ namespace Canvas3D {
return webgl.isContextLost ? undefined : pickPass.identify(x, y)
}
- async function commit(renderObjects?: readonly GraphicsRenderObject[]) {
- scene.update(renderObjects, false)
+ function commit(isSynchronous: boolean = false) {
+ const allCommited = commitScene(isSynchronous);
+ // Only reset the camera after the full scene has been commited.
+ if (allCommited) resolveCameraReset();
+ }
- return runTask(scene.commit()).then(() => {
- if (cameraResetRequested && !scene.isCommiting) {
- const { center, radius } = scene.boundingSphere
- camera.focus(center, radius, radius)
- cameraResetRequested = false
- }
- if (debugHelper.isEnabled) debugHelper.update()
- requestDraw(true)
- reprCount.next(reprRenderObjects.size)
- })
+ function resolveCameraReset() {
+ if (!cameraResetRequested) return;
+ const { center, radius } = scene.boundingSphere;
+ const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration
+ camera.focus(center, radius, radius, duration);
+ nextCameraResetDuration = void 0;
+ cameraResetRequested = false;
+ }
+
+ const sceneCommitTimeoutMs = 250;
+ function commitScene(isSynchronous: boolean) {
+ if (!scene.needsCommit) return true;
+
+ if (!scene.commit(isSynchronous ? void 0 : sceneCommitTimeoutMs)) return false;
+
+ if (debugHelper.isEnabled) debugHelper.update();
+ reprCount.next(reprRenderObjects.size);
+ return true;
}
function add(repr: Representation.Any) {
+ registerAutoUpdate(repr);
+
const oldRO = reprRenderObjects.get(repr)
const newRO = new Set<GraphicsRenderObject>()
repr.renderObjects.forEach(o => newRO.add(o))
@@ -303,7 +323,35 @@ namespace Canvas3D {
repr.renderObjects.forEach(o => scene.add(o))
}
reprRenderObjects.set(repr, newRO)
- return commit(repr.renderObjects)
+
+ scene.update(repr.renderObjects, false)
+ }
+
+ function remove(repr: Representation.Any) {
+ unregisterAutoUpdate(repr);
+
+ const renderObjects = reprRenderObjects.get(repr)
+ if (renderObjects) {
+ renderObjects.forEach(o => scene.remove(o))
+ reprRenderObjects.delete(repr)
+ scene.update(repr.renderObjects, false, true)
+ }
+ }
+
+ function registerAutoUpdate(repr: Representation.Any) {
+ if (reprUpdatedSubscriptions.has(repr)) return;
+
+ reprUpdatedSubscriptions.set(repr, repr.updated.subscribe(_ => {
+ if (!repr.state.syncManually) add(repr);
+ }))
+ }
+
+ function unregisterAutoUpdate(repr: Representation.Any) {
+ const updatedSubscription = reprUpdatedSubscriptions.get(repr);
+ if (updatedSubscription) {
+ updatedSubscription.unsubscribe();
+ reprUpdatedSubscriptions.delete(repr);
+ }
}
handleResize()
@@ -311,25 +359,9 @@ namespace Canvas3D {
return {
webgl,
- add: (repr: Representation.Any) => {
- reprUpdatedSubscriptions.set(repr, repr.updated.subscribe(_ => {
- if (!repr.state.syncManually) add(repr)
- }))
- return add(repr)
- },
- remove: (repr: Representation.Any) => {
- const updatedSubscription = reprUpdatedSubscriptions.get(repr)
- if (updatedSubscription) {
- updatedSubscription.unsubscribe()
- }
- const renderObjects = reprRenderObjects.get(repr)
- if (renderObjects) {
- renderObjects.forEach(o => scene.remove(o))
- reprRenderObjects.delete(repr)
- return commit()
- }
- return Promise.resolve()
- },
+ add,
+ remove,
+ commit,
update: (repr, keepSphere) => {
if (repr) {
if (!reprRenderObjects.has(repr)) return;
@@ -356,14 +388,9 @@ namespace Canvas3D {
getLoci,
handleResize,
- resetCamera: () => {
- if (scene.isCommiting) {
- cameraResetRequested = true
- } else {
- const { center, radius } = scene.boundingSphere
- camera.focus(center, radius, radius, p.cameraResetDurationMs)
- requestDraw(true);
- }
+ requestCameraReset: (durationMs) => {
+ nextCameraResetDuration = durationMs;
+ cameraResetRequested = true;
},
camera,
boundingSphere: scene.boundingSphere,
diff --git a/src/mol-canvas3d/helper/bounding-sphere-helper.ts b/src/mol-canvas3d/helper/bounding-sphere-helper.ts
index 4d0d18e2c026da2e68c7490c944144ba005974ea..69f69194144483bc2560bfe4d9bafbb56e3eddd6 100644
--- a/src/mol-canvas3d/helper/bounding-sphere-helper.ts
+++ b/src/mol-canvas3d/helper/bounding-sphere-helper.ts
@@ -82,7 +82,7 @@ export class BoundingSphereHelper {
})
this.scene.update(void 0, false)
- this.scene.syncCommit()
+ this.scene.commit()
}
syncVisibility() {
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index 1f25b531ea611511f567c059028320ce2ce7b227..8f242202ca93a747e465b0587c6fa6d8d7f1fee8 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -37,7 +37,7 @@ namespace Column {
export type Coordinate = { '@type': 'coord', T: number } & Base<'float'>
export type Tensor = { '@type': 'tensor', T: Tensors.Data, space: Tensors.Space, baseType: Int | Float } & Base<'tensor'>
- export type Aliased<T> = { '@type': 'aliased', T: T } & Base<'str' | 'int'>
+ export type Aliased<T> = { '@type': 'aliased', T: T } & Base<T extends string ? 'str' : 'int'>
export type List<T extends number|string> = { '@type': 'list', T: T[], separator: string, itemParse: (x: string) => T } & Base<'list'>
export const str: Str = { '@type': 'str', T: '', valueType: 'str' };
@@ -137,6 +137,14 @@ namespace Column {
return arrayColumn({ array, schema: Schema.str });
}
+ export function ofStringAliasArray<T extends string>(array: ArrayLike<T>) {
+ return arrayColumn<Schema.Aliased<T>>({ array, schema: Schema.Aliased(Schema.str) });
+ }
+
+ export function ofStringListArray<T extends string>(array: ArrayLike<T[]>, separator = ',') {
+ return arrayColumn<Schema.List<T>>({ array, schema: Schema.List<T>(separator, x => x as T) });
+ }
+
export function ofIntTokens(tokens: Tokens) {
const { count, data, indices } = tokens
return lambdaColumn({
diff --git a/src/mol-data/db/table.ts b/src/mol-data/db/table.ts
index 693fe3cd077b9c74434a450e259891ca75cd019c..b202468232b649e0591a39a496fc178bdf5d2f5a 100644
--- a/src/mol-data/db/table.ts
+++ b/src/mol-data/db/table.ts
@@ -9,7 +9,7 @@ import { sortArray } from '../util/sort'
import { StringBuilder } from '../../mol-util';
/** A collection of columns */
-type Table<Schema extends Table.Schema> = {
+type Table<Schema extends Table.Schema = any> = {
readonly _rowCount: number,
readonly _columns: ReadonlyArray<string>,
readonly _schema: Schema
@@ -21,7 +21,8 @@ namespace Table {
export type Columns<S extends Schema> = { [C in keyof S]: Column<S[C]['T']> }
export type Row<S extends Schema> = { [C in keyof S]: S[C]['T'] }
export type Arrays<S extends Schema> = { [C in keyof S]: ArrayLike<S[C]['T']> }
- export type PartialTable<S extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & { [C in keyof S]?: Column<S[C]['T']> }
+ export type PartialColumns<S extends Schema> = { [C in keyof S]?: Column<S[C]['T']> }
+ export type PartialTable<S extends Table.Schema> = { readonly _rowCount: number, readonly _columns: ReadonlyArray<string> } & PartialColumns<S>
export function is(t: any): t is Table<any> {
return t && typeof t._rowCount === 'number' && !!t._columns && !!t._schema;
@@ -47,6 +48,19 @@ namespace Table {
return { _rowCount, _columns, _schema: schema, ...(columns as any) };
}
+ export function ofPartialColumns<S extends Schema, R extends Table<S> = Table<S>>(schema: S, partialColumns: PartialColumns<S>, rowCount: number): R {
+ const ret = Object.create(null);
+ const columns = Object.keys(schema);
+ ret._rowCount = rowCount;
+ ret._columns = columns;
+ ret._schema = schema;
+ for (const k of columns) {
+ if (k in partialColumns) ret[k] = partialColumns[k]
+ else ret[k] = Column.Undefined(rowCount, schema[k])
+ }
+ return ret;
+ }
+
export function ofUndefinedColumns<S extends Schema, R extends Table<S> = Table<S>>(schema: S, rowCount: number): R {
const ret = Object.create(null);
const columns = Object.keys(schema);
@@ -59,7 +73,7 @@ namespace Table {
return ret;
}
- export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, rows: ArrayLike<Partial<Row<S>>>): R {
+ export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: S, rows: ArrayLike<Partial<Row<S>>>): R {
const ret = Object.create(null);
const rowCount = rows.length;
const columns = Object.keys(schema);
@@ -77,14 +91,19 @@ namespace Table {
return ret as R;
}
- export function ofArrays<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, arrays: Arrays<S>): R {
+ export function ofArrays<S extends Schema, R extends Table<S> = Table<S>>(schema: S, arrays: Partial<Arrays<S>>): R {
const ret = Object.create(null);
const columns = Object.keys(schema);
- ret._rowCount = arrays[columns[0]].length;
+ ret._rowCount = 0;
ret._columns = columns;
ret._schema = schema;
for (const k of columns) {
- (ret as any)[k] = typeof arrays[k] !== 'undefined' ? Column.ofArray({ array: arrays[k], schema: schema[k] }) : Column.Undefined(ret._rowCount, schema[k]);
+ if (typeof arrays[k] !== 'undefined') {
+ (ret as any)[k] = Column.ofArray({ array: arrays[k]!, schema: schema[k] });
+ ret._rowCount = arrays[k]?.length;
+ } else {
+ (ret as any)[k] = Column.Undefined(ret._rowCount, schema[k]);
+ }
}
return ret as R;
}
@@ -153,7 +172,7 @@ namespace Table {
}
/** Sort and return a new table */
- export function sort<T extends Table<S>, S extends Schema>(table: T, cmp: (i: number, j: number) => number) {
+ export function sort<T extends Table>(table: T, cmp: (i: number, j: number) => number) {
const indices = new Int32Array(table._rowCount);
for (let i = 0, _i = indices.length; i < _i; i++) indices[i] = i;
sortArray(indices, (_, i, j) => cmp(i, j));
@@ -177,7 +196,7 @@ namespace Table {
return ret;
}
- export function areEqual<T extends Table<Schema>>(a: T, b: T) {
+ export function areEqual<T extends Table<any>>(a: T, b: T) {
if (a._rowCount !== b._rowCount) return false;
if (a._columns.length !== b._columns.length) return false;
for (const c of a._columns) {
diff --git a/src/mol-gl/_spec/renderer.spec.ts b/src/mol-gl/_spec/renderer.spec.ts
index 4f85148b16f86c502ecfe73c3d91b4592aa82b9c..c9fdde6ddda907376edb2dfab6f54cf894516b1d 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -121,7 +121,7 @@ describe('renderer', () => {
const points = createPoints()
scene.add(points)
- await scene.commit().run()
+ scene.commit()
expect(ctx.stats.resourceCounts.attribute).toBe(4);
expect(ctx.stats.resourceCounts.texture).toBe(5);
expect(ctx.stats.resourceCounts.vertexArray).toBe(5);
@@ -129,7 +129,7 @@ describe('renderer', () => {
expect(ctx.stats.resourceCounts.shader).toBe(10);
scene.remove(points)
- await scene.commit().run()
+ scene.commit()
expect(ctx.stats.resourceCounts.attribute).toBe(0);
expect(ctx.stats.resourceCounts.texture).toBe(0);
expect(ctx.stats.resourceCounts.vertexArray).toBe(0);
diff --git a/src/mol-gl/commit-queue.ts b/src/mol-gl/commit-queue.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2cfd37d6206dcdde6c600c8d0fe7e074be551d5b
--- /dev/null
+++ b/src/mol-gl/commit-queue.ts
@@ -0,0 +1,55 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { LinkedList } from '../mol-data/generic'
+import { GraphicsRenderObject } from './render-object'
+
+type N = LinkedList.Node<GraphicsRenderObject>
+
+export class CommitQueue {
+ private removeList = LinkedList<GraphicsRenderObject>();
+ private removeMap = new Map<GraphicsRenderObject, N>();
+ private addList = LinkedList<GraphicsRenderObject>();
+ private addMap = new Map<GraphicsRenderObject, N>();
+
+ get isEmpty() {
+ return this.removeList.count === 0 && this.addList.count === 0;
+ }
+
+ add(o: GraphicsRenderObject) {
+ if (this.removeMap.has(o)) {
+ const a = this.removeMap.get(o)!;
+ this.removeMap.delete(o);
+ this.removeList.remove(a);
+ }
+ if (this.addMap.has(o)) return;
+ const b = this.addList.addLast(o);
+ this.addMap.set(o, b);
+ }
+
+ remove(o: GraphicsRenderObject) {
+ if (this.addMap.has(o)) {
+ const a = this.addMap.get(o)!;
+ this.addMap.delete(o);
+ this.addList.remove(a);
+ }
+ if (this.removeMap.has(o)) return;
+ const b = this.removeList.addLast(o);
+ this.removeMap.set(o, b);
+ }
+
+ tryGetRemove() {
+ const o = this.removeList.removeFirst();
+ if (o) this.removeMap.delete(o);
+ return o;
+ }
+
+ tryGetAdd() {
+ const o = this.addList.removeFirst();
+ if (o) this.addMap.delete(o);
+ return o;
+ }
+}
diff --git a/src/mol-gl/scene.ts b/src/mol-gl/scene.ts
index e47ae7f194970625aa738054fa9569dd7069caa6..ecfbbad30634189da8dcba6c39c2564c37937d4f 100644
--- a/src/mol-gl/scene.ts
+++ b/src/mol-gl/scene.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
import { Renderable } from './renderable'
@@ -12,8 +13,9 @@ import { Object3D } from './object3d';
import { Sphere3D } from '../mol-math/geometry';
import { Vec3 } from '../mol-math/linear-algebra';
import { BoundaryHelper } from '../mol-math/geometry/boundary-helper';
-import { RuntimeContext, Task } from '../mol-task';
-import { AsyncQueue } from '../mol-util/async-queue';
+import { CommitQueue } from './commit-queue';
+import { now } from '../mol-util/now';
+import { arraySetRemove } from '../mol-util/array';
const boundaryHelper = new BoundaryHelper();
function calculateBoundingSphere(renderables: Renderable<RenderableValues & BaseValues>[], boundingSphere: Sphere3D): Sphere3D {
@@ -56,13 +58,12 @@ interface Scene extends Object3D {
readonly count: number
readonly renderables: ReadonlyArray<Renderable<RenderableValues & BaseValues>>
readonly boundingSphere: Sphere3D
- readonly isCommiting: boolean
- update: (objects: ArrayLike<GraphicsRenderObject> | undefined, keepBoundingSphere: boolean) => void
+ update: (objects: ArrayLike<GraphicsRenderObject> | undefined, keepBoundingSphere: boolean, isRemoving?: boolean) => void
add: (o: GraphicsRenderObject) => void // Renderable<any>
remove: (o: GraphicsRenderObject) => void
- syncCommit: () => void
- commit: () => Task<void>
+ commit: (maxTimeMs?: number) => boolean
+ readonly needsCommit: boolean
has: (o: GraphicsRenderObject) => boolean
clear: () => void
forEach: (callbackFn: (value: Renderable<RenderableValues & BaseValues>, key: GraphicsRenderObject) => void) => void
@@ -78,7 +79,7 @@ namespace Scene {
const object3d = Object3D.create()
- const add = (o: GraphicsRenderObject) => {
+ function add(o: GraphicsRenderObject) {
if (!renderableMap.has(o)) {
const renderable = createRenderable(ctx, o)
renderables.push(renderable)
@@ -91,47 +92,50 @@ namespace Scene {
}
}
- const remove = (o: GraphicsRenderObject) => {
+ function remove(o: GraphicsRenderObject) {
const renderable = renderableMap.get(o)
if (renderable) {
renderable.dispose()
- renderables.splice(renderables.indexOf(renderable), 1)
+ arraySetRemove(renderables, renderable);
renderableMap.delete(o)
boundingSphereDirty = true
}
}
- const commitQueue = new AsyncQueue<any>();
- const toAdd: GraphicsRenderObject[] = []
- const toRemove: GraphicsRenderObject[] = []
+ const commitBulkSize = 100;
+ function commit(maxTimeMs: number) {
+ const start = now();
- type CommitParams = { toAdd: GraphicsRenderObject[], toRemove: GraphicsRenderObject[] }
+ let i = 0;
- const step = 100
- const handle = async (ctx: RuntimeContext, arr: GraphicsRenderObject[], fn: (o: GraphicsRenderObject) => void, message: string) => {
- for (let i = 0, il = arr.length; i < il; i += step) {
- if (ctx.shouldUpdate) await ctx.update({ message, current: i, max: il })
- for (let j = i, jl = Math.min(i + step, il); j < jl; ++j) {
- fn(arr[j])
- }
+ while (true) {
+ const o = commitQueue.tryGetRemove();
+ if (!o) break;
+ remove(o);
+ if (++i % commitBulkSize === 0 && now() - start > maxTimeMs) return false;
+ }
+
+ while (true) {
+ const o = commitQueue.tryGetAdd();
+ if (!o) break;
+ add(o);
+ if (++i % commitBulkSize === 0 && now() - start > maxTimeMs) return false;
}
- }
- const commit = async (ctx: RuntimeContext, p: CommitParams) => {
- await handle(ctx, p.toRemove, remove, 'Removing GraphicsRenderObjects')
- await handle(ctx, p.toAdd, add, 'Adding GraphicsRenderObjects')
- if (ctx.shouldUpdate) await ctx.update({ message: 'Sorting GraphicsRenderObjects' })
renderables.sort(renderableSort)
+ return true;
}
+ const commitQueue = new CommitQueue();
+
return {
get view () { return object3d.view },
get position () { return object3d.position },
get direction () { return object3d.direction },
get up () { return object3d.up },
- get isCommiting () { return commitQueue.length > 0 },
+ // get isCommiting () { return commitQueue.length > 0 },
- update(objects, keepBoundingSphere) {
+ update(objects, keepBoundingSphere, isRemoving) {
Object3D.update(object3d)
if (objects) {
for (let i = 0, il = objects.length; i < il; ++i) {
@@ -139,44 +143,17 @@ namespace Scene {
if (!o) continue;
o.update();
}
- } else {
+ } else if (!isRemoving) {
for (let i = 0, il = renderables.length; i < il; ++i) {
renderables[i].update()
}
}
if (!keepBoundingSphere) boundingSphereDirty = true
},
- add: (o: GraphicsRenderObject) => {
- toAdd.push(o)
- },
- remove: (o: GraphicsRenderObject) => {
- toRemove.push(o)
- },
- syncCommit: () => {
- for (let i = 0, il = toRemove.length; i < il; ++i) remove(toRemove[i])
- toRemove.length = 0
- for (let i = 0, il = toAdd.length; i < il; ++i) add(toAdd[i])
- toAdd.length = 0
- renderables.sort(renderableSort)
- },
- commit: () => {
- const params = { toAdd: [ ...toAdd ], toRemove: [ ...toRemove ] }
- toAdd.length = 0
- toRemove.length = 0
-
- return Task.create('Commiting GraphicsRenderObjects', async ctx => {
- const removed = await commitQueue.enqueue(params);
- if (!removed) return;
-
- try {
- await commit(ctx, params);
- } finally {
- commitQueue.handled(params);
- }
- }, () => {
- commitQueue.remove(params);
- })
- },
+ add: (o: GraphicsRenderObject) => commitQueue.add(o),
+ remove: (o: GraphicsRenderObject) => commitQueue.remove(o),
+ commit: (maxTime = Number.MAX_VALUE) => commit(maxTime),
+ get needsCommit() { return !commitQueue.isEmpty; },
has: (o: GraphicsRenderObject) => {
return renderableMap.has(o)
},
diff --git a/src/mol-io/reader/_spec/cif.spec.ts b/src/mol-io/reader/_spec/cif.spec.ts
index f8823d1309adb2141bbedbe99089c3cdd054aa90..8b25cf7b17b3aef5dd5708b24ad913316c01e8d1 100644
--- a/src/mol-io/reader/_spec/cif.spec.ts
+++ b/src/mol-io/reader/_spec/cif.spec.ts
@@ -8,6 +8,7 @@
import * as Data from '../cif/data-model'
import * as Schema from '../cif/schema'
import { Column } from '../../../mol-data/db'
+import parse from '../cif/text/parser';
const columnData = `123abc d,e,f '4 5 6'`;
// 123abc d,e,f '4 5 6'
@@ -36,6 +37,24 @@ namespace TestSchema {
export const schema = { test }
}
+test('cif triple quote', async () => {
+ const data = `data_test
+_test.field1 '''123 " '' 1'''
+_test.field2 ''' c glide reflection through the plane (x,1/4,z)
+chosen as one of the generators of the space group'''`;
+
+ const result = await parse(data).run();
+ if (result.isError) {
+ expect(false).toBe(true);
+ return;
+ }
+
+ const cat = result.result.blocks[0].categories['test'];
+ expect(cat.getField('field1')!.str(0)).toBe(`123 " '' 1`);
+ expect(cat.getField('field2')!.str(0)).toBe(` c glide reflection through the plane (x,1/4,z)
+chosen as one of the generators of the space group`);
+});
+
describe('schema', () => {
const db = Schema.toDatabase(TestSchema.schema, testBlock);
it('property access', () => {
diff --git a/src/mol-io/reader/cif.ts b/src/mol-io/reader/cif.ts
index 436e3137c4e258f1ead1438cc41690af5168784d..63883a2fdf4a219d3f125dff0ece117db244264f 100644
--- a/src/mol-io/reader/cif.ts
+++ b/src/mol-io/reader/cif.ts
@@ -14,7 +14,7 @@ import { CCD_Schema, CCD_Database } from './cif/schema/ccd'
import { BIRD_Schema, BIRD_Database } from './cif/schema/bird'
import { dic_Schema, dic_Database } from './cif/schema/dic'
import { DensityServer_Data_Schema, DensityServer_Data_Database } from './cif/schema/density-server'
-import { cifCore_Database, cifCore_Schema, cifCore_Aliases } from './cif/schema/cif-core'
+import { CifCore_Database, CifCore_Schema, CifCore_Aliases } from './cif/schema/cif-core'
export const CIF = {
parse: (data: string|Uint8Array) => typeof data === 'string' ? parseText(data) : parseBinary(data),
@@ -27,7 +27,7 @@ export const CIF = {
CCD: (frame: CifFrame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame),
BIRD: (frame: CifFrame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame),
dic: (frame: CifFrame) => toDatabase<dic_Schema, dic_Database>(dic_Schema, frame),
- cifCore: (frame: CifFrame) => toDatabase<cifCore_Schema, cifCore_Database>(cifCore_Schema, frame, cifCore_Aliases),
+ cifCore: (frame: CifFrame) => toDatabase<CifCore_Schema, CifCore_Database>(CifCore_Schema, frame, CifCore_Aliases),
densityServer: (frame: CifFrame) => toDatabase<DensityServer_Data_Schema, DensityServer_Data_Database>(DensityServer_Data_Schema, frame),
}
}
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index 6a1912e5f3e55814706997eb11807912dc65abc0..6e87afbd818f490f10cbd99bfa696df40ff45a33 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.08, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -78,7 +78,7 @@ export const BIRD_Schema = {
/**
* Defines how this entity is represented in PDB data files.
*/
- represent_as: Aliased<'polymer' | 'single molecule'>(str),
+ represent_as: Aliased<'polymer' | 'single molecule' | 'branched'>(str),
/**
* For entities represented as single molecules, the identifier
* corresponding to the chemical definition for the molecule.
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index ba71621291228682e276d0c02d2add2de407f71d..ae08d364df297f9d7e6bacc05f670c8a2f8ea926 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.08, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/cif-core.ts b/src/mol-io/reader/cif/schema/cif-core.ts
index ddde84aaa47f344030ebe90a6d3750ab80acd1ef..e3de62df551ace8ad31174e095b522150402058f 100644
--- a/src/mol-io/reader/cif/schema/cif-core.ts
+++ b/src/mol-io/reader/cif/schema/cif-core.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'cifCore' schema file. Dictionary versions: CifCore 3.0.11.
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.11.
*
* @author molstar/ciftools package
*/
@@ -14,7 +14,7 @@ const int = Schema.int;
const float = Schema.float;
const str = Schema.str;
-export const cifCore_Schema = {
+export const CifCore_Schema = {
/**
* The CATEGORY of data items used to describe the parameters of
* the crystal unit cell and their measurement.
@@ -585,7 +585,7 @@ export const cifCore_Schema = {
},
}
-export const cifCore_Aliases = {
+export const CifCore_Aliases = {
'space_group.name_H-M_full': [
'symmetry_space_group_name_H-M',
],
@@ -633,5 +633,5 @@ export const cifCore_Aliases = {
],
}
-export type cifCore_Schema = typeof cifCore_Schema;
-export interface cifCore_Database extends Database<cifCore_Schema> {}
\ No newline at end of file
+export type CifCore_Schema = typeof CifCore_Schema;
+export interface CifCore_Database extends Database<CifCore_Schema> {}
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index d52d5763ed69b64273f3cbe77d6ded6601f50a88..484c694f06e0a44e735b072a1db878ba761f31de 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.323, IHM 1.08, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -1880,6 +1880,23 @@ export const mmCIF_Schema = {
*/
name: str,
},
+ /**
+ * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
+ */
+ pdbx_chem_comp_synonyms: {
+ /**
+ * The synonym of this particular chemical component.
+ */
+ name: str,
+ /**
+ * The chemical component for which this synonym applies.
+ */
+ comp_id: str,
+ /**
+ * The provenance of this synonym.
+ */
+ provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
+ },
/**
* Data items in the CHEM_COMP_IDENTIFIER category provide
* identifiers for chemical components.
@@ -3665,7 +3682,7 @@ export const mmCIF_Schema = {
/**
* The type of crosslinker used.
*/
- linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'Other'>(str),
+ linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'CYS' | 'Other'>(str),
/**
* Identifier to the crosslinking dataset.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -4584,23 +4601,6 @@ export const mmCIF_Schema = {
*/
auth_mon_id: str,
},
- /**
- * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
- */
- pdbx_chem_comp_synonyms: {
- /**
- * The synonym of this particular chemical component.
- */
- name: str,
- /**
- * The chemical component for which this synonym applies.
- */
- comp_id: str,
- /**
- * The provenance of this synonym.
- */
- provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
- },
/**
* PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
*/
diff --git a/src/mol-io/reader/cif/text/parser.ts b/src/mol-io/reader/cif/text/parser.ts
index c593e25ddf4d176b39f2fc289da025058a34687c..693754053e9743d122d4b07f94ef6ffca1067883 100644
--- a/src/mol-io/reader/cif/text/parser.ts
+++ b/src/mol-io/reader/cif/text/parser.ts
@@ -131,6 +131,28 @@ function eatEscaped(state: TokenizerState, esc: number) {
state.tokenEnd = state.position;
}
+/**
+ * Eats an escaped value "triple quote" (''') value.
+ */
+function eatTripleQuote(state: TokenizerState) {
+ // skip the '''
+ state.position += 3;
+ while (state.position < state.length) {
+ if (state.data.charCodeAt(state.position) === 39 /* ' */ && isTripleQuoteAtPosition(state)) {
+ // get rid of the quotes.
+ state.tokenStart += 3;
+ state.tokenEnd = state.position;
+ state.isEscaped = true;
+ state.position += 3;
+ return;
+ }
+
+ ++state.position;
+ }
+
+ state.tokenEnd = state.position;
+}
+
/**
* Eats a multiline token of the form NL;....NL;
*/
@@ -235,6 +257,18 @@ function skipWhitespace(state: TokenizerState): number {
return prev;
}
+
+/**
+ * Returns true if there are two consecutive ' in +1 and +2 positions.
+ */
+function isTripleQuoteAtPosition(state: TokenizerState): boolean {
+ if (state.length - state.position < 2) return false;
+ if (state.data.charCodeAt(state.position + 1) !== 39) return false; // '
+ if (state.data.charCodeAt(state.position + 2) !== 39) return false; // '
+
+ return true;
+}
+
function isData(state: TokenizerState): boolean {
// here we already assume the 5th char is _ and that the length >= 5
@@ -393,8 +427,13 @@ function moveNextInternal(state: TokenizerState) {
skipCommentLine(state);
state.tokenType = CifTokenType.Comment;
break;
- case 34: // ", escaped value
case 39: // ', escaped value
+ if (isTripleQuoteAtPosition(state)) {
+ eatTripleQuote(state);
+ state.tokenType = CifTokenType.Value;
+ break;
+ }
+ case 34: // ", escaped value
eatEscaped(state, c);
state.tokenType = CifTokenType.Value;
break;
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 9c0b8a743f3377edd90527b13977b95165fbfe03..74079dcfa2a64b80cdb19ca1461643ea8233bfb8 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -199,7 +199,7 @@ export namespace Category {
getFormat(cat, field) { return void 0; }
}
- export function ofTable(table: Table<Table.Schema>, indices?: ArrayLike<number>): Category.Instance {
+ export function ofTable(table: Table, indices?: ArrayLike<number>): Category.Instance {
if (indices) {
return {
fields: cifFieldsFromTableSchema(table._schema),
diff --git a/src/mol-model-formats/structure/3dg.ts b/src/mol-model-formats/structure/3dg.ts
index f72aff712cfc7d96f4bd3d7a33bd2d30d7942f17..74d5eba815f6560164c043e521319fb44401f6f8 100644
--- a/src/mol-model-formats/structure/3dg.ts
+++ b/src/mol-model-formats/structure/3dg.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,16 +7,15 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { Column } from '../../mol-data/db';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { Column, Table } from '../../mol-data/db';
import { EntityBuilder } from './common/entity';
import { File3DG } from '../../mol-io/reader/3dg/parser';
import { fillSerial } from '../../mol-util/array';
import { MoleculeType } from '../../mol-model/structure/model/types';
+import { BasicSchema, createBasic } from './basic/schema';
+import { createModels } from './basic/parser';
-function getCategories(table: File3DG['table']) {
+function getBasic(table: File3DG['table']) {
const entityIds = new Array<string>(table._rowCount)
const entityBuilder = new EntityBuilder()
@@ -33,47 +32,52 @@ function getCategories(table: File3DG['table']) {
seqIdEnds[i] = seqIdStarts[i] + stride - 1
}
- const ihm_sphere_obj_site: CifCategory.SomeFields<mmCIF_Schema['ihm_sphere_obj_site']> = {
- id: CifField.ofNumbers(fillSerial(new Uint32Array(table._rowCount))),
- entity_id: CifField.ofStrings(entityIds),
- seq_id_begin: CifField.ofNumbers(seqIdStarts),
- seq_id_end: CifField.ofNumbers(seqIdEnds),
- asym_id: CifField.ofColumn(table.chromosome),
+ const ihm_sphere_obj_site = Table.ofPartialColumns(BasicSchema.ihm_sphere_obj_site, {
+ id: Column.ofIntArray(fillSerial(new Uint32Array(table._rowCount))),
+ entity_id: Column.ofStringArray(entityIds),
+ seq_id_begin: Column.ofIntArray(seqIdStarts),
+ seq_id_end: Column.ofIntArray(seqIdEnds),
+ asym_id: table.chromosome,
- Cartn_x: CifField.ofNumbers(Column.mapToArray(table.x, x => x * 10, Float32Array)),
- Cartn_y: CifField.ofNumbers(Column.mapToArray(table.y, y => y * 10, Float32Array)),
- Cartn_z: CifField.ofNumbers(Column.mapToArray(table.z, z => z * 10, Float32Array)),
+ Cartn_x: Column.ofFloatArray(Column.mapToArray(table.x, x => x * 10, Float32Array)),
+ Cartn_y: Column.ofFloatArray(Column.mapToArray(table.y, y => y * 10, Float32Array)),
+ Cartn_z: Column.ofFloatArray(Column.mapToArray(table.z, z => z * 10, Float32Array)),
- object_radius: CifField.ofColumn(Column.ofConst(objectRadius, table._rowCount, Column.Schema.float)),
- rmsf: CifField.ofColumn(Column.ofConst(0, table._rowCount, Column.Schema.float)),
- model_id: CifField.ofColumn(Column.ofConst(1, table._rowCount, Column.Schema.int)),
- }
+ object_radius: Column.ofConst(objectRadius, table._rowCount, Column.Schema.float),
+ rmsf: Column.ofConst(0, table._rowCount, Column.Schema.float),
+ model_id: Column.ofConst(1, table._rowCount, Column.Schema.int),
+ }, table._rowCount)
- return {
- entity: entityBuilder.getEntityCategory(),
- ihm_model_list: CifCategory.ofFields('ihm_model_list', {
- model_id: CifField.ofNumbers([1]),
- model_name: CifField.ofStrings(['3DG Model']),
- }),
- ihm_sphere_obj_site: CifCategory.ofFields('ihm_sphere_obj_site', ihm_sphere_obj_site)
- }
+ return createBasic({
+ entity: entityBuilder.getEntityTable(),
+ ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
+ model_id: Column.ofIntArray([1]),
+ model_name: Column.ofStringArray(['3DG Model']),
+ }, 1),
+ ihm_sphere_obj_site
+ })
}
-async function mmCifFrom3dg(file3dg: File3DG) {
- const categories = getCategories(file3dg.table)
+//
+
+export { Format3dg }
- return {
- header: '3DG',
- categoryNames: Object.keys(categories),
- categories
- };
+type Format3dg = ModelFormat<File3DG>
+
+namespace Format3dg {
+ export function is(x: ModelFormat): x is Format3dg {
+ return x.kind === '3dg'
+ }
+
+ export function from3dg(file3dg: File3DG): Format3dg {
+ return { kind: '3dg', name: '3DG', data: file3dg };
+ }
}
export function trajectoryFrom3DG(file3dg: File3DG): Task<Model.Trajectory> {
return Task.create('Parse 3DG', async ctx => {
- await ctx.update('Converting to mmCIF');
- const cif = await mmCifFrom3dg(file3dg);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = Format3dg.from3dg(file3dg);
+ const basic = getBasic(file3dg.table)
+ return createModels(basic, format, ctx);
})
}
diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/basic/atomic.ts
similarity index 86%
rename from src/mol-model-formats/structure/mmcif/atomic.ts
rename to src/mol-model-formats/structure/basic/atomic.ts
index 81346a2ce981d0643e8d60ed04ed9f729dba9bae..277026770b18b7f084bf6df2c6ef9da23a2234de 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -7,7 +7,6 @@
import { Column, Table } from '../../../mol-data/db';
import { Interval, Segmentation } from '../../../mol-data/int';
-import { mmCIF_Database } from '../../../mol-io/reader/cif/schema/mmcif';
import UUID from '../../../mol-util/uuid';
import { ElementIndex } from '../../../mol-model/structure';
import { Model } from '../../../mol-model/structure/model/model';
@@ -16,9 +15,7 @@ import { getAtomicIndex } from '../../../mol-model/structure/model/properties/ut
import { ElementSymbol } from '../../../mol-model/structure/model/types';
import { Entities } from '../../../mol-model/structure/model/properties/common';
import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
-import { FormatData } from './parser';
-
-type AtomSite = mmCIF_Database['atom_site']
+import { AtomSite } from './schema';
function findHierarchyOffsets(atom_site: AtomSite) {
if (atom_site._rowCount === 0) return { residues: [], chains: [] };
@@ -93,12 +90,12 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
// TODO need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
- return Table.areEqual(a.chains as Table<ChainsSchema>, b.chains as Table<ChainsSchema>)
- && Table.areEqual(a.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
- && Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
+ return Table.areEqual(a.chains, b.chains)
+ && Table.areEqual(a.residues, b.residues)
+ && Table.areEqual(a.atoms, b.atoms)
}
-function getAtomicHierarchy(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model) {
+function getAtomicHierarchy(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, chemicalComponentMap: Model['properties']['chemicalComponentMap'], previous?: Model) {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, sourceIndex, hierarchyOffsets);
@@ -115,13 +112,13 @@ function getAtomicHierarchy(atom_site: AtomSite, sourceIndex: Column<number>, en
}
const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
- const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
+ const derived = getAtomicDerivedData(hierarchyData, index, chemicalComponentMap);
const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, index, derived };
return { sameAsPrevious: false, hierarchy };
}
-export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model) {
- const { sameAsPrevious, hierarchy } = getAtomicHierarchy(atom_site, sourceIndex, entities, formatData, previous)
+export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, chemicalComponentMap: Model['properties']['chemicalComponentMap'], previous?: Model) {
+ const { sameAsPrevious, hierarchy } = getAtomicHierarchy(atom_site, sourceIndex, entities, chemicalComponentMap, previous)
const conformation = getConformation(atom_site)
return { sameAsPrevious, hierarchy, conformation };
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/ihm.ts b/src/mol-model-formats/structure/basic/coarse.ts
similarity index 74%
rename from src/mol-model-formats/structure/mmcif/ihm.ts
rename to src/mol-model-formats/structure/basic/coarse.ts
index 7ce1eb9fd8b03eb2f6709a9cafc8297951c64a26..7cb248ec5f9cdd75753331e3072363e4deb572f4 100644
--- a/src/mol-model-formats/structure/mmcif/ihm.ts
+++ b/src/mol-model-formats/structure/basic/coarse.ts
@@ -1,10 +1,10 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { mmCIF_Database as mmCIF, mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif'
import { CoarseHierarchy, CoarseConformation, CoarseElementData, CoarseSphereConformation, CoarseGaussianConformation } from '../../../mol-model/structure/model/properties/coarse'
import { Entities } from '../../../mol-model/structure/model/properties/common';
import { Column } from '../../../mol-data/db';
@@ -14,35 +14,36 @@ import { Segmentation, Interval } from '../../../mol-data/int';
import { Mat3, Tensor } from '../../../mol-math/linear-algebra';
import { ElementIndex, ChainIndex } from '../../../mol-model/structure/model/indexing';
import { getCoarseRanges } from '../../../mol-model/structure/model/properties/utils/coarse-ranges';
-import { FormatData } from './parser';
+import { IhmSphereObjSite, IhmGaussianObjSite, AtomSite, BasicSchema } from './schema';
+import { Model } from '../../../mol-model/structure';
-export interface IHMData {
+export interface CoarseData {
model_id: number,
model_name: string,
model_group_name: string,
entities: Entities,
- atom_site: mmCIF['atom_site'],
+ atom_site: AtomSite,
atom_site_sourceIndex: Column<number>,
- ihm_sphere_obj_site: mmCIF['ihm_sphere_obj_site'],
- ihm_gaussian_obj_site: mmCIF['ihm_gaussian_obj_site']
+ ihm_sphere_obj_site: IhmSphereObjSite,
+ ihm_gaussian_obj_site: IhmGaussianObjSite
}
-export const EmptyIHMCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any }
+export const EmptyCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any }
-export function getIHMCoarse(data: IHMData, formatData: FormatData): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
+export function getCoarse(data: CoarseData, properties: Model['properties']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
const { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;
- if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyIHMCoarse;
+ if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyCoarse;
const sphereData = getData(ihm_sphere_obj_site);
const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
const sphereKeys = getCoarseKeys(sphereData, data.entities);
- const sphereRanges = getCoarseRanges(sphereData, formatData.chemicalComponentMap);
+ const sphereRanges = getCoarseRanges(sphereData, properties.chemicalComponentMap);
const gaussianData = getData(ihm_gaussian_obj_site);
const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
- const gaussianRanges = getCoarseRanges(gaussianData, formatData.chemicalComponentMap);
+ const gaussianRanges = getCoarseRanges(gaussianData, properties.chemicalComponentMap);
return {
hierarchy: {
@@ -58,7 +59,7 @@ export function getIHMCoarse(data: IHMData, formatData: FormatData): { hierarchy
};
}
-function getSphereConformation(data: mmCIF['ihm_sphere_obj_site']): CoarseSphereConformation {
+function getSphereConformation(data: IhmSphereObjSite): CoarseSphereConformation {
return {
x: data.Cartn_x.toArray({ array: Float32Array }),
y: data.Cartn_y.toArray({ array: Float32Array }),
@@ -68,8 +69,8 @@ function getSphereConformation(data: mmCIF['ihm_sphere_obj_site']): CoarseSphere
};
}
-function getGaussianConformation(data: mmCIF['ihm_gaussian_obj_site']): CoarseGaussianConformation {
- const matrix_space = mmCIF_Schema.ihm_gaussian_obj_site.covariance_matrix.space;
+function getGaussianConformation(data: IhmGaussianObjSite): CoarseGaussianConformation {
+ const matrix_space = BasicSchema.ihm_gaussian_obj_site.covariance_matrix.space;
const covariance_matrix: Mat3[] = [];
const { covariance_matrix: cm } = data;
@@ -98,7 +99,7 @@ function getSegments(asym_id: Column<string>, seq_id_begin: Column<number>, seq_
}
}
-function getData(data: mmCIF['ihm_sphere_obj_site'] | mmCIF['ihm_gaussian_obj_site']): CoarseElementData {
+function getData(data: IhmSphereObjSite | IhmGaussianObjSite): CoarseElementData {
const { entity_id, seq_id_begin, seq_id_end, asym_id } = data;
return { count: entity_id.rowCount, entity_id, asym_id, seq_id_begin, seq_id_end, ...getSegments(asym_id, seq_id_begin, seq_id_end) };
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/entities.ts b/src/mol-model-formats/structure/basic/entities.ts
new file mode 100644
index 0000000000000000000000000000000000000000..77d1468297bc84d448c8f22e7ca112fe8cb5be7b
--- /dev/null
+++ b/src/mol-model-formats/structure/basic/entities.ts
@@ -0,0 +1,122 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../../mol-data/db';
+import { Entities, EntitySubtype } from '../../../mol-model/structure/model/properties/common';
+import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/model/types';
+import { ElementIndex, EntityIndex } from '../../../mol-model/structure/model';
+import { BasicData, BasicSchema, Entity } from './schema';
+
+export function getEntities(data: BasicData): Entities {
+ let entityData: Entity
+
+ if (!data.entity.id.isDefined) {
+ const entityIds = new Set<string>()
+
+ const ids: ReturnType<Entity['id']['value']>[] = []
+ const types: ReturnType<Entity['type']['value']>[] = []
+
+ const { label_entity_id, label_comp_id } = data.atom_site;
+ for (let i = 0 as ElementIndex, il = data.atom_site._rowCount; i < il; i++) {
+ const entityId = label_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ ids.push(entityId)
+ types.push(getEntityType(label_comp_id.value(i)))
+ entityIds.add(entityId)
+ }
+ }
+
+ const { entity_id: sphere_entity_id } = data.ihm_sphere_obj_site;
+ for (let i = 0 as ElementIndex, il = data.ihm_sphere_obj_site._rowCount; i < il; i++) {
+ const entityId = sphere_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ ids.push(entityId)
+ types.push('polymer')
+ entityIds.add(entityId)
+ }
+ }
+
+ const { entity_id: gaussian_entity_id } = data.ihm_gaussian_obj_site;
+ for (let i = 0 as ElementIndex, il = data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
+ const entityId = gaussian_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ ids.push(entityId)
+ types.push('polymer')
+ entityIds.add(entityId)
+ }
+ }
+
+ entityData = Table.ofPartialColumns(BasicSchema.entity, {
+ id: Column.ofArray({ array: ids, schema: BasicSchema.entity.id }),
+ type: Column.ofArray({ array: types, schema: BasicSchema.entity.type }),
+ }, ids.length)
+ } else {
+ entityData = data.entity;
+ }
+
+ const getEntityIndex = Column.createIndexer<string, EntityIndex>(entityData.id)
+
+ //
+
+ const subtypes: EntitySubtype[] = new Array(entityData._rowCount)
+ subtypes.fill('other')
+
+ const entityIds = new Set<string>()
+ let assignSubtype = false
+
+ if (data.entity_poly && data.entity_poly.type.isDefined) {
+ const { entity_id, type, _rowCount } = data.entity_poly
+ for (let i = 0; i < _rowCount; ++i) {
+ const entityId = entity_id.value(i)
+ subtypes[getEntityIndex(entityId)] = type.value(i)
+ entityIds.add(entityId)
+ }
+ } else {
+ assignSubtype = true
+ }
+
+ if (data.pdbx_entity_branch && data.pdbx_entity_branch.entity_id.isDefined) {
+ const { entity_id, type, _rowCount } = data.pdbx_entity_branch
+ for (let i = 0; i < _rowCount; ++i) {
+ const entityId = entity_id.value(i)
+ subtypes[getEntityIndex(entityId)] = type.value(i)
+ entityIds.add(entityId)
+ }
+ } else {
+ assignSubtype = true
+ }
+
+ if (assignSubtype) {
+ const chemCompType = new Map<string, string>()
+ if (data.chem_comp) {
+ const { id, type } = data.chem_comp;
+ for (let i = 0, il = data.chem_comp._rowCount; i < il; i++) {
+ chemCompType.set(id.value(i), type.value(i))
+ }
+ }
+
+ if (data.atom_site) {
+ const { label_entity_id, label_comp_id } = data.atom_site;
+ for (let i = 0 as ElementIndex, il = data.atom_site._rowCount; i < il; i++) {
+ const entityId = label_entity_id.value(i);
+ if (!entityIds.has(entityId)) {
+ const compId = label_comp_id.value(i)
+ const compType = chemCompType.get(compId) || ''
+ subtypes[getEntityIndex(entityId)] = getEntitySubtype(compId, compType)
+ entityIds.add(entityId)
+ }
+ }
+ }
+ // TODO how to handle coarse?
+ }
+
+ const subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype })
+
+ //
+
+ return { data: entityData, subtype: subtypeColumn, getEntityIndex };
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/parser.ts b/src/mol-model-formats/structure/basic/parser.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cf41cd1866c7c82aef5f6b339cdf6d5f28a8e402
--- /dev/null
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -0,0 +1,210 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../../mol-data/db';
+import { RuntimeContext } from '../../../mol-task';
+import UUID from '../../../mol-util/uuid';
+import { Model } from '../../../mol-model/structure/model/model';
+import { Entities } from '../../../mol-model/structure/model/properties/common';
+import { CustomProperties } from '../../../mol-model/structure';
+import { getAtomicHierarchyAndConformation } from './atomic';
+import { getCoarse, EmptyCoarse, CoarseData } from './coarse';
+import { getSequence } from './sequence';
+import { sortAtomSite } from './sort';
+import { ModelFormat } from '../format';
+import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
+import { AtomSite, BasicData } from './schema';
+import { getProperties } from './properties';
+import { getEntities } from './entities';
+import { getModelGroupName } from './util';
+
+export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
+ const properties = getProperties(data)
+ return data.ihm_model_list._rowCount > 0
+ ? await readIntegrative(ctx, data, properties, format)
+ : await readStandard(ctx, data, properties, format);
+}
+
+/** Standard atomic model */
+function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: Model['properties'], format: ModelFormat, previous?: Model): Model {
+
+ const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, properties.chemicalComponentMap, previous);
+ const modelNum = atom_site.pdbx_PDB_model_num.value(0)
+ if (previous && atomic.sameAsPrevious) {
+ return {
+ ...previous,
+ id: UUID.create22(),
+ modelNum,
+ atomicConformation: atomic.conformation,
+ _dynamicPropertyData: Object.create(null)
+ };
+ }
+
+ const coarse = EmptyCoarse;
+ const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy, properties.modifiedResidues.parentId)
+ const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence)
+
+ const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
+ ? data.entry.id.value(0) : format.name;
+
+ const label: string[] = []
+ if (entry) label.push(entry)
+ if (data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(data.struct.title.value(0))
+
+ return {
+ id: UUID.create22(),
+ entryId: entry,
+ label: label.join(' | '),
+ entry,
+ sourceData: format,
+ modelNum,
+ entities,
+ sequence,
+ atomicHierarchy: atomic.hierarchy,
+ atomicConformation: atomic.conformation,
+ atomicRanges,
+ coarseHierarchy: coarse.hierarchy,
+ coarseConformation: coarse.conformation,
+ properties,
+ customProperties: new CustomProperties(),
+ _staticPropertyData: Object.create(null),
+ _dynamicPropertyData: Object.create(null)
+ };
+}
+
+/** Integrative model with atomic/coarse parts */
+function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Model['properties'], format: ModelFormat): Model {
+ const atomic = getAtomicHierarchyAndConformation(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap);
+ const coarse = getCoarse(ihm, properties);
+ const sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy, properties.modifiedResidues.parentId)
+ const atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence)
+
+ const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
+ ? data.entry.id.value(0) : format.name;
+
+ const label: string[] = []
+ if (entry) label.push(entry)
+ if (data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(data.struct.title.value(0))
+ if (ihm.model_name) label.push(ihm.model_name)
+ if (ihm.model_group_name) label.push(ihm.model_group_name)
+
+ return {
+ id: UUID.create22(),
+ entryId: entry,
+ label: label.join(' | '),
+ entry,
+ sourceData: format,
+ modelNum: ihm.model_id,
+ entities: ihm.entities,
+ sequence,
+ atomicHierarchy: atomic.hierarchy,
+ atomicConformation: atomic.conformation,
+ atomicRanges,
+ coarseHierarchy: coarse.hierarchy,
+ coarseConformation: coarse.conformation,
+ properties,
+ customProperties: new CustomProperties(),
+ _staticPropertyData: Object.create(null),
+ _dynamicPropertyData: Object.create(null)
+ };
+}
+
+function findModelEnd(num: Column<number>, startIndex: number) {
+ const rowCount = num.rowCount;
+ if (!num.isDefined) return rowCount;
+ let endIndex = startIndex + 1;
+ while (endIndex < rowCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
+ return endIndex;
+}
+
+async function readStandard(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
+ const models: Model[] = [];
+
+ if (data.atom_site) {
+ const atomCount = data.atom_site.id.rowCount;
+ const entities = getEntities(data)
+
+ let modelStart = 0;
+ while (modelStart < atomCount) {
+ const modelEnd = findModelEnd(data.atom_site.pdbx_PDB_model_num, modelStart);
+ const { atom_site, sourceIndex } = await sortAtomSite(ctx, data.atom_site, modelStart, modelEnd);
+ const model = createStandardModel(data, atom_site, sourceIndex, entities, properties, format, models.length > 0 ? models[models.length - 1] : void 0);
+ models.push(model);
+ modelStart = modelEnd;
+ }
+ }
+ return models;
+}
+
+function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
+ const ret = new Map<number, { table: T, start: number, end: number }>()
+ const rowCount = table._rowCount;
+ let modelStart = 0;
+ while (modelStart < rowCount) {
+ const modelEnd = findModelEnd(col, modelStart);
+ const id = col.value(modelStart);
+ ret.set(id, {
+ table: Table.window(table, table._schema, modelStart, modelEnd) as T,
+ start: modelStart,
+ end: modelEnd
+ });
+ modelStart = modelEnd;
+ }
+ return ret;
+}
+
+
+
+async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
+ const entities = getEntities(data)
+ // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
+ const atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
+ ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num
+ const atom_sites = splitTable(data.atom_site, atom_sites_modelColumn)
+
+ // TODO: will coarse IHM records require sorting or will we trust it?
+ // ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
+ // If the sorting is implemented, updated mol-model/structure/properties: atom.sourceIndex
+ const sphere_sites = splitTable(data.ihm_sphere_obj_site, data.ihm_sphere_obj_site.model_id);
+ const gauss_sites = splitTable(data.ihm_gaussian_obj_site, data.ihm_gaussian_obj_site.model_id);
+
+ const models: Model[] = [];
+
+ if (data.ihm_model_list) {
+ const { model_id, model_name } = data.ihm_model_list;
+ for (let i = 0; i < data.ihm_model_list._rowCount; i++) {
+ const id = model_id.value(i);
+
+ let atom_site, atom_site_sourceIndex;
+ if (atom_sites.has(id)) {
+ const e = atom_sites.get(id)!;
+ // need to sort `data.atom_site` as `e.start` and `e.end` are indices into that
+ const { atom_site: sorted, sourceIndex } = await sortAtomSite(ctx, data.atom_site, e.start, e.end);
+ atom_site = sorted;
+ atom_site_sourceIndex = sourceIndex;
+ } else {
+ atom_site = Table.window(data.atom_site, data.atom_site._schema, 0, 0);
+ atom_site_sourceIndex = Column.ofIntArray([]);
+ }
+
+ const ihm: CoarseData = {
+ model_id: id,
+ model_name: model_name.value(i),
+ model_group_name: getModelGroupName(id, data),
+ entities: entities,
+ atom_site,
+ atom_site_sourceIndex,
+ ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(data.ihm_sphere_obj_site, data.ihm_sphere_obj_site._schema, 0, 0),
+ ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)!.table : Table.window(data.ihm_gaussian_obj_site, data.ihm_gaussian_obj_site._schema, 0, 0)
+ };
+ const model = createIntegrativeModel(data, ihm, properties, format);
+ models.push(model);
+ }
+ }
+
+ return models;
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/properties.ts b/src/mol-model-formats/structure/basic/properties.ts
new file mode 100644
index 0000000000000000000000000000000000000000..45ecd6e5d17ee6f0d4e13803c91981b6cf0369b0
--- /dev/null
+++ b/src/mol-model-formats/structure/basic/properties.ts
@@ -0,0 +1,134 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Model } from '../../../mol-model/structure/model/model';
+import { ChemicalComponent, MissingResidue } from '../../../mol-model/structure/model/properties/common';
+import { getMoleculeType, MoleculeType, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
+import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { memoize1 } from '../../../mol-util/memoize';
+import { BasicData } from './schema';
+import { Table } from '../../../mol-data/db';
+
+function getModifiedResidueNameMap(data: BasicData): Model['properties']['modifiedResidues'] {
+ const parentId = new Map<string, string>();
+ const details = new Map<string, string>();
+
+ const c = data.pdbx_struct_mod_residue;
+ const comp_id = c.label_comp_id.isDefined ? c.label_comp_id : c.auth_comp_id;
+ const parent_id = c.parent_comp_id, details_data = c.details;
+
+ for (let i = 0; i < c._rowCount; i++) {
+ const id = comp_id.value(i);
+ parentId.set(id, parent_id.value(i));
+ details.set(id, details_data.value(i));
+ }
+
+ return { parentId, details };
+}
+
+function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
+ const map = new Map<string, MissingResidue>();
+ const getKey = (model_num: number, asym_id: string, seq_id: number) => {
+ return `${model_num}|${asym_id}|${seq_id}`
+ }
+
+ const c = data.pdbx_unobs_or_zero_occ_residues
+ for (let i = 0, il = c._rowCount; i < il; ++i) {
+ const key = getKey(c.PDB_model_num.value(i), c.label_asym_id.value(i), c.label_seq_id.value(i))
+ map.set(key, { polymer_flag: c.polymer_flag.value(i), occupancy_flag: c.occupancy_flag.value(i) })
+ }
+
+ return {
+ has: (model_num: number, asym_id: string, seq_id: number) => {
+ return map.has(getKey(model_num, asym_id, seq_id))
+ },
+ get: (model_num: number, asym_id: string, seq_id: number) => {
+ return map.get(getKey(model_num, asym_id, seq_id))
+ },
+ size: map.size
+ }
+}
+
+function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
+ const map = new Map<string, ChemicalComponent>();
+
+ if (data.chem_comp._rowCount > 0) {
+ const { id } = data.chem_comp
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ map.set(id.value(i), Table.getRow(data.chem_comp, i))
+ }
+ } else {
+ const uniqueNames = getUniqueComponentNames(data);
+ uniqueNames.forEach(n => {
+ map.set(n, getDefaultChemicalComponent(n));
+ });
+ }
+ return map
+}
+
+function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
+ const map = new Map<string, SaccharideComponent>();
+
+ if (data.pdbx_chem_comp_identifier._rowCount > 0) {
+ // note that `pdbx_chem_comp_identifier` does not contain
+ // a 'SNFG CARBOHYDRATE SYMBOL' entry for 'Unknown' saccharide components
+ // so we always need to check `chem_comp` for those
+ const { comp_id, type, identifier } = data.pdbx_chem_comp_identifier
+ for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
+ if (type.value(i) === 'SNFG CARBOHYDRATE SYMBOL' ||
+ type.value(i) === 'SNFG CARB SYMBOL' // legacy, to be removed from mmCIF dictionary
+ ) {
+ const snfgName = identifier.value(i)
+ const saccharideComp = SaccharidesSnfgMap.get(snfgName)
+ if (saccharideComp) {
+ map.set(comp_id.value(i), saccharideComp)
+ } else {
+ console.warn(`Unknown SNFG name '${snfgName}'`)
+ }
+ }
+ }
+ }
+
+ if (data.chem_comp._rowCount > 0) {
+ const { id, type } = data.chem_comp
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ const _id = id.value(i)
+ if (map.has(_id)) continue
+ const _type = type.value(i)
+ if (SaccharideCompIdMap.has(_id)) {
+ map.set(_id, SaccharideCompIdMap.get(_id)!)
+ } else if (getMoleculeType(_type, _id) === MoleculeType.Saccharide) {
+ map.set(_id, UnknownSaccharideComponent)
+ }
+ }
+ } else {
+ const uniqueNames = getUniqueComponentNames(data)
+ SaccharideCompIdMap.forEach((v, k) => {
+ if (!map.has(k) && uniqueNames.has(k)) map.set(k, v)
+ })
+ }
+ return map
+}
+
+const getUniqueComponentNames = memoize1((data: BasicData) => {
+ const uniqueNames = new Set<string>()
+ const { label_comp_id, auth_comp_id } = data.atom_site
+ const comp_id = label_comp_id.isDefined ? label_comp_id : auth_comp_id;
+ for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
+ uniqueNames.add(comp_id.value(i))
+ }
+ return uniqueNames
+})
+
+export function getProperties(data: BasicData): Model['properties'] {
+ return {
+ modifiedResidues: getModifiedResidueNameMap(data),
+ missingResidues: getMissingResidues(data),
+ chemicalComponentMap: getChemicalComponentMap(data),
+ saccharideComponentMap: getSaccharideComponentMap(data)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/schema.ts b/src/mol-model-formats/structure/basic/schema.ts
new file mode 100644
index 0000000000000000000000000000000000000000..dea7e328e8a9db387542f49ee8c057e7fb9f73aa
--- /dev/null
+++ b/src/mol-model-formats/structure/basic/schema.ts
@@ -0,0 +1,81 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { Table } from '../../../mol-data/db';
+
+// TODO split into conformation and hierarchy parts
+// TODO extract `pdbx_struct_mod_residue` as property?
+
+export type Entry = Table<mmCIF_Schema['entry']>
+export type Struct = Table<mmCIF_Schema['struct']>
+export type StructAsym = Table<mmCIF_Schema['struct_asym']>
+export type IhmModelList = Table<mmCIF_Schema['ihm_model_list']>
+export type IhmModelGroup = Table<mmCIF_Schema['ihm_model_group']>
+export type IhmModelGroupLink = Table<mmCIF_Schema['ihm_model_group_link']>
+export type Entity = Table<mmCIF_Schema['entity']>
+export type EntityPoly = Table<mmCIF_Schema['entity_poly']>
+export type EntityPolySeq = Table<mmCIF_Schema['entity_poly_seq']>
+export type EntityBranch = Table<mmCIF_Schema['pdbx_entity_branch']>
+export type ChemComp = Table<mmCIF_Schema['chem_comp']>
+export type ChemCompIdentifier = Table<mmCIF_Schema['pdbx_chem_comp_identifier']>
+export type StructModResidue = Table<mmCIF_Schema['pdbx_struct_mod_residue']>
+export type AtomSite = Table<mmCIF_Schema['atom_site']>
+export type IhmSphereObjSite = Table<mmCIF_Schema['ihm_sphere_obj_site']>
+export type IhmGaussianObjSite =Table<mmCIF_Schema['ihm_gaussian_obj_site']>
+export type UnobsOrZeroOccResidues =Table<mmCIF_Schema['pdbx_unobs_or_zero_occ_residues']>
+
+export const BasicSchema = {
+ entry: mmCIF_Schema.entry,
+ struct: mmCIF_Schema.struct,
+ struct_asym: mmCIF_Schema.struct_asym,
+ ihm_model_list: mmCIF_Schema.ihm_model_list,
+ ihm_model_group: mmCIF_Schema.ihm_model_group,
+ ihm_model_group_link: mmCIF_Schema.ihm_model_group_link,
+ entity: mmCIF_Schema.entity,
+ entity_poly: mmCIF_Schema.entity_poly,
+ entity_poly_seq: mmCIF_Schema.entity_poly_seq,
+ pdbx_entity_branch: mmCIF_Schema.pdbx_entity_branch,
+ chem_comp: mmCIF_Schema.chem_comp,
+ pdbx_chem_comp_identifier: mmCIF_Schema.pdbx_chem_comp_identifier,
+ pdbx_struct_mod_residue: mmCIF_Schema.pdbx_struct_mod_residue,
+ atom_site: mmCIF_Schema.atom_site,
+ ihm_sphere_obj_site: mmCIF_Schema.ihm_sphere_obj_site,
+ ihm_gaussian_obj_site: mmCIF_Schema.ihm_gaussian_obj_site,
+ pdbx_unobs_or_zero_occ_residues: mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
+}
+
+export interface BasicData {
+ entry: Entry
+ struct: Struct
+ struct_asym: StructAsym
+ ihm_model_list: IhmModelList
+ ihm_model_group: IhmModelGroup
+ ihm_model_group_link: IhmModelGroupLink
+ entity: Entity
+ entity_poly: EntityPoly
+ entity_poly_seq: EntityPolySeq
+ pdbx_entity_branch: EntityBranch
+ chem_comp: ChemComp
+ pdbx_chem_comp_identifier: ChemCompIdentifier
+ pdbx_struct_mod_residue: StructModResidue
+ atom_site: AtomSite
+ ihm_sphere_obj_site: IhmSphereObjSite
+ ihm_gaussian_obj_site: IhmGaussianObjSite
+ pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues
+}
+
+export function createBasic(data: Partial<BasicData>): BasicData {
+ const basic = Object.create(null)
+ for (const name of Object.keys(BasicSchema)) {
+ if (name in data) {
+ basic[name] = data[name as keyof typeof BasicSchema]
+ } else {
+ basic[name] = Table.ofUndefinedColumns(BasicSchema[name as keyof typeof BasicSchema], 0)
+ }
+ }
+ return basic
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/sequence.ts b/src/mol-model-formats/structure/basic/sequence.ts
similarity index 77%
rename from src/mol-model-formats/structure/mmcif/sequence.ts
rename to src/mol-model-formats/structure/basic/sequence.ts
index 2b455a2a74c9103ed984be005c0b93a6886c41ec..d73a6f84a50bf48ff02504a0002813012f49d417 100644
--- a/src/mol-model-formats/structure/mmcif/sequence.ts
+++ b/src/mol-model-formats/structure/basic/sequence.ts
@@ -1,24 +1,24 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { mmCIF_Database as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
import StructureSequence from '../../../mol-model/structure/model/properties/sequence'
import { Column } from '../../../mol-data/db';
import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
import { Entities } from '../../../mol-model/structure/model/properties/common';
import { Sequence } from '../../../mol-model/sequence';
import { CoarseHierarchy } from '../../../mol-model/structure/model/properties/coarse';
+import { BasicData } from './schema';
-export function getSequence(cif: mmCIF, entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy, modResMap: ReadonlyMap<string, string>): StructureSequence {
- if (!cif.entity_poly_seq._rowCount) {
+export function getSequence(data: BasicData, entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy, modResMap: ReadonlyMap<string, string>): StructureSequence {
+ if (!data.entity_poly_seq || !data.entity_poly_seq._rowCount) {
return StructureSequence.fromHierarchy(entities, atomicHierarchy, coarseHierarchy, modResMap);
}
- const { entity_id, num, mon_id } = cif.entity_poly_seq;
+ const { entity_id, num, mon_id } = data.entity_poly_seq;
const byEntityKey: StructureSequence['byEntityKey'] = {};
const sequences: StructureSequence.Entity[] = [];
diff --git a/src/mol-model-formats/structure/mmcif/sort.ts b/src/mol-model-formats/structure/basic/sort.ts
similarity index 86%
rename from src/mol-model-formats/structure/mmcif/sort.ts
rename to src/mol-model-formats/structure/basic/sort.ts
index a6e450b40076403d40a2fac796ceb0ab7b6233c9..51b939afdad6718564068c2c38047ae8f4c6c9f0 100644
--- a/src/mol-model-formats/structure/mmcif/sort.ts
+++ b/src/mol-model-formats/structure/basic/sort.ts
@@ -4,12 +4,15 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { mmCIF_Database } from '../../../mol-io/reader/cif/schema/mmcif';
import { createRangeArray, makeBuckets } from '../../../mol-data/util';
import { Column, Table } from '../../../mol-data/db';
import { RuntimeContext } from '../../../mol-task';
+import { AtomSite } from './schema';
-export type SortedAtomSite = mmCIF_Database['atom_site'] & { sourceIndex: Column<number> }
+export type SortedAtomSite = {
+ atom_site: AtomSite
+ sourceIndex: Column<number>
+}
function isIdentity(xs: ArrayLike<number>) {
for (let i = 0, _i = xs.length; i < _i; i++) {
@@ -18,7 +21,7 @@ function isIdentity(xs: ArrayLike<number>) {
return true;
}
-export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Database['atom_site'], start: number, end: number) {
+export async function sortAtomSite(ctx: RuntimeContext, atom_site: AtomSite, start: number, end: number): Promise<SortedAtomSite> {
const indices = createRangeArray(start, end - 1);
const { label_entity_id, label_asym_id, label_seq_id } = atom_site;
@@ -42,7 +45,7 @@ export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Databas
}
return {
- atom_site: Table.view(atom_site, atom_site._schema, indices) as mmCIF_Database['atom_site'],
+ atom_site: Table.view(atom_site, atom_site._schema, indices) as AtomSite,
sourceIndex: Column.ofIntArray(indices)
};
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/util.ts b/src/mol-model-formats/structure/basic/util.ts
new file mode 100644
index 0000000000000000000000000000000000000000..daf0d3a8a3ebeaddf5e9c373843e602cc46bb2d7
--- /dev/null
+++ b/src/mol-model-formats/structure/basic/util.ts
@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { BasicData } from './schema';
+import { Table } from '../../../mol-data/db';
+
+export function getModelGroupName(model_id: number, data: BasicData) {
+ const { ihm_model_group, ihm_model_group_link } = data;
+
+ const link = Table.pickRow(ihm_model_group_link, i => ihm_model_group_link.model_id.value(i) === model_id)
+ if (link) {
+ const group = Table.pickRow(ihm_model_group, i => ihm_model_group.id.value(i) === link.group_id)
+ if (group) return group.name
+ }
+ return ''
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index 30f201b86c2f344560749e26fdd71ecdbb34f46a..483ac6e95369b33506deee7132a663104a8a7b91 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -1,15 +1,14 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { _parse_mmCif } from '../mmcif/parser';
-import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { Table, Column } from '../../../mol-data/db';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { WaterNames } from '../../../mol-model/structure/model/types';
import { SetUtils } from '../../../mol-util/set';
+import { BasicSchema } from '../basic/schema';
type Component = Table.Row<Pick<mmCIF_Schema['chem_comp'], 'id' | 'name' | 'type'>>
@@ -137,13 +136,12 @@ export class ComponentBuilder {
return this.get(compId)!
}
- getChemCompCategory() {
- const chemComp: CifCategory.SomeFields<mmCIF_Schema['chem_comp']> = {
- id: CifField.ofStrings(this.ids),
- name: CifField.ofStrings(this.names),
- type: CifField.ofStrings(this.types),
- }
- return CifCategory.ofFields('chem_comp', chemComp)
+ getChemCompTable() {
+ return Table.ofPartialColumns(BasicSchema.chem_comp, {
+ id: Column.ofStringArray(this.ids),
+ name: Column.ofStringArray(this.names),
+ type: Column.ofStringAliasArray(this.types),
+ }, this.ids.length)
}
setNames(names: [string, string][]) {
diff --git a/src/mol-model-formats/structure/common/entity.ts b/src/mol-model-formats/structure/common/entity.ts
index d44fefb2f7f9e7d5117333b80731f81d7181c604..3de2bfefd7c42951082f68b0f654d059d2dba716 100644
--- a/src/mol-model-formats/structure/common/entity.ts
+++ b/src/mol-model-formats/structure/common/entity.ts
@@ -1,20 +1,23 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { MoleculeType, isPolymer } from '../../../mol-model/structure/model/types';
-import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { Column, Table } from '../../../mol-data/db';
+import { BasicSchema } from '../basic/schema';
export type EntityCompound = { chains: string[], description: string }
+// TODO add support for `branched`
+type EntityType = 'water' | 'polymer' | 'non-polymer'
+
export class EntityBuilder {
private count = 0
private ids: string[] = []
- private types: string[] = []
- private descriptions: string[] = []
+ private types: EntityType[] = []
+ private descriptions: string[][] = []
private compoundsMap = new Map<string, string>()
private namesMap = new Map<string, string>()
@@ -22,11 +25,11 @@ export class EntityBuilder {
private chainMap = new Map<string, string>()
private waterId?: string
- private set(type: string, description: string) {
+ private set(type: EntityType, description: string) {
this.count += 1
this.ids.push(`${this.count}`)
this.types.push(type)
- this.descriptions.push(description)
+ this.descriptions.push([description])
}
getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
@@ -55,13 +58,12 @@ export class EntityBuilder {
}
}
- getEntityCategory() {
- const entity: CifCategory.SomeFields<mmCIF_Schema['entity']> = {
- id: CifField.ofStrings(this.ids),
- type: CifField.ofStrings(this.types),
- pdbx_description: CifField.ofStrings(this.descriptions),
- }
- return CifCategory.ofFields('entity', entity)
+ getEntityTable() {
+ return Table.ofPartialColumns(BasicSchema.entity, {
+ id: Column.ofStringArray(this.ids),
+ type: Column.ofStringAliasArray(this.types),
+ pdbx_description: Column.ofStringListArray(this.descriptions),
+ }, this.count)
}
setCompounds(compounds: EntityCompound[]) {
diff --git a/src/mol-model-formats/structure/common/property.ts b/src/mol-model-formats/structure/common/property.ts
new file mode 100644
index 0000000000000000000000000000000000000000..44bae5f2f3e0e1642a01a9fc10b3a302dde39f69
--- /dev/null
+++ b/src/mol-model-formats/structure/common/property.ts
@@ -0,0 +1,55 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
+import { ModelFormat } from '../format';
+
+class FormatRegistry<T> {
+ map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
+
+ add(kind: ModelFormat['kind'], obtain: (model: Model) => T | undefined) {
+ this.map.set(kind, obtain)
+ }
+
+ get(kind: ModelFormat['kind']) {
+ return this.map.get(kind)
+ }
+}
+
+export { FormatPropertyProvider as FormatPropertyProvider }
+
+interface FormatPropertyProvider<T> {
+ readonly descriptor: CustomPropertyDescriptor
+ readonly formatRegistry: FormatRegistry<T>
+ get(model: Model): T | undefined
+ set(model: Model, value: T): void
+}
+
+namespace FormatPropertyProvider {
+ export function create<T>(descriptor: CustomPropertyDescriptor): FormatPropertyProvider<T> {
+ const { name } = descriptor
+ const formatRegistry = new FormatRegistry<T>()
+
+ return {
+ descriptor,
+ formatRegistry,
+ get(model: Model): T | undefined {
+ if (model._staticPropertyData[name]) return model._staticPropertyData[name]
+ if (model.customProperties.has(descriptor)) return
+
+ const obtain = formatRegistry.get(model.sourceData.kind)
+ if (!obtain) return
+
+ model._staticPropertyData[name] = obtain(model)
+ model.customProperties.add(descriptor)
+ return model._staticPropertyData[name]
+ },
+ set(model: Model, value: T) {
+ model._staticPropertyData[name] = value
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/format.ts b/src/mol-model-formats/structure/format.ts
index 08d0d3b3ffdb70973b46e3a9fd22c4a75cde6161..a3cb77eb5327320f34972b02f43fc71995851534 100644
--- a/src/mol-model-formats/structure/format.ts
+++ b/src/mol-model-formats/structure/format.ts
@@ -1,18 +1,8 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
-import { CIF, CifFrame } from '../../mol-io/reader/cif';
-
-type ModelFormat =
- | ModelFormat.mmCIF
-
-namespace ModelFormat {
- export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database, frame: CifFrame }
- export function mmCIF(frame: CifFrame, data?: mmCIF_Database): mmCIF { return { kind: 'mmCIF', data: data || CIF.schema.mmCIF(frame), frame }; }
-}
-
-export { ModelFormat }
\ No newline at end of file
+export interface ModelFormat<T = unknown> { readonly kind: string, name: string, data: T }
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index 8f141ea1c98305df18e3b54a5dd6ecf64a5b027a..c38beca49164cb7d98d322036b10db9d83a2a316 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,22 +7,21 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
import { GroFile, GroAtoms } from '../../mol-io/reader/gro/schema';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { Column } from '../../mol-data/db';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { Column, Table } from '../../mol-data/db';
import { guessElementSymbolString } from './util';
import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { ComponentBuilder } from './common/component';
import { getChainId } from './common/util';
import { EntityBuilder } from './common/entity';
+import { BasicData, BasicSchema, createBasic } from './basic/schema';
+import { createModels } from './basic/parser';
// TODO multi model files
-function getCategories(atoms: GroAtoms) {
- const auth_atom_id = CifField.ofColumn(atoms.atomName)
- const auth_comp_id = CifField.ofColumn(atoms.residueName)
+function getBasic(atoms: GroAtoms): BasicData {
+ const auth_atom_id = atoms.atomName
+ const auth_comp_id = atoms.residueName
const entityIds = new Array<string>(atoms.count)
const asymIds = new Array<string>(atoms.count)
@@ -69,57 +68,57 @@ function getCategories(atoms: GroAtoms) {
ids[i] = i
}
- const auth_asym_id = CifField.ofColumn(Column.ofStringArray(asymIds))
+ const auth_asym_id = Column.ofStringArray(asymIds)
- const atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+ const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id,
auth_atom_id,
auth_comp_id,
- auth_seq_id: CifField.ofColumn(atoms.residueNumber),
- B_iso_or_equiv: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_x: CifField.ofNumbers(Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
- Cartn_y: CifField.ofNumbers(Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
- Cartn_z: CifField.ofNumbers(Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
- group_PDB: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- id: CifField.ofColumn(Column.ofIntArray(ids)),
-
- label_alt_id: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
+ auth_seq_id: atoms.residueNumber,
+ Cartn_x: Column.ofFloatArray(Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
+ Cartn_y: Column.ofFloatArray(Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
+ Cartn_z: Column.ofFloatArray(Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
+ id: Column.ofIntArray(ids),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
- label_seq_id: CifField.ofColumn(Column.ofIntArray(seqIds)),
- label_entity_id: CifField.ofColumn(Column.ofStringArray(entityIds)),
+ label_seq_id: Column.ofIntArray(seqIds),
+ label_entity_id: Column.ofStringArray(entityIds),
- occupancy: CifField.ofColumn(Column.ofConst(1, atoms.count, Column.Schema.float)),
- type_symbol: CifField.ofStrings(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+ occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+ type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
- pdbx_PDB_ins_code: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
- }
+ pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+ }, atoms.count)
- return {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
- atom_site: CifCategory.ofFields('atom_site', atom_site)
- }
+ return createBasic({
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
+ atom_site
+ })
}
-function groToMmCif(gro: GroFile) {
- const categories = getCategories(gro.structures[0].atoms)
+//
+
+export { GroFormat }
- return {
- header: gro.structures[0].header.title,
- categoryNames: Object.keys(categories),
- categories
- };
+type GroFormat = ModelFormat<GroFile>
+
+namespace GroFormat {
+ export function is(x: ModelFormat): x is GroFormat {
+ return x.kind === 'gro'
+ }
+
+ export function fromGro(gro: GroFile): GroFormat {
+ return { kind: 'gro', name: gro.structures[0].header.title, data: gro };
+ }
}
export function trajectoryFromGRO(gro: GroFile): Task<Model.Trajectory> {
return Task.create('Parse GRO', async ctx => {
- await ctx.update('Converting to mmCIF');
- const cif = groToMmCif(gro);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = GroFormat.fromGro(gro);
+ const basic = getBasic(gro.structures[0].atoms)
+ return createModels(basic, format, ctx);
})
}
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index ea8c6de0653c21bb9f0542f25e4fa69123be5462..d52f7898ce97b0431e80ea59a6e726efa58e3660 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,9 +8,90 @@
import { Model } from '../../mol-model/structure/model/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
-import { CifFrame } from '../../mol-io/reader/cif';
+import { CifFrame, CIF } from '../../mol-io/reader/cif';
+import { mmCIF_Database, mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { createModels } from './basic/parser';
+import { ModelSymmetry } from './property/symmetry';
+import { ModelSecondaryStructure } from './property/secondary-structure';
+import { Table } from '../../mol-data/db';
+import { AtomSiteAnisotrop } from './property/anisotropic';
+import { ComponentBond } from './property/bonds/comp';
+import { StructConn } from './property/bonds/struct_conn';
+import { ModelCrossLinkRestraint } from './property/pair-restraints/cross-links';
+
+function modelSymmetryFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ return ModelSymmetry.fromData(model.sourceData.data.db)
+}
+ModelSymmetry.Provider.formatRegistry.add('mmCIF', modelSymmetryFromMmcif)
+
+function secondaryStructureFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { struct_conf, struct_sheet_range } = model.sourceData.data.db
+ return ModelSecondaryStructure.fromStruct(struct_conf, struct_sheet_range, model.atomicHierarchy)
+}
+ModelSecondaryStructure.Provider.formatRegistry.add('mmCIF', secondaryStructureFromMmcif)
+
+function atomSiteAnisotropFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { atom_site_anisotrop } = model.sourceData.data.db
+ const data = Table.ofColumns(mmCIF_Schema['atom_site_anisotrop'], atom_site_anisotrop);
+ const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model, data)
+ return { data, elementToAnsiotrop }
+}
+AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif)
+
+function componentBondFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { chem_comp_bond } = model.sourceData.data.db;
+ if (chem_comp_bond._rowCount === 0) return;
+ return {
+ data: chem_comp_bond,
+ entries: ComponentBond.getEntriesFromChemCompBond(chem_comp_bond)
+ }
+}
+ComponentBond.Provider.formatRegistry.add('mmCIF', componentBondFromMmcif)
+
+function structConnFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { struct_conn } = model.sourceData.data.db;
+ if (struct_conn._rowCount === 0) return;
+ const entries = StructConn.getEntriesFromStructConn(struct_conn, model)
+ return {
+ data: struct_conn,
+ byAtomIndex: StructConn.getAtomIndexFromEntries(entries),
+ entries,
+ }
+}
+StructConn.Provider.formatRegistry.add('mmCIF', structConnFromMmcif)
+
+function crossLinkRestraintFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { ihm_cross_link_restraint } = model.sourceData.data.db;
+ if (ihm_cross_link_restraint._rowCount === 0) return;
+ return ModelCrossLinkRestraint.fromTable(ihm_cross_link_restraint, model)
+}
+ModelCrossLinkRestraint.Provider.formatRegistry.add('mmCIF', crossLinkRestraintFromMmcif)
+
+//
+
+export { MmcifFormat }
+
+type MmcifFormat = ModelFormat<MmcifFormat.Data>
+
+namespace MmcifFormat {
+ export type Data = { db: mmCIF_Database, frame: CifFrame }
+ export function is(x: ModelFormat): x is MmcifFormat {
+ return x.kind === 'mmCIF'
+ }
+
+ export function fromFrame(frame: CifFrame, db?: mmCIF_Database): MmcifFormat {
+ if (!db) db = CIF.schema.mmCIF(frame)
+ return { kind: 'mmCIF', name: db._name, data: { db, frame } };
+ }
+}
export function trajectoryFromMmCIF(frame: CifFrame): Task<Model.Trajectory> {
- return Task.create('Create mmCIF Model', ctx => _parse_mmCif(ModelFormat.mmCIF(frame), ctx));
+ const format = MmcifFormat.fromFrame(frame)
+ return Task.create('Create mmCIF Model', ctx => createModels(format.data.db, format, ctx));
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/anisotropic.ts b/src/mol-model-formats/structure/mmcif/anisotropic.ts
deleted file mode 100644
index b4ae035eb11be2951a3ad627edebb06c66964cf4..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/anisotropic.ts
+++ /dev/null
@@ -1,88 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Table } from '../../../mol-data/db';
-import { Model, CustomPropertyDescriptor } from '../../../mol-model/structure';
-import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { CifWriter } from '../../../mol-io/writer/cif';
-
-export interface AtomSiteAnisotrop {
- data: Table<AtomSiteAnisotrop.Schema['atom_site_anisotrop']>
- /** maps atom_site-index to atom_site_anisotrop-index */
- elementToAnsiotrop: Int32Array
-}
-
-export namespace AtomSiteAnisotrop {
- export function getAtomSiteAnisotrop(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const { atom_site_anisotrop } = model.sourceData.data
- return Table.ofColumns(Schema.atom_site_anisotrop, atom_site_anisotrop);
- }
-
- export const PropName = '__AtomSiteAnisotrop__';
- export function get(model: Model): AtomSiteAnisotrop | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName]
- if (!model.customProperties.has(Descriptor)) return void 0;
-
- const data = getAtomSiteAnisotrop(model);
- if (!data) return void 0;
-
- const prop = { data, elementToAnsiotrop: getElementToAnsiotrop(model, data) }
- set(model, prop)
-
- return prop;
- }
- function set(model: Model, prop: AtomSiteAnisotrop) {
- (model._staticPropertyData[PropName] as AtomSiteAnisotrop) = prop;
- }
-
- export const Schema = { atom_site_anisotrop: mmCIF_Schema['atom_site_anisotrop'] };
- export type Schema = typeof Schema
-
- export const Descriptor: CustomPropertyDescriptor = {
- name: 'atom_site_anisotrop',
- cifExport: {
- prefix: '',
- categories: [{
- name: 'atom_site_anisotrop',
- instance(ctx) {
- const atom_site_anisotrop = getAtomSiteAnisotrop(ctx.firstModel);
- if (!atom_site_anisotrop) return CifWriter.Category.Empty;
- return CifWriter.Category.ofTable(atom_site_anisotrop);
- }
- }]
- }
- };
-
- function getElementToAnsiotrop(model: Model, data: Table<Schema['atom_site_anisotrop']>) {
- const { atomId } = model.atomicConformation
- const atomIdToElement = new Int32Array(atomId.rowCount)
- atomIdToElement.fill(-1)
- for (let i = 0, il = atomId.rowCount; i < il; i++) {
- atomIdToElement[atomId.value(i)] = i
- }
-
- const { id } = data
- const elementToAnsiotrop = new Int32Array(atomId.rowCount)
- elementToAnsiotrop.fill(-1)
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- const ei = atomIdToElement[id.value(i)]
- if (ei !== -1) elementToAnsiotrop[ei] = i
- }
-
- return elementToAnsiotrop
- }
-
- export async function attachFromMmCif(model: Model) {
- if (model.customProperties.has(Descriptor)) return true;
- if (model.sourceData.kind !== 'mmCIF') return false;
- const atomSiteAnisotrop = getAtomSiteAnisotrop(model);
- if (!atomSiteAnisotrop || atomSiteAnisotrop._rowCount === 0) return false;
-
- model.customProperties.add(Descriptor);
- return true;
- }
-}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/bonds.ts b/src/mol-model-formats/structure/mmcif/bonds.ts
deleted file mode 100644
index 0f69970236251826f5c529d481726b6d2c82b8fc..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/bonds.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-/**
- * Copyright (c) 2017-2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export * from './bonds/comp'
-export * from './bonds/struct_conn'
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
deleted file mode 100644
index 8c8edd3857bd15ebaa93119853bcec9dc611fc69..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
+++ /dev/null
@@ -1,250 +0,0 @@
-/**
- * Copyright (c) 2017-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Model } from '../../../../mol-model/structure/model/model'
-import { Structure } from '../../../../mol-model/structure'
-import { BondType } from '../../../../mol-model/structure/model/types'
-import { findEntityIdByAsymId, findAtomIndexByLabelName } from '../util'
-import { Column } from '../../../../mol-data/db'
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
-import { mmCIF_Database } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { SortedArray } from '../../../../mol-data/int';
-import { CifWriter } from '../../../../mol-io/writer/cif'
-import { ElementIndex, ResidueIndex } from '../../../../mol-model/structure/model/indexing';
-import { getInterBondOrderFromTable } from '../../../../mol-model/structure/model/properties/atomic/bonds';
-
-export interface StructConn {
- getResidueEntries(residueAIndex: ResidueIndex, residueBIndex: ResidueIndex): ReadonlyArray<StructConn.Entry>,
- getAtomEntries(atomIndex: ElementIndex): ReadonlyArray<StructConn.Entry>,
- readonly entries: ReadonlyArray<StructConn.Entry>
-}
-
-export namespace StructConn {
- export const Descriptor: CustomPropertyDescriptor = {
- name: 'struct_conn',
- cifExport: {
- prefix: '',
- categories: [{
- name: 'struct_conn',
- instance(ctx) {
- const structure = ctx.structures[0], model = structure.model;
- const struct_conn = getStructConn(model);
- if (!struct_conn) return CifWriter.Category.Empty;
-
- const strConn = get(model);
- if (!strConn || strConn.entries.length === 0) return CifWriter.Category.Empty;
-
- const foundAtoms = new Set<ElementIndex>();
- const indices: number[] = [];
- for (const entry of strConn.entries) {
- const { partners } = entry;
- let hasAll = true;
- for (let i = 0, _i = partners.length; i < _i; i++) {
- const atom = partners[i].atomIndex;
- if (foundAtoms.has(atom)) continue;
- if (hasAtom(structure, atom)) {
- foundAtoms.add(atom);
- } else {
- hasAll = false;
- break;
- }
- }
- if (hasAll) {
- indices[indices.length] = entry.rowIndex;
- }
- }
-
- return CifWriter.Category.ofTable(struct_conn, indices);
- }
- }]
- }
- }
-
- function hasAtom({ units }: Structure, element: ElementIndex) {
- for (let i = 0, _i = units.length; i < _i; i++) {
- if (SortedArray.indexOf(units[i].elements, element) >= 0) return true;
- }
- return false;
- }
-
- function _resKey(rA: number, rB: number) {
- if (rA < rB) return `${rA}-${rB}`;
- return `${rB}-${rA}`;
- }
- const _emptyEntry: Entry[] = [];
-
- class StructConnImpl implements StructConn {
- private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
- private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
-
- private getResiduePairIndex() {
- if (this._residuePairIndex) return this._residuePairIndex;
- this._residuePairIndex = new Map();
- for (const e of this.entries) {
- const ps = e.partners;
- const l = ps.length;
- for (let i = 0; i < l - 1; i++) {
- for (let j = i + i; j < l; j++) {
- const key = _resKey(ps[i].residueIndex, ps[j].residueIndex);
- if (this._residuePairIndex.has(key)) {
- this._residuePairIndex.get(key)!.push(e);
- } else {
- this._residuePairIndex.set(key, [e]);
- }
- }
- }
- }
- return this._residuePairIndex;
- }
-
- private getAtomIndex() {
- if (this._atomIndex) return this._atomIndex;
- this._atomIndex = new Map();
- for (const e of this.entries) {
- for (const p of e.partners) {
- const key = p.atomIndex;
- if (this._atomIndex.has(key)) {
- this._atomIndex.get(key)!.push(e);
- } else {
- this._atomIndex.set(key, [e]);
- }
- }
- }
- return this._atomIndex;
- }
-
- getResidueEntries(residueAIndex: ResidueIndex, residueBIndex: ResidueIndex): ReadonlyArray<StructConn.Entry> {
- return this.getResiduePairIndex().get(_resKey(residueAIndex, residueBIndex)) || _emptyEntry;
- }
-
- getAtomEntries(atomIndex: ElementIndex): ReadonlyArray<StructConn.Entry> {
- return this.getAtomIndex().get(atomIndex) || _emptyEntry;
- }
-
- constructor(public entries: StructConn.Entry[]) {
- }
- }
-
- export interface Entry {
- rowIndex: number,
- distance: number,
- order: number,
- flags: number,
- partners: { residueIndex: ResidueIndex, atomIndex: ElementIndex, symmetry: string }[]
- }
-
- export function attachFromMmCif(model: Model): boolean {
- if (model.customProperties.has(Descriptor)) return true;
- if (model.sourceData.kind !== 'mmCIF') return false;
- const { struct_conn } = model.sourceData.data;
- if (struct_conn._rowCount === 0) return false;
- model.customProperties.add(Descriptor);
- model._staticPropertyData.__StructConnData__ = struct_conn;
- return true;
- }
-
- function getStructConn(model: Model) {
- return model._staticPropertyData.__StructConnData__ as mmCIF_Database['struct_conn'];
- }
-
- export const PropName = '__StructConn__';
- export function get(model: Model): StructConn | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
- if (!model.customProperties.has(Descriptor)) return void 0;
-
- const struct_conn = getStructConn(model);
-
- const { conn_type_id, pdbx_dist_value, pdbx_value_order } = struct_conn;
- const p1 = {
- label_asym_id: struct_conn.ptnr1_label_asym_id,
- label_seq_id: struct_conn.ptnr1_label_seq_id,
- auth_seq_id: struct_conn.ptnr1_auth_seq_id,
- label_atom_id: struct_conn.ptnr1_label_atom_id,
- label_alt_id: struct_conn.pdbx_ptnr1_label_alt_id,
- ins_code: struct_conn.pdbx_ptnr1_PDB_ins_code,
- symmetry: struct_conn.ptnr1_symmetry
- };
- const p2: typeof p1 = {
- label_asym_id: struct_conn.ptnr2_label_asym_id,
- label_seq_id: struct_conn.ptnr2_label_seq_id,
- auth_seq_id: struct_conn.ptnr2_auth_seq_id,
- label_atom_id: struct_conn.ptnr2_label_atom_id,
- label_alt_id: struct_conn.pdbx_ptnr2_label_alt_id,
- ins_code: struct_conn.pdbx_ptnr2_PDB_ins_code,
- symmetry: struct_conn.ptnr2_symmetry
- };
-
- const _p = (row: number, ps: typeof p1) => {
- if (ps.label_asym_id.valueKind(row) !== Column.ValueKind.Present) return void 0;
- const asymId = ps.label_asym_id.value(row);
- const residueIndex = model.atomicHierarchy.index.findResidue(
- findEntityIdByAsymId(model, asymId),
- asymId,
- ps.auth_seq_id.value(row),
- ps.ins_code.value(row)
- );
- if (residueIndex < 0) return void 0;
- const atomName = ps.label_atom_id.value(row);
- // turns out "mismat" records might not have atom name value
- if (!atomName) return void 0;
- const atomIndex = findAtomIndexByLabelName(model, residueIndex, atomName, ps.label_alt_id.value(row));
- if (atomIndex < 0) return void 0;
- return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) || '1_555' };
- }
-
- const _ps = (row: number) => {
- const ret = [];
- let p = _p(row, p1);
- if (p) ret.push(p);
- p = _p(row, p2);
- if (p) ret.push(p);
- return ret;
- }
-
- const entries: StructConn.Entry[] = [];
- for (let i = 0; i < struct_conn._rowCount; i++) {
- const partners = _ps(i);
- if (partners.length < 2) continue;
-
- const type = conn_type_id.value(i)
- const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
- let flags = BondType.Flag.None;
- let order = 1;
-
- switch (orderType) {
- case 'sing': order = 1; break;
- case 'doub': order = 2; break;
- case 'trip': order = 3; break;
- case 'quad': order = 4; break;
- default:
- order = getInterBondOrderFromTable(
- struct_conn.ptnr1_label_comp_id.value(i),
- struct_conn.ptnr1_label_atom_id.value(i),
- struct_conn.ptnr2_label_comp_id.value(i),
- struct_conn.ptnr2_label_atom_id.value(i)
- )
- }
-
- switch (type) {
- case 'covale':
- flags = BondType.Flag.Covalent;
- break;
- case 'disulf': flags = BondType.Flag.Covalent | BondType.Flag.Disulfide; break;
- case 'hydrog':
- flags = BondType.Flag.HydrogenBond;
- break;
- case 'metalc': flags = BondType.Flag.MetallicCoordination; break;
- }
-
- entries.push({ rowIndex: i, flags, order, distance: pdbx_dist_value.value(i), partners });
- }
-
- const ret = new StructConnImpl(entries);
- model._staticPropertyData[PropName] = ret;
- return ret;
- }
-}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/pair-restraint.ts b/src/mol-model-formats/structure/mmcif/pair-restraint.ts
deleted file mode 100644
index 40cec49d41786cc3576f29bca18c357e87cb715e..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/pair-restraint.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export * from './pair-restraints/cross-links'
-// export * from './pair-restraints/predicted-contacts'
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
deleted file mode 100644
index 8f19909479f858d24406f421f324863c1b10f291..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ /dev/null
@@ -1,529 +0,0 @@
-/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Column, Table } from '../../../mol-data/db';
-import { mmCIF_Database, mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry';
-import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
-import { RuntimeContext } from '../../../mol-task';
-import UUID from '../../../mol-util/uuid';
-import { Model } from '../../../mol-model/structure/model/model';
-import { Entities, ChemicalComponent, MissingResidue, EntitySubtype } from '../../../mol-model/structure/model/properties/common';
-import { CustomProperties } from '../../../mol-model/structure';
-import { ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry';
-import { createAssemblies } from './assembly';
-import { getAtomicHierarchyAndConformation } from './atomic';
-import { ComponentBond } from './bonds';
-import { getIHMCoarse, EmptyIHMCoarse, IHMData } from './ihm';
-import { getSecondaryStructure } from './secondary-structure';
-import { getSequence } from './sequence';
-import { sortAtomSite } from './sort';
-import { StructConn } from './bonds/struct_conn';
-import { getMoleculeType, MoleculeType, getEntityType, getEntitySubtype, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
-import { ModelFormat } from '../format';
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
-import mmCIF_Format = ModelFormat.mmCIF
-import { memoize1 } from '../../../mol-util/memoize';
-import { ElementIndex, EntityIndex } from '../../../mol-model/structure/model';
-import { AtomSiteAnisotrop } from './anisotropic';
-import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
-
-export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
- const formatData = getFormatData(format)
- const isIHM = format.data.ihm_model_list._rowCount > 0;
- return isIHM ? await readIHM(ctx, format, formatData) : await readStandard(ctx, format, formatData);
-}
-
-type AtomSite = mmCIF_Database['atom_site']
-
-function getSymmetry(format: mmCIF_Format): ModelSymmetry {
- const assemblies = createAssemblies(format);
- const spacegroup = getSpacegroup(format);
- const isNonStandardCrytalFrame = checkNonStandardCrystalFrame(format, spacegroup);
- return { assemblies, spacegroup, isNonStandardCrytalFrame, ncsOperators: getNcsOperators(format) };
-}
-
-function checkNonStandardCrystalFrame(format: mmCIF_Format, spacegroup: Spacegroup) {
- const { atom_sites } = format.data;
- if (atom_sites._rowCount === 0) return false;
- // TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
- return false;
-}
-
-function getSpacegroupNameOrNumber(symmetry: mmCIF_Format['data']['symmetry']) {
- const groupNumber = symmetry['Int_Tables_number'].value(0);
- const groupName = symmetry['space_group_name_H-M'].value(0);
- if (!symmetry['Int_Tables_number'].isDefined) return groupName
- if (!symmetry['space_group_name_H-M'].isDefined) return groupNumber
- return groupName
-}
-
-function getSpacegroup(format: mmCIF_Format): Spacegroup {
- const { symmetry, cell } = format.data;
- if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
- const nameOrNumber = getSpacegroupNameOrNumber(symmetry)
- const spaceCell = SpacegroupCell.create(nameOrNumber,
- Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
- Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
-
- return Spacegroup.create(spaceCell);
-}
-
-function getNcsOperators(format: mmCIF_Format) {
- const { struct_ncs_oper } = format.data;
- if (struct_ncs_oper._rowCount === 0) return void 0;
- const { id, matrix, vector } = struct_ncs_oper;
-
- const matrixSpace = mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmCIF_Schema.struct_ncs_oper.vector.space;
-
- const opers: SymmetryOperator[] = [];
- for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
- const m = Tensor.toMat3(Mat3(), matrixSpace, matrix.value(i));
- const v = Tensor.toVec3(Vec3(), vectorSpace, vector.value(i));
- if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue;
- // ignore non-identity 'given' NCS operators
- if (struct_ncs_oper.code.value(i) === 'given' && !Mat3.isIdentity(m) && !Vec3.isZero(v)) continue;
- const ncsId = id.value(i)
- opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${ncsId}`, m, v, ncsId);
- }
- return opers;
-}
-
-function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['modifiedResidues'] {
- const data = format.data.pdbx_struct_mod_residue;
- const parentId = new Map<string, string>();
- const details = new Map<string, string>();
- const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
- const parent_id = data.parent_comp_id, details_data = data.details;
-
- for (let i = 0; i < data._rowCount; i++) {
- const id = comp_id.value(i);
- parentId.set(id, parent_id.value(i));
- details.set(id, details_data.value(i));
- }
-
- return { parentId, details };
-}
-
-function getMissingResidues(format: mmCIF_Format): Model['properties']['missingResidues'] {
- const map = new Map<string, MissingResidue>();
- const c = format.data.pdbx_unobs_or_zero_occ_residues
-
- const getKey = (model_num: number, asym_id: string, seq_id: number) => {
- return `${model_num}|${asym_id}|${seq_id}`
- }
-
- for (let i = 0, il = c._rowCount; i < il; ++i) {
- const key = getKey(c.PDB_model_num.value(i), c.label_asym_id.value(i), c.label_seq_id.value(i))
- map.set(key, { polymer_flag: c.polymer_flag.value(i), occupancy_flag: c.occupancy_flag.value(i) })
- }
-
- return {
- has: (model_num: number, asym_id: string, seq_id: number) => {
- return map.has(getKey(model_num, asym_id, seq_id))
- },
- get: (model_num: number, asym_id: string, seq_id: number) => {
- return map.get(getKey(model_num, asym_id, seq_id))
- },
- size: map.size
- }
-}
-
-function getChemicalComponentMap(format: mmCIF_Format): Model['properties']['chemicalComponentMap'] {
- const map = new Map<string, ChemicalComponent>();
- const { chem_comp } = format.data
-
- if (chem_comp._rowCount > 0) {
- const { id } = chem_comp
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- map.set(id.value(i), Table.getRow(chem_comp, i))
- }
- } else {
- const uniqueNames = getUniqueComponentNames(format);
- uniqueNames.forEach(n => {
- map.set(n, getDefaultChemicalComponent(n));
- });
- }
- return map
-}
-
-function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
- const map = new Map<string, SaccharideComponent>();
-
- if (format.data.pdbx_chem_comp_identifier._rowCount > 0) {
- // note that `pdbx_chem_comp_identifier` does not contain
- // a 'SNFG CARBOHYDRATE SYMBOL' entry for 'Unknown' saccharide components
- // so we always need to check `chem_comp` for those
- const { comp_id, type, identifier } = format.data.pdbx_chem_comp_identifier
- for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
- if (type.value(i) === 'SNFG CARBOHYDRATE SYMBOL' ||
- type.value(i) === 'SNFG CARB SYMBOL' // legacy, to be removed from mmCIF dictionary
- ) {
- const snfgName = identifier.value(i)
- const saccharideComp = SaccharidesSnfgMap.get(snfgName)
- if (saccharideComp) {
- map.set(comp_id.value(i), saccharideComp)
- } else {
- console.warn(`Unknown SNFG name '${snfgName}'`)
- }
- }
- }
- }
-
- if (format.data.chem_comp._rowCount > 0) {
- const { id, type } = format.data.chem_comp
- for (let i = 0, il = id.rowCount; i < il; ++i) {
- const _id = id.value(i)
- if (map.has(_id)) continue
- const _type = type.value(i)
- if (SaccharideCompIdMap.has(_id)) {
- map.set(_id, SaccharideCompIdMap.get(_id)!)
- } else if (getMoleculeType(_type, _id) === MoleculeType.Saccharide) {
- map.set(_id, UnknownSaccharideComponent)
- }
- }
- } else {
- const uniqueNames = getUniqueComponentNames(format)
- SaccharideCompIdMap.forEach((v, k) => {
- if (!map.has(k) && uniqueNames.has(k)) map.set(k, v)
- })
- }
- return map
-}
-
-const getUniqueComponentNames = memoize1((format: mmCIF_Format) => {
- const uniqueNames = new Set<string>()
- const data = format.data.atom_site
- const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
- for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
- uniqueNames.add(comp_id.value(i))
- }
- return uniqueNames
-})
-
-export interface FormatData {
- modifiedResidues: Model['properties']['modifiedResidues']
- missingResidues: Model['properties']['missingResidues']
- chemicalComponentMap: Model['properties']['chemicalComponentMap']
- saccharideComponentMap: Model['properties']['saccharideComponentMap']
-}
-
-function getFormatData(format: mmCIF_Format): FormatData {
- return {
- modifiedResidues: getModifiedResidueNameMap(format),
- missingResidues: getMissingResidues(format),
- chemicalComponentMap: getChemicalComponentMap(format),
- saccharideComponentMap: getSaccharideComponentMap(format)
- }
-}
-
-function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model): Model {
- const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, formatData, previous);
- const modelNum = atom_site.pdbx_PDB_model_num.value(0)
- if (previous && atomic.sameAsPrevious) {
- return {
- ...previous,
- id: UUID.create22(),
- modelNum,
- atomicConformation: atomic.conformation,
- _dynamicPropertyData: Object.create(null)
- };
- }
-
- const coarse = EmptyIHMCoarse;
- const sequence = getSequence(format.data, entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
- const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence)
-
- const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
- ? format.data.entry.id.value(0)
- : format.data._name;
-
- const label: string[] = []
- if (entry) label.push(entry)
- if (format.data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(format.data.struct.title.value(0))
-
- return {
- id: UUID.create22(),
- entryId: entry,
- label: label.join(' | '),
- entry,
- sourceData: format,
- modelNum,
- entities,
- symmetry: getSymmetry(format),
- sequence,
- atomicHierarchy: atomic.hierarchy,
- atomicConformation: atomic.conformation,
- atomicRanges,
- coarseHierarchy: coarse.hierarchy,
- coarseConformation: coarse.conformation,
- properties: {
- secondaryStructure: getSecondaryStructure(format.data, atomic.hierarchy),
- ...formatData
- },
- customProperties: new CustomProperties(),
- _staticPropertyData: Object.create(null),
- _dynamicPropertyData: Object.create(null)
- };
-}
-
-function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
- const atomic = getAtomicHierarchyAndConformation(data.atom_site, data.atom_site_sourceIndex, data.entities, formatData);
- const coarse = getIHMCoarse(data, formatData);
- const sequence = getSequence(format.data, data.entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
- const atomicRanges = getAtomicRanges(atomic.hierarchy, data.entities, atomic.conformation, sequence)
-
- const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
- ? format.data.entry.id.value(0)
- : format.data._name;
-
- const label: string[] = []
- if (entry) label.push(entry)
- if (format.data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(format.data.struct.title.value(0))
- if (data.model_group_name) label.push(data.model_name)
- if (data.model_group_name) label.push(data.model_group_name)
-
- return {
- id: UUID.create22(),
- entryId: entry,
- label: label.join(' | '),
- entry,
- sourceData: format,
- modelNum: data.model_id,
- entities: data.entities,
- symmetry: getSymmetry(format),
- sequence,
- atomicHierarchy: atomic.hierarchy,
- atomicConformation: atomic.conformation,
- atomicRanges,
- coarseHierarchy: coarse.hierarchy,
- coarseConformation: coarse.conformation,
- properties: {
- secondaryStructure: getSecondaryStructure(format.data, atomic.hierarchy),
- ...formatData
- },
- customProperties: new CustomProperties(),
- _staticPropertyData: Object.create(null),
- _dynamicPropertyData: Object.create(null)
- };
-}
-
-function attachProps(model: Model) {
- ComponentBond.attachFromMmCif(model);
- StructConn.attachFromMmCif(model);
- AtomSiteAnisotrop.attachFromMmCif(model);
-}
-
-function findModelEnd(num: Column<number>, startIndex: number) {
- const rowCount = num.rowCount;
- if (!num.isDefined) return rowCount;
- let endIndex = startIndex + 1;
- while (endIndex < rowCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
- return endIndex;
-}
-
-function getEntities(format: mmCIF_Format): Entities {
- let entityData: Table<mmCIF_Schema['entity']>
-
- if (!format.data.entity.id.isDefined) {
- const entityIds = new Set<string>()
-
- const ids: mmCIF_Schema['entity']['id']['T'][] = []
- const types: mmCIF_Schema['entity']['type']['T'][] = []
-
- const { label_entity_id, label_comp_id } = format.data.atom_site;
- for (let i = 0 as ElementIndex, il = format.data.atom_site._rowCount; i < il; i++) {
- const entityId = label_entity_id.value(i);
- if (!entityIds.has(entityId)) {
- ids.push(entityId)
- types.push(getEntityType(label_comp_id.value(i)))
- entityIds.add(entityId)
- }
- }
-
- const { entity_id: sphere_entity_id } = format.data.ihm_sphere_obj_site;
- for (let i = 0 as ElementIndex, il = format.data.ihm_sphere_obj_site._rowCount; i < il; i++) {
- const entityId = sphere_entity_id.value(i);
- if (!entityIds.has(entityId)) {
- ids.push(entityId)
- types.push('polymer')
- entityIds.add(entityId)
- }
- }
-
- const { entity_id: gaussian_entity_id } = format.data.ihm_gaussian_obj_site;
- for (let i = 0 as ElementIndex, il = format.data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
- const entityId = gaussian_entity_id.value(i);
- if (!entityIds.has(entityId)) {
- ids.push(entityId)
- types.push('polymer')
- entityIds.add(entityId)
- }
- }
-
- entityData = Table.ofColumns(mmCIF_Schema.entity, {
- ...format.data.entity,
- id: Column.ofArray({ array: ids, schema: mmCIF_Schema.entity.id }),
- type: Column.ofArray({ array: types, schema: mmCIF_Schema.entity.type }),
- })
- } else {
- entityData = format.data.entity;
- }
-
- const getEntityIndex = Column.createIndexer<string, EntityIndex>(entityData.id)
-
- //
-
- const subtypes: EntitySubtype[] = new Array(entityData._rowCount)
- subtypes.fill('other')
-
- const entityIds = new Set<string>()
- let assignSubtype = false
-
- if (format.data.entity_poly.entity_id.isDefined) {
- const { entity_id, type, _rowCount } = format.data.entity_poly
- for (let i = 0; i < _rowCount; ++i) {
- const entityId = entity_id.value(i)
- subtypes[getEntityIndex(entityId)] = type.value(i)
- entityIds.add(entityId)
- }
- } else {
- assignSubtype = true
- }
-
- if (format.data.pdbx_entity_branch.entity_id.isDefined) {
- const { entity_id, type, _rowCount } = format.data.pdbx_entity_branch
- for (let i = 0; i < _rowCount; ++i) {
- const entityId = entity_id.value(i)
- subtypes[getEntityIndex(entityId)] = type.value(i)
- entityIds.add(entityId)
- }
- } else {
- assignSubtype = true
- }
-
- if (assignSubtype) {
- const chemCompType = new Map<string, string>()
- const { id, type } = format.data.chem_comp;
- for (let i = 0, il = format.data.chem_comp._rowCount; i < il; i++) {
- chemCompType.set(id.value(i), type.value(i))
- }
-
- const { label_entity_id, label_comp_id } = format.data.atom_site;
- for (let i = 0 as ElementIndex, il = format.data.atom_site._rowCount; i < il; i++) {
- const entityId = label_entity_id.value(i);
- if (!entityIds.has(entityId)) {
- const compId = label_comp_id.value(i)
- const compType = chemCompType.get(compId) || ''
- subtypes[getEntityIndex(entityId)] = getEntitySubtype(compId, compType)
- entityIds.add(entityId)
- }
- }
- // TODO how to handle coarse?
- }
-
- const subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype })
-
- //
-
- return { data: entityData, subtype: subtypeColumn, getEntityIndex };
-}
-
-async function readStandard(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
- const atomCount = format.data.atom_site._rowCount;
- const entities = getEntities(format)
-
- const models: Model[] = [];
- let modelStart = 0;
- while (modelStart < atomCount) {
- const modelEnd = findModelEnd(format.data.atom_site.pdbx_PDB_model_num, modelStart);
- const { atom_site, sourceIndex } = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
- const model = createStandardModel(format, atom_site, sourceIndex, entities, formatData, models.length > 0 ? models[models.length - 1] : void 0);
- attachProps(model);
- models.push(model);
- modelStart = modelEnd;
- }
- return models;
-}
-
-function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
- const ret = new Map<number, { table: T, start: number, end: number }>()
- const rowCount = table._rowCount;
- let modelStart = 0;
- while (modelStart < rowCount) {
- const modelEnd = findModelEnd(col, modelStart);
- const id = col.value(modelStart);
- ret.set(id, {
- table: Table.window(table, table._schema, modelStart, modelEnd) as T,
- start: modelStart,
- end: modelEnd
- });
- modelStart = modelEnd;
- }
- return ret;
-}
-
-function getModelGroupName(model_id: number, format: mmCIF_Format) {
- const { ihm_model_group, ihm_model_group_link } = format.data;
-
- const link = Table.pickRow(ihm_model_group_link, i => ihm_model_group_link.model_id.value(i) === model_id)
- if (link) {
- const group = Table.pickRow(ihm_model_group, i => ihm_model_group.id.value(i) === link.group_id)
- if (group) return group.name
- }
- return ''
-}
-
-async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
- // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
- const atom_sites_modelColumn = format.data.atom_site.ihm_model_id.isDefined ? format.data.atom_site.ihm_model_id : format.data.atom_site.pdbx_PDB_model_num
-
- const { ihm_model_list } = format.data;
- const entities = getEntities(format)
-
- const atom_sites = splitTable(format.data.atom_site, atom_sites_modelColumn);
- // TODO: will coarse IHM records require sorting or will we trust it?
- // ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
- // If the sorting is implemented, updated mol-model/structure/properties: atom.sourceIndex
- const sphere_sites = splitTable(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site.model_id);
- const gauss_sites = splitTable(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site.model_id);
-
- const models: Model[] = [];
-
- const { model_id, model_name } = ihm_model_list;
- for (let i = 0; i < ihm_model_list._rowCount; i++) {
- const id = model_id.value(i);
-
- let atom_site, atom_site_sourceIndex;
- if (atom_sites.has(id)) {
- const e = atom_sites.get(id)!;
- // need to sort `format.data.atom_site` as `e.start` and `e.end` are indices into that
- const { atom_site: sorted, sourceIndex } = await sortAtomSite(ctx, format.data.atom_site, e.start, e.end);
- atom_site = sorted;
- atom_site_sourceIndex = sourceIndex;
- } else {
- atom_site = Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0);
- atom_site_sourceIndex = Column.ofIntArray([]);
- }
-
- const data: IHMData = {
- model_id: id,
- model_name: model_name.value(i),
- model_group_name: getModelGroupName(id, format),
- entities: entities,
- atom_site,
- atom_site_sourceIndex,
- ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site._schema, 0, 0),
- ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)!.table : Table.window(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site._schema, 0, 0)
- };
- const model = createModelIHM(format, data, formatData);
- attachProps(model);
- models.push(model);
- }
-
- return models;
-}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/util.ts b/src/mol-model-formats/structure/mmcif/util.ts
deleted file mode 100644
index 71d7ac58cc5810b6fda966b26b4966e4a01ee93f..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/util.ts
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Model } from '../../../mol-model/structure/model'
-import { ElementIndex } from '../../../mol-model/structure/model/indexing';
-
-export function findEntityIdByAsymId(model: Model, asymId: string) {
- if (model.sourceData.kind !== 'mmCIF') return ''
- const { struct_asym } = model.sourceData.data
- for (let i = 0, n = struct_asym._rowCount; i < n; ++i) {
- if (struct_asym.id.value(i) === asymId) return struct_asym.entity_id.value(i)
- }
- return ''
-}
-
-export function findAtomIndexByLabelName(model: Model, residueIndex: number, atomName: string, altLoc: string | null): ElementIndex {
- const { offsets } = model.atomicHierarchy.residueAtomSegments;
- const { label_atom_id, label_alt_id } = model.atomicHierarchy.atoms;
- for (let i = offsets[residueIndex], n = offsets[residueIndex + 1]; i < n; ++i) {
- if (label_atom_id.value(i) === atomName && (!altLoc || label_alt_id.value(i) === altLoc)) return i as ElementIndex;
- }
- return -1 as ElementIndex;
-}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/pdb.ts b/src/mol-model-formats/structure/pdb.ts
index 525ec39cccfa76c405fbb2d44b231b213ab0a946..c77392ec26435bf213bec83521a7f74f95836c17 100644
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.ts
@@ -1,21 +1,22 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PdbFile } from '../../mol-io/reader/pdb/schema';
import { pdbToMmCif } from './pdb/to-cif';
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
+import { MmcifFormat } from './mmcif';
+import { createModels } from './basic/parser';
export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
return Task.create('Parse PDB', async ctx => {
await ctx.update('Converting to mmCIF');
const cif = await pdbToMmCif(pdb);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = MmcifFormat.fromFrame(cif)
+ return createModels(format.data.db, format, ctx)
})
}
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index cf967d4359bbb2a6437f4973a3eb3a20069646b8..05e0f8592689d7a48a0d44b3cac74e06f83284d5 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -162,8 +162,8 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
const categories = {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
atom_site: CifCategory.ofFields('atom_site', getAtomSite(atomSite)),
atom_site_anisotrop: CifCategory.ofFields('atom_site_anisotrop', getAnisotropic(anisotropic))
} as any;
diff --git a/src/mol-model-formats/structure/property/anisotropic.ts b/src/mol-model-formats/structure/property/anisotropic.ts
new file mode 100644
index 0000000000000000000000000000000000000000..156fcb8926083d77d75dd277a22e48621530d972
--- /dev/null
+++ b/src/mol-model-formats/structure/property/anisotropic.ts
@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Table } from '../../../mol-data/db';
+import { Model, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { CifWriter } from '../../../mol-io/writer/cif';
+import { FormatPropertyProvider } from '../common/property';
+
+export { AtomSiteAnisotrop }
+
+type Anisotrop = Table<mmCIF_Schema['atom_site_anisotrop']>
+
+interface AtomSiteAnisotrop {
+ data: Anisotrop
+ /** maps atom_site-index to atom_site_anisotrop-index */
+ elementToAnsiotrop: Int32Array
+}
+
+namespace AtomSiteAnisotrop {
+ export const Descriptor: CustomPropertyDescriptor = {
+ name: 'atom_site_anisotrop',
+ cifExport: {
+ prefix: '',
+ categories: [{
+ name: 'atom_site_anisotrop',
+ instance(ctx) {
+ const p = Provider.get(ctx.firstModel);
+ if (!p) return CifWriter.Category.Empty;
+ // TODO filter to write only data for elements that exist in model
+ return CifWriter.Category.ofTable(p.data);
+ }
+ }]
+ }
+ };
+
+ export const Provider = FormatPropertyProvider.create<AtomSiteAnisotrop>(Descriptor)
+
+ export function getElementToAnsiotrop(model: Model, data: Anisotrop) {
+ const { atomId } = model.atomicConformation
+ const atomIdToElement = new Int32Array(atomId.rowCount)
+ atomIdToElement.fill(-1)
+ for (let i = 0, il = atomId.rowCount; i < il; i++) {
+ atomIdToElement[atomId.value(i)] = i
+ }
+
+ const { id } = data
+ const elementToAnsiotrop = new Int32Array(atomId.rowCount)
+ elementToAnsiotrop.fill(-1)
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ const ei = atomIdToElement[id.value(i)]
+ if (ei !== -1) elementToAnsiotrop[ei] = i
+ }
+
+ return elementToAnsiotrop
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/assembly.ts b/src/mol-model-formats/structure/property/assembly.ts
similarity index 84%
rename from src/mol-model-formats/structure/mmcif/assembly.ts
rename to src/mol-model-formats/structure/property/assembly.ts
index 46720eb26c5bd1560c93ef14b83e696fc359540e..f253cf1edfb65483a01a8ef7ec1733b589bc0644 100644
--- a/src/mol-model-formats/structure/mmcif/assembly.ts
+++ b/src/mol-model-formats/structure/property/assembly.ts
@@ -9,17 +9,20 @@ import { SymmetryOperator } from '../../../mol-math/geometry/symmetry-operator'
import { Assembly, OperatorGroup, OperatorGroups } from '../../../mol-model/structure/model/properties/symmetry'
import { Queries as Q } from '../../../mol-model/structure'
import { StructureProperties } from '../../../mol-model/structure';
-import { ModelFormat } from '../format';
-import mmCIF_Format = ModelFormat.mmCIF
+import { Table } from '../../../mol-data/db';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-export function createAssemblies(format: mmCIF_Format): ReadonlyArray<Assembly> {
- const { pdbx_struct_assembly } = format.data;
+type StructAssembly = Table<mmCIF_Schema['pdbx_struct_assembly']>
+type StructAssemblyGen = Table<mmCIF_Schema['pdbx_struct_assembly_gen']>
+type StructOperList = Table<mmCIF_Schema['pdbx_struct_oper_list']>
+
+export function createAssemblies(pdbx_struct_assembly: StructAssembly, pdbx_struct_assembly_gen: StructAssemblyGen, pdbx_struct_oper_list: StructOperList): ReadonlyArray<Assembly> {
if (!pdbx_struct_assembly._rowCount) return [];
- const matrices = getMatrices(format);
+ const matrices = getMatrices(pdbx_struct_oper_list);
const assemblies: Assembly[] = [];
for (let i = 0; i < pdbx_struct_assembly._rowCount; i++) {
- assemblies[assemblies.length] = createAssembly(format, i, matrices);
+ assemblies[assemblies.length] = createAssembly(pdbx_struct_assembly, pdbx_struct_assembly_gen, i, matrices);
}
return assemblies;
}
@@ -27,9 +30,7 @@ export function createAssemblies(format: mmCIF_Format): ReadonlyArray<Assembly>
type Matrices = Map<string, Mat4>
type Generator = { assemblyId: string, expression: string, asymIds: string[] }
-function createAssembly(format: mmCIF_Format, index: number, matrices: Matrices): Assembly {
- const { pdbx_struct_assembly, pdbx_struct_assembly_gen } = format.data;
-
+function createAssembly(pdbx_struct_assembly: StructAssembly, pdbx_struct_assembly_gen: StructAssemblyGen, index: number, matrices: Matrices): Assembly {
const id = pdbx_struct_assembly.id.value(index);
const details = pdbx_struct_assembly.details.value(index);
const generators: Generator[] = [];
@@ -70,8 +71,7 @@ function operatorGroupsProvider(generators: Generator[], matrices: Matrices): ()
}
}
-function getMatrices({ data }: mmCIF_Format): Matrices {
- const { pdbx_struct_oper_list } = data;
+function getMatrices(pdbx_struct_oper_list: StructOperList): Matrices {
const { id, matrix, vector, _schema } = pdbx_struct_oper_list;
const matrices = new Map<string, Mat4>();
diff --git a/src/mol-model-formats/structure/mmcif/bonds/comp.ts b/src/mol-model-formats/structure/property/bonds/comp.ts
similarity index 51%
rename from src/mol-model-formats/structure/mmcif/bonds/comp.ts
rename to src/mol-model-formats/structure/property/bonds/comp.ts
index 4ae1bfc330dff8550ebaf441fc0d78ff351622c3..21eafaa7f9f979a8aee88031e8d66a047a201015 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/comp.ts
+++ b/src/mol-model-formats/structure/property/bonds/comp.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,12 +8,14 @@
import { Model } from '../../../../mol-model/structure/model/model'
import { BondType } from '../../../../mol-model/structure/model/types'
import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
-import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../../mol-io/writer/cif'
import { Table } from '../../../../mol-data/db';
+import { FormatPropertyProvider } from '../../common/property';
export interface ComponentBond {
- entries: Map<string, ComponentBond.Entry>
+ readonly data: Table<mmCIF_Schema['chem_comp_bond']>
+ readonly entries: ReadonlyMap<string, ComponentBond.Entry>
}
export namespace ComponentBond {
@@ -24,7 +26,9 @@ export namespace ComponentBond {
categories: [{
name: 'chem_comp_bond',
instance(ctx) {
- const chem_comp_bond = getChemCompBond(ctx.firstModel);
+ const p = Provider.get(ctx.firstModel);
+ if (!p) return CifWriter.Category.Empty;
+ const chem_comp_bond = p.data;
if (!chem_comp_bond) return CifWriter.Category.Empty;
const comp_names = ctx.structures[0].uniqueResidueNames;
@@ -40,73 +44,27 @@ export namespace ComponentBond {
}
}
- export function attachFromMmCif(model: Model): boolean {
- if (model.customProperties.has(Descriptor)) return true;
- if (model.sourceData.kind !== 'mmCIF') return false;
- const { chem_comp_bond } = model.sourceData.data;
- if (chem_comp_bond._rowCount === 0) return false;
+ export const Provider = FormatPropertyProvider.create<ComponentBond>(Descriptor)
- model.customProperties.add(Descriptor);
- model._staticPropertyData.__ComponentBondData__ = chem_comp_bond;
- return true;
- }
-
- export function attachFromExternalData(model: Model, table: mmCIF_Database['chem_comp_bond'], force = false) {
- if (!force && model.customProperties.has(Descriptor)) return true;
- if (model._staticPropertyData.__ComponentBondData__) delete model._staticPropertyData.__ComponentBondData__;
- const chem_comp_bond = chemCompBondFromTable(model, table);
- if (chem_comp_bond._rowCount === 0) return false;
-
- model.customProperties.add(Descriptor);
- model._staticPropertyData.__ComponentBondData__ = chem_comp_bond;
- return true;
- }
-
- function chemCompBondFromTable(model: Model, table: mmCIF_Database['chem_comp_bond']): mmCIF_Database['chem_comp_bond'] {
+ export function chemCompBondFromTable(model: Model, table: Table<mmCIF_Schema['chem_comp_bond']>): Table<mmCIF_Schema['chem_comp_bond']> {
return Table.pick(table, mmCIF_Schema.chem_comp_bond, (i: number) => {
return model.properties.chemicalComponentMap.has(table.comp_id.value(i))
})
}
- export class ComponentBondImpl implements ComponentBond {
- entries: Map<string, ComponentBond.Entry> = new Map();
+ export function getEntriesFromChemCompBond(data: Table<mmCIF_Schema['chem_comp_bond']>) {
+ const entries: Map<string, Entry> = new Map();
- addEntry(id: string) {
+ function addEntry(id: string) {
let e = new Entry(id);
- this.entries.set(id, e);
+ entries.set(id, e);
return e;
}
- }
- export class Entry {
- map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
-
- add(a: string, b: string, order: number, flags: number, swap = true) {
- let e = this.map.get(a);
- if (e !== void 0) {
- let f = e.get(b);
- if (f === void 0) {
- e.set(b, { order, flags });
- }
- } else {
- let map = new Map<string, { order: number, flags: number }>();
- map.set(b, { order, flags });
- this.map.set(a, map);
- }
+ const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount } = data;
- if (swap) this.add(b, a, order, flags, false);
- }
-
- constructor(public id: string) {
- }
- }
-
- export function parseChemCompBond(data: mmCIF_Database['chem_comp_bond']): ComponentBond {
- const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount: rowCount } = data;
-
- const compBond = new ComponentBondImpl();
- let entry = compBond.addEntry(comp_id.value(0)!);
- for (let i = 0; i < rowCount; i++) {
+ let entry = addEntry(comp_id.value(0)!);
+ for (let i = 0; i < _rowCount; i++) {
const id = comp_id.value(i)!;
const nameA = atom_id_1.value(i)!;
const nameB = atom_id_2.value(i)!;
@@ -114,7 +72,7 @@ export namespace ComponentBond {
const aromatic = pdbx_aromatic_flag.value(i) === 'Y';
if (entry.id !== id) {
- entry = compBond.addEntry(id);
+ entry = addEntry(id);
}
let flags: number = BondType.Flag.Covalent;
@@ -132,23 +90,28 @@ export namespace ComponentBond {
entry.add(nameA, nameB, ord, flags);
}
- return compBond;
+ return entries
}
- function getChemCompBond(model: Model) {
- return model._staticPropertyData.__ComponentBondData__ as mmCIF_Database['chem_comp_bond'];
- }
+ export class Entry {
+ readonly map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
- export const PropName = '__ComponentBond__';
- export function get(model: Model): ComponentBond | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
- if (!model.customProperties.has(Descriptor)) return void 0;
+ add(a: string, b: string, order: number, flags: number, swap = true) {
+ let e = this.map.get(a);
+ if (e !== void 0) {
+ let f = e.get(b);
+ if (f === void 0) {
+ e.set(b, { order, flags });
+ }
+ } else {
+ let map = new Map<string, { order: number, flags: number }>();
+ map.set(b, { order, flags });
+ this.map.set(a, map);
+ }
- const chem_comp_bond = getChemCompBond(model);
- if (!chem_comp_bond) return void 0;
+ if (swap) this.add(b, a, order, flags, false);
+ }
- const chemComp = parseChemCompBond(chem_comp_bond);
- model._staticPropertyData[PropName] = chemComp;
- return chemComp;
+ constructor(public readonly id: string) { }
}
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/bonds/index-pair.ts b/src/mol-model-formats/structure/property/bonds/index-pair.ts
similarity index 54%
rename from src/mol-model-formats/structure/mmcif/bonds/index-pair.ts
rename to src/mol-model-formats/structure/property/bonds/index-pair.ts
index 22af2913d7f403ee6a42fcf01b2408f933eff851..8cc29e892471b5d9847dffb075c82efbf1d52d9d 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -1,13 +1,13 @@
/**
- * Copyright (c) 2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Model } from '../../../../mol-model/structure/model/model'
import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
import { IntAdjacencyGraph } from '../../../../mol-math/graph';
import { Column } from '../../../../mol-data/db';
+import { FormatPropertyProvider } from '../../common/property';
export type IndexPairBonds = IntAdjacencyGraph<number, { readonly order: ArrayLike<number> }>
@@ -27,6 +27,8 @@ export namespace IndexPairBonds {
name: 'index_pair_bonds',
}
+ export const Provider = FormatPropertyProvider.create<IndexPairBonds>(Descriptor)
+
export type Data = {
pairs: {
indexA: Column<number>,
@@ -36,33 +38,11 @@ export namespace IndexPairBonds {
count: number
}
- export function attachFromData(model: Model, data: Data): boolean {
- if (model.customProperties.has(Descriptor)) return true;
-
- model.customProperties.add(Descriptor);
- model._staticPropertyData.__IndexPairBondsData__ = data;
- return true;
- }
-
- function getIndexPairBonds(model: Model) {
- return model._staticPropertyData.__IndexPairBondsData__ as Data;
- }
-
- export const PropName = '__IndexPairBonds__';
- export function get(model: Model): IndexPairBonds | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
- if (!model.customProperties.has(Descriptor)) return void 0;
-
- const data = getIndexPairBonds(model);
- if (!data) return void 0;
+ export function fromData(data: Data) {
const { pairs, count } = data
-
const indexA = pairs.indexA.toArray()
const indexB = pairs.indexB.toArray()
const order = pairs.order.toArray()
-
- const indexPairBonds = getGraph(indexA, indexB, order, count);
- model._staticPropertyData[PropName] = indexPairBonds;
- return indexPairBonds;
+ return getGraph(indexA, indexB, order, count);
}
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/property/bonds/struct_conn.ts b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4462ebe20da53b2081ef4ec4961a3e9f98832728
--- /dev/null
+++ b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
@@ -0,0 +1,168 @@
+/**
+ * Copyright (c) 2017-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Model } from '../../../../mol-model/structure/model/model'
+import { Structure } from '../../../../mol-model/structure'
+import { BondType } from '../../../../mol-model/structure/model/types'
+import { Column, Table } from '../../../../mol-data/db'
+import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { SortedArray } from '../../../../mol-data/int';
+import { CifWriter } from '../../../../mol-io/writer/cif'
+import { ElementIndex, ResidueIndex } from '../../../../mol-model/structure/model/indexing';
+import { getInterBondOrderFromTable } from '../../../../mol-model/structure/model/properties/atomic/bonds';
+import { FormatPropertyProvider } from '../../common/property';
+
+export interface StructConn {
+ readonly data: Table<mmCIF_Schema['struct_conn']>
+ readonly byAtomIndex: Map<ElementIndex, ReadonlyArray<StructConn.Entry>>
+ readonly entries: ReadonlyArray<StructConn.Entry>
+}
+
+export namespace StructConn {
+ export const Descriptor: CustomPropertyDescriptor = {
+ name: 'struct_conn',
+ cifExport: {
+ prefix: '',
+ categories: [{
+ name: 'struct_conn',
+ instance(ctx) {
+ const p = Provider.get(ctx.firstModel);
+ if (!p || p.entries.length === 0) return CifWriter.Category.Empty;
+
+ const structure = ctx.structures[0]
+
+ const indices: number[] = [];
+ for (const e of p.entries) {
+ if (hasAtom(structure, e.partnerA.atomIndex) &&
+ hasAtom(structure, e.partnerB.atomIndex)) {
+ indices[indices.length] = e.rowIndex;
+ }
+ }
+
+ return CifWriter.Category.ofTable(p.data, indices);
+ }
+ }]
+ }
+ }
+
+ export const Provider = FormatPropertyProvider.create<StructConn>(Descriptor)
+
+ function hasAtom({ units }: Structure, element: ElementIndex) {
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ if (SortedArray.indexOf(units[i].elements, element) >= 0) return true;
+ }
+ return false;
+ }
+
+ export function getAtomIndexFromEntries(entries: StructConn['entries']) {
+ const m = new Map();
+ for (const e of entries) {
+ const { partnerA: { atomIndex: iA }, partnerB: { atomIndex: iB } } = e;
+ if (m.has(iA)) m.get(iA)!.push(e);
+ else m.set(iA, [e]);
+
+ if (m.has(iB)) m.get(iB)!.push(e);
+ else m.set(iB, [e]);
+ }
+ return m;
+ }
+
+ export interface Entry {
+ rowIndex: number,
+ distance: number,
+ order: number,
+ flags: number,
+ partnerA: { residueIndex: ResidueIndex, atomIndex: ElementIndex, symmetry: string },
+ partnerB: { residueIndex: ResidueIndex, atomIndex: ElementIndex, symmetry: string }
+ }
+
+ export function getEntriesFromStructConn(struct_conn: Table<mmCIF_Schema['struct_conn']>, model: Model): StructConn['entries'] {
+ const { conn_type_id, pdbx_dist_value, pdbx_value_order } = struct_conn;
+ const p1 = {
+ label_asym_id: struct_conn.ptnr1_label_asym_id,
+ label_seq_id: struct_conn.ptnr1_label_seq_id,
+ auth_seq_id: struct_conn.ptnr1_auth_seq_id,
+ label_atom_id: struct_conn.ptnr1_label_atom_id,
+ label_alt_id: struct_conn.pdbx_ptnr1_label_alt_id,
+ ins_code: struct_conn.pdbx_ptnr1_PDB_ins_code,
+ symmetry: struct_conn.ptnr1_symmetry
+ };
+ const p2: typeof p1 = {
+ label_asym_id: struct_conn.ptnr2_label_asym_id,
+ label_seq_id: struct_conn.ptnr2_label_seq_id,
+ auth_seq_id: struct_conn.ptnr2_auth_seq_id,
+ label_atom_id: struct_conn.ptnr2_label_atom_id,
+ label_alt_id: struct_conn.pdbx_ptnr2_label_alt_id,
+ ins_code: struct_conn.pdbx_ptnr2_PDB_ins_code,
+ symmetry: struct_conn.ptnr2_symmetry
+ };
+
+ const _p = (row: number, ps: typeof p1) => {
+ if (ps.label_asym_id.valueKind(row) !== Column.ValueKind.Present) return void 0;
+ const asymId = ps.label_asym_id.value(row);
+ const entityIndex = model.atomicHierarchy.index.findEntity(asymId);
+ if (entityIndex < 0) return void 0;
+ const residueIndex = model.atomicHierarchy.index.findResidue(
+ model.entities.data.id.value(entityIndex),
+ asymId,
+ ps.auth_seq_id.value(row),
+ ps.ins_code.value(row)
+ );
+ if (residueIndex < 0) return void 0;
+ const atomName = ps.label_atom_id.value(row);
+ // turns out "mismat" records might not have atom name value
+ if (!atomName) return void 0;
+ const atomIndex = model.atomicHierarchy.index.findAtomOnResidue(residueIndex, atomName, ps.label_alt_id.value(row));
+ if (atomIndex < 0) return void 0;
+ return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) };
+ }
+
+ const entries: StructConn.Entry[] = [];
+ for (let i = 0; i < struct_conn._rowCount; i++) {
+ const partnerA = _p(i, p1)
+ const partnerB = _p(i, p2)
+ if (partnerA === undefined || partnerB === undefined) continue;
+
+ const type = conn_type_id.value(i)
+ const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
+ let flags = BondType.Flag.None;
+ let order = 1;
+
+ switch (orderType) {
+ case 'sing': order = 1; break;
+ case 'doub': order = 2; break;
+ case 'trip': order = 3; break;
+ case 'quad': order = 4; break;
+ default:
+ order = getInterBondOrderFromTable(
+ struct_conn.ptnr1_label_comp_id.value(i),
+ struct_conn.ptnr1_label_atom_id.value(i),
+ struct_conn.ptnr2_label_comp_id.value(i),
+ struct_conn.ptnr2_label_atom_id.value(i)
+ )
+ }
+
+ switch (type) {
+ case 'covale':
+ flags = BondType.Flag.Covalent;
+ break;
+ case 'disulf': flags = BondType.Flag.Covalent | BondType.Flag.Disulfide; break;
+ case 'hydrog':
+ flags = BondType.Flag.HydrogenBond;
+ break;
+ case 'metalc': flags = BondType.Flag.MetallicCoordination; break;
+ }
+
+ entries.push({
+ rowIndex: i, flags, order, distance: pdbx_dist_value.value(i), partnerA, partnerB
+ });
+ }
+
+ return entries;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/pair-restraints/cross-links.ts b/src/mol-model-formats/structure/property/pair-restraints/cross-links.ts
similarity index 57%
rename from src/mol-model-formats/structure/mmcif/pair-restraints/cross-links.ts
rename to src/mol-model-formats/structure/property/pair-restraints/cross-links.ts
index 62305d3e942cefc6f3cbef76c598aba74de7caf4..484645a3a921c46bc2aa3f63aa26766043b3569d 100644
--- a/src/mol-model-formats/structure/mmcif/pair-restraints/cross-links.ts
+++ b/src/mol-model-formats/structure/property/pair-restraints/cross-links.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,43 +7,39 @@
import { Model } from '../../../../mol-model/structure/model/model'
import { Table } from '../../../../mol-data/db'
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
-import { findAtomIndexByLabelName } from '../util';
-import { Unit } from '../../../../mol-model/structure';
+import { Unit, CustomPropertyDescriptor } from '../../../../mol-model/structure';
import { ElementIndex } from '../../../../mol-model/structure/model/indexing';
+import { FormatPropertyProvider } from '../../common/property';
-function findAtomIndex(model: Model, entityId: string, asymId: string, seqId: number, atomId: string) {
- if (!model.atomicHierarchy.atoms.auth_atom_id.isDefined) return -1
- const residueIndex = model.atomicHierarchy.index.findResidue(entityId, asymId, seqId)
- if (residueIndex < 0) return -1
- return findAtomIndexByLabelName(model, residueIndex, atomId, '') as ElementIndex
-}
+export { ModelCrossLinkRestraint }
-export interface IHMCrossLinkRestraint {
+interface ModelCrossLinkRestraint {
getIndicesByElement: (element: ElementIndex, kind: Unit.Kind) => number[]
data: Table<mmCIF_Schema['ihm_cross_link_restraint']>
}
-export namespace IHMCrossLinkRestraint {
- export const PropName = '__CrossLinkRestraint__';
- export function fromModel(model: Model): IHMCrossLinkRestraint | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName]
+namespace ModelCrossLinkRestraint {
+ export const Descriptor: CustomPropertyDescriptor = {
+ name: 'ihm_cross_link_restraint',
+ // TODO cifExport
+ }
+
+ export const Provider = FormatPropertyProvider.create<ModelCrossLinkRestraint>(Descriptor)
- if (model.sourceData.kind !== 'mmCIF') return
- const { ihm_cross_link_restraint } = model.sourceData.data;
- if (!ihm_cross_link_restraint._rowCount) return
+ export function fromTable(table: Table<mmCIF_Schema['ihm_cross_link_restraint']>, model: Model): ModelCrossLinkRestraint {
const p1 = {
- entity_id: ihm_cross_link_restraint.entity_id_1,
- asym_id: ihm_cross_link_restraint.asym_id_1,
- seq_id: ihm_cross_link_restraint.seq_id_1,
- atom_id: ihm_cross_link_restraint.atom_id_1,
+ entity_id: table.entity_id_1,
+ asym_id: table.asym_id_1,
+ seq_id: table.seq_id_1,
+ atom_id: table.atom_id_1,
}
const p2: typeof p1 = {
- entity_id: ihm_cross_link_restraint.entity_id_2,
- asym_id: ihm_cross_link_restraint.asym_id_2,
- seq_id: ihm_cross_link_restraint.seq_id_2,
- atom_id: ihm_cross_link_restraint.atom_id_2,
+ entity_id: table.entity_id_2,
+ asym_id: table.asym_id_2,
+ seq_id: table.seq_id_2,
+ atom_id: table.atom_id_2,
}
function _add(map: Map<ElementIndex, number[]>, element: ElementIndex, row: number) {
@@ -57,8 +53,13 @@ export namespace IHMCrossLinkRestraint {
const asymId = ps.asym_id.value(row)
const seqId = ps.seq_id.value(row)
- if (ihm_cross_link_restraint.model_granularity.value(row) === 'by-atom') {
- const atomicElement = findAtomIndex(model, entityId, asymId, seqId, ps.atom_id.value(row))
+ if (table.model_granularity.value(row) === 'by-atom') {
+ const atomicElement = model.atomicHierarchy.index.findAtom({
+ auth_seq_id: seqId,
+ label_asym_id: asymId,
+ label_atom_id: ps.atom_id.value(row),
+ label_entity_id: entityId,
+ })
if (atomicElement >= 0) _add(atomicElementMap, atomicElement as ElementIndex, row)
} else if (model.coarseHierarchy.isDefined) {
const sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId)
@@ -88,20 +89,18 @@ export namespace IHMCrossLinkRestraint {
const emptyIndexArray: number[] = [];
- for (let i = 0; i < ihm_cross_link_restraint._rowCount; ++i) {
+ for (let i = 0; i < table._rowCount; ++i) {
add(i, p1)
add(i, p2)
}
- const crossLinkRestraint = {
+ return {
getIndicesByElement: (element: ElementIndex, kind: Unit.Kind) => {
const map = getMapByKind(kind)
const idx = map.get(element)
return idx !== undefined ? idx : emptyIndexArray
},
- data: ihm_cross_link_restraint
+ data: table
}
- model._staticPropertyData[PropName] = crossLinkRestraint
- return crossLinkRestraint
}
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/pair-restraints/predicted-contacts.ts b/src/mol-model-formats/structure/property/pair-restraints/predicted-contacts.ts
similarity index 100%
rename from src/mol-model-formats/structure/mmcif/pair-restraints/predicted-contacts.ts
rename to src/mol-model-formats/structure/property/pair-restraints/predicted-contacts.ts
diff --git a/src/mol-model-formats/structure/mmcif/secondary-structure.ts b/src/mol-model-formats/structure/property/secondary-structure.ts
similarity index 77%
rename from src/mol-model-formats/structure/mmcif/secondary-structure.ts
rename to src/mol-model-formats/structure/property/secondary-structure.ts
index 73c454a8dea08a44966f700330153503568a1043..d1be73086b1cff12372e6ad2406aa78118fa593e 100644
--- a/src/mol-model-formats/structure/mmcif/secondary-structure.ts
+++ b/src/mol-model-formats/structure/property/secondary-structure.ts
@@ -1,36 +1,51 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { mmCIF_Database as mmCIF, mmCIF_Database } from '../../../mol-io/reader/cif/schema/mmcif'
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif'
import { SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
import { SecondaryStructure } from '../../../mol-model/structure/model/properties/seconday-structure';
-import { Column } from '../../../mol-data/db';
+import { Column, Table } from '../../../mol-data/db';
import { ChainIndex, ResidueIndex } from '../../../mol-model/structure/model/indexing';
+import { FormatPropertyProvider } from '../common/property';
+import { CustomPropertyDescriptor } from '../../../mol-model/structure';
-export function getSecondaryStructure(data: mmCIF_Database, hierarchy: AtomicHierarchy): SecondaryStructure {
- const map: SecondaryStructureMap = new Map();
- const elements: SecondaryStructure.Element[] = [{ kind: 'none' }];
- addHelices(data.struct_conf, map, elements);
- // must add Helices 1st because of 'key' value assignment.
- addSheets(data.struct_sheet_range, map, data.struct_conf._rowCount, elements);
+export { ModelSecondaryStructure }
- const n = hierarchy.residues._rowCount
- const getIndex = (rI: ResidueIndex) => rI
+type StructConf = Table<mmCIF_Schema['struct_conf']>
+type StructSheetRange = Table<mmCIF_Schema['struct_sheet_range']>
- const secStruct: SecondaryStructureData = {
- type: new Int32Array(n) as any,
- key: new Int32Array(n) as any,
- elements
+namespace ModelSecondaryStructure {
+ export const Descriptor: CustomPropertyDescriptor = {
+ name: 'model_secondary_structure',
};
- if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
- return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements, getIndex);
+ export const Provider = FormatPropertyProvider.create<SecondaryStructure>(Descriptor)
+
+ export function fromStruct(conf: StructConf, sheetRange: StructSheetRange, hierarchy: AtomicHierarchy): SecondaryStructure {
+ const map: SecondaryStructureMap = new Map();
+ const elements: SecondaryStructure.Element[] = [{ kind: 'none' }];
+ addHelices(conf, map, elements);
+ // must add Helices 1st because of 'key' value assignment.
+ addSheets(sheetRange, map, conf._rowCount, elements);
+
+ const n = hierarchy.residues._rowCount
+ const getIndex = (rI: ResidueIndex) => rI
+
+ const secStruct: SecondaryStructureData = {
+ type: new Int32Array(n) as any,
+ key: new Int32Array(n) as any,
+ elements
+ };
+
+ if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
+ return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements, getIndex);
+ }
}
type SecondaryStructureEntry = {
@@ -44,7 +59,7 @@ type SecondaryStructureEntry = {
type SecondaryStructureMap = Map<string, Map<number, SecondaryStructureEntry[]>>
type SecondaryStructureData = { type: SecondaryStructureType[], key: number[], elements: SecondaryStructure.Element[] }
-function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
+function addHelices(cat: StructConf, map: SecondaryStructureMap, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
@@ -90,7 +105,7 @@ function addHelices(cat: mmCIF['struct_conf'], map: SecondaryStructureMap, eleme
}
}
-function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap, sheetCount: number, elements: SecondaryStructure.Element[]) {
+function addSheets(cat: StructSheetRange, map: SecondaryStructureMap, sheetCount: number, elements: SecondaryStructure.Element[]) {
if (!cat._rowCount) return;
const { beg_label_asym_id, beg_label_seq_id, pdbx_beg_PDB_ins_code } = cat;
diff --git a/src/mol-model-formats/structure/property/symmetry.ts b/src/mol-model-formats/structure/property/symmetry.ts
new file mode 100644
index 0000000000000000000000000000000000000000..487509249aefa9567915ca4b994aa715cf4e7f6d
--- /dev/null
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -0,0 +1,85 @@
+/**
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry';
+import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
+import { Symmetry as _ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry';
+import { createAssemblies } from './assembly';
+import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { FormatPropertyProvider } from '../common/property';
+import { Table } from '../../../mol-data/db';
+
+export { ModelSymmetry }
+
+namespace ModelSymmetry {
+ export const Descriptor: CustomPropertyDescriptor = {
+ name: 'model_symmetry',
+ };
+
+ export const Provider = FormatPropertyProvider.create<_ModelSymmetry>(Descriptor)
+
+ type Data = {
+ symmetry: Table<mmCIF_Schema['symmetry']>
+ cell: Table<mmCIF_Schema['cell']>
+ struct_ncs_oper: Table<mmCIF_Schema['struct_ncs_oper']>
+ atom_sites: Table<mmCIF_Schema['atom_sites']>
+ pdbx_struct_assembly: Table<mmCIF_Schema['pdbx_struct_assembly']>
+ pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_struct_assembly_gen']>
+ pdbx_struct_oper_list: Table<mmCIF_Schema['pdbx_struct_oper_list']>
+ }
+
+ export function fromData(data: Data): _ModelSymmetry {
+ const assemblies = createAssemblies(data.pdbx_struct_assembly, data.pdbx_struct_assembly_gen, data.pdbx_struct_oper_list);
+ const spacegroup = getSpacegroup(data.symmetry, data.cell);
+ const isNonStandardCrytalFrame = checkNonStandardCrystalFrame(data.atom_sites, spacegroup);
+ return { assemblies, spacegroup, isNonStandardCrytalFrame, ncsOperators: getNcsOperators(data.struct_ncs_oper) };
+ }
+}
+
+function checkNonStandardCrystalFrame(atom_sites: Table<mmCIF_Schema['atom_sites']>, spacegroup: Spacegroup) {
+ if (atom_sites._rowCount === 0) return false;
+ // TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
+ return false;
+}
+
+function getSpacegroupNameOrNumber(symmetry: Table<mmCIF_Schema['symmetry']>) {
+ const groupNumber = symmetry['Int_Tables_number'].value(0);
+ const groupName = symmetry['space_group_name_H-M'].value(0);
+ if (!symmetry['Int_Tables_number'].isDefined) return groupName
+ if (!symmetry['space_group_name_H-M'].isDefined) return groupNumber
+ return groupName
+}
+
+function getSpacegroup(symmetry: Table<mmCIF_Schema['symmetry']>, cell: Table<mmCIF_Schema['cell']>): Spacegroup {
+ if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
+ const nameOrNumber = getSpacegroupNameOrNumber(symmetry)
+ const spaceCell = SpacegroupCell.create(nameOrNumber,
+ Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
+ Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+
+ return Spacegroup.create(spaceCell);
+}
+
+function getNcsOperators(struct_ncs_oper: Table<mmCIF_Schema['struct_ncs_oper']>) {
+ if (struct_ncs_oper._rowCount === 0) return void 0;
+ const { id, matrix, vector } = struct_ncs_oper;
+
+ const matrixSpace = mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmCIF_Schema.struct_ncs_oper.vector.space;
+
+ const opers: SymmetryOperator[] = [];
+ for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
+ const m = Tensor.toMat3(Mat3(), matrixSpace, matrix.value(i));
+ const v = Tensor.toVec3(Vec3(), vectorSpace, vector.value(i));
+ if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue;
+ // ignore non-identity 'given' NCS operators
+ if (struct_ncs_oper.code.value(i) === 'given' && !Mat3.isIdentity(m) && !Vec3.isZero(v)) continue;
+ const ncsId = id.value(i)
+ opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${ncsId}`, m, v, ncsId);
+ }
+ return opers;
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/psf.ts b/src/mol-model-formats/structure/psf.ts
index ab4eae3e12a7c9c2a7d441f554fbe9d9b80dc59d..88e5a53d64a8e3f6dfdf798b15f8e61f580dccbf 100644
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -1,26 +1,24 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PsfFile } from '../../mol-io/reader/psf/parser';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
-import { Column } from '../../mol-data/db';
+import { Column, Table } from '../../mol-data/db';
import { EntityBuilder } from './common/entity';
import { ComponentBuilder } from './common/component';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
import { guessElementSymbolString } from './util';
import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { getChainId } from './common/util';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
import { Topology } from '../../mol-model/structure/topology/topology';
+import { createBasic, BasicSchema } from './basic/schema';
-// TODO: shares most of the code with ./gro.ts#getCategories
-function getCategories(atoms: PsfFile['atoms']) {
- const auth_atom_id = CifField.ofColumn(atoms.atomName)
- const auth_comp_id = CifField.ofColumn(atoms.residueName)
+function getBasic(atoms: PsfFile['atoms']) {
+ const auth_atom_id = atoms.atomName
+ const auth_comp_id = atoms.residueName
const entityIds = new Array<string>(atoms.count)
const asymIds = new Array<string>(atoms.count)
@@ -62,57 +60,54 @@ function getCategories(atoms: PsfFile['atoms']) {
ids[i] = i
}
- const auth_asym_id = CifField.ofColumn(Column.ofStringArray(asymIds))
+ const auth_asym_id = Column.ofStringArray(asymIds)
- const atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+ const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id,
auth_atom_id,
auth_comp_id,
- auth_seq_id: CifField.ofColumn(atoms.residueId),
- B_iso_or_equiv: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_x: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_y: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_z: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- group_PDB: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- id: CifField.ofColumn(Column.ofIntArray(ids)),
-
- label_alt_id: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
+ auth_seq_id: atoms.residueId,
+ id: Column.ofIntArray(ids),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
- label_seq_id: CifField.ofColumn(Column.ofIntArray(seqIds)),
- label_entity_id: CifField.ofColumn(Column.ofStringArray(entityIds)),
+ label_seq_id: Column.ofIntArray(seqIds),
+ label_entity_id: Column.ofStringArray(entityIds),
- occupancy: CifField.ofColumn(Column.ofConst(1, atoms.count, Column.Schema.float)),
- type_symbol: CifField.ofStrings(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+ occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+ type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
- pdbx_PDB_ins_code: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
- }
+ pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+ }, atoms.count)
- return {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
- atom_site: CifCategory.ofFields('atom_site', atom_site)
- }
+ return createBasic({
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
+ atom_site
+ })
}
-function psfToMmCif(psf: PsfFile) {
- const categories = getCategories(psf.atoms)
+//
+
+export { PsfFormat }
- return {
- header: psf.id,
- categoryNames: Object.keys(categories),
- categories
- };
+type PsfFormat = ModelFormat<PsfFile>
+
+namespace PsfFormat {
+ export function is(x: ModelFormat): x is PsfFormat {
+ return x.kind === 'psf'
+ }
+
+ export function fromPsf(psf: PsfFile): PsfFormat {
+ return { kind: 'psf', name: psf.id, data: psf };
+ }
}
export function topologyFromPsf(psf: PsfFile): Task<Topology> {
return Task.create('Parse PSF', async ctx => {
- const label = psf.id
- const cif = psfToMmCif(psf);
- const format = ModelFormat.mmCIF(cif);
+ const format = PsfFormat.fromPsf(psf);
+ const basic = getBasic(psf.atoms)
const { atomIdA, atomIdB } = psf.bonds
@@ -130,6 +125,6 @@ export function topologyFromPsf(psf: PsfFile): Task<Topology> {
order: Column.ofConst(1, psf.bonds.count, Column.Schema.int)
}
- return Topology.create(label, format, bonds)
+ return Topology.create(psf.id, basic, bonds, format)
})
}
\ No newline at end of file
diff --git a/src/mol-model-props/common/custom-property.ts b/src/mol-model-props/common/custom-property.ts
index f8bc99821856b6d095ca2f86d0dcc0aabeeeaf46..24dbbd7a9adb19634b9a79184ca97814aa152687 100644
--- a/src/mol-model-props/common/custom-property.ts
+++ b/src/mol-model-props/common/custom-property.ts
@@ -41,21 +41,32 @@ namespace CustomProperty {
/** Get params for all applicable property providers */
getParams(data?: Data) {
- const params: PD.Params = {}
+ const propertiesParams: PD.Params = {}
+ const autoAttachOptions: [string, string][] = []
+ const autoAttachDefault: string[] = []
if (data) {
- const values = this.providers.values();
+ const values = this.providers.values();
while (true) {
const v = values.next()
if (v.done) break
+
const provider = v.value
if (!provider.isApplicable(data)) continue
- params[provider.descriptor.name] = PD.Group({
- autoAttach: PD.Boolean(this.defaultAutoAttachValues.get(provider.descriptor.name)!),
- ...provider.getParams(data),
- }, { label: v.value.label })
+
+ autoAttachOptions.push([provider.descriptor.name, provider.label])
+ if (this.defaultAutoAttachValues.get(provider.descriptor.name)) {
+ autoAttachDefault.push(provider.descriptor.name)
+ }
+
+ propertiesParams[provider.descriptor.name] = PD.Group({
+ ...provider.getParams(data)
+ }, { label: provider.label })
}
}
- return params
+ return {
+ autoAttach: PD.MultiSelect(autoAttachDefault, autoAttachOptions),
+ properties: PD.Group(propertiesParams, { isFlat: true })
+ }
}
setDefaultAutoAttach(name: string, value: boolean) {
diff --git a/src/mol-model-props/common/wrapper.ts b/src/mol-model-props/common/wrapper.ts
index 21c57e124e18ad5ab3193eb9a67774cc8a0abd51..7f3523515dbfc88602fe798e05c7a6c79328b8f0 100644
--- a/src/mol-model-props/common/wrapper.ts
+++ b/src/mol-model-props/common/wrapper.ts
@@ -7,6 +7,7 @@
import { CifWriter } from '../../mol-io/writer/cif';
import { Model } from '../../mol-model/structure';
import { dateToUtcString } from '../../mol-util/date';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
interface PropertyWrapper<Data> {
info: PropertyWrapper.Info,
@@ -40,11 +41,11 @@ namespace PropertyWrapper {
];
export function tryGetInfoFromCif(categoryName: string, model: Model): Info | undefined {
- if (model.sourceData.kind !== 'mmCIF' || !model.sourceData.frame.categoryNames.includes(categoryName)) {
+ if (!MmcifFormat.is(model.sourceData) || !model.sourceData.data.frame.categoryNames.includes(categoryName)) {
return;
}
- const timestampField = model.sourceData.frame.categories[categoryName].getField('updated_datetime_utc');
+ const timestampField = model.sourceData.data.frame.categories[categoryName].getField('updated_datetime_utc');
if (!timestampField || timestampField.rowCount === 0) return;
return { timestamp_utc: timestampField.str(0) || dateToUtcString(new Date()) };
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
index 5097af98adc5d27078e239c9aa1cb1e580bd6aaf..fd93549b530d56b99679fc68644cab989513a5c6 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
@@ -31,10 +31,11 @@ export async function computeArea(runtime: RuntimeContext, ctx: ShrakeRupleyCont
const aPos = Vec3();
const bPos = Vec3();
const testPoint = Vec3();
-const aLoc = StructureElement.Location.create()
-const bLoc = StructureElement.Location.create()
+const aLoc = StructureElement.Location.create(void 0 as any)
+const bLoc = StructureElement.Location.create(void 0 as any)
function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
+ l.structure = structure;
l.unit = structure.units[structure.serialMapping.unitIndices[serialIndex]]
l.element = structure.serialMapping.elementIndices[serialIndex]
return l
@@ -63,7 +64,7 @@ function computeRange(ctx: ShrakeRupleyContext, begin: number, end: number) {
const neighbors = []; // TODO reuse
for (let iI = 0; iI < count; ++iI) {
const bUnit = units[iI]
- StructureElement.Location.set(bLoc, bUnit, bUnit.elements[indices[iI]])
+ StructureElement.Location.set(bLoc, ctx.structure, bUnit, bUnit.elements[indices[iI]])
const bI = cumulativeUnitElementCount[unitIndexMap.get(bUnit.id)] + indices[iI]
const radius2 = VdWLookup[atomRadiusType[bI]];
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
index 32520eda0599b1296a6edab429419d020a05a9ab..cc9ac3f5a0ad31f4d8f69b7769c9622636bbf0c7 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
@@ -12,7 +12,7 @@ import { VdwRadius } from '../../../../mol-model/structure/model/properties/atom
import { StructureElement, StructureProperties } from '../../../../mol-model/structure/structure';
import { getElementMoleculeType } from '../../../../mol-model/structure/util';
-const l = StructureElement.Location.create()
+const l = StructureElement.Location.create(void 0)
export function assignRadiusForHeavyAtoms(ctx: ShrakeRupleyContext) {
const { label_comp_id, key } = StructureProperties.residue
@@ -23,6 +23,7 @@ export function assignRadiusForHeavyAtoms(ctx: ShrakeRupleyContext) {
let residueIdx = 0
let serialResidueIdx = -1
+ l.structure = structure;
for (let i = 0, m = 0, il = structure.units.length; i < il; ++i) {
const unit = structure.units[i]
const { elements } = unit
diff --git a/src/mol-model-props/computed/interactions/interactions.ts b/src/mol-model-props/computed/interactions/interactions.ts
index c7e1e409bdf03c41522bd470ca22bf5c163bf416..881163733e3549460322b933d2297b734621be20 100644
--- a/src/mol-model-props/computed/interactions/interactions.ts
+++ b/src/mol-model-props/computed/interactions/interactions.ts
@@ -39,6 +39,7 @@ interface Interactions {
namespace Interactions {
export interface Element {
+ structure: Structure,
unitA: Unit
/** Index into features of unitA */
indexA: Features.FeatureIndex
@@ -48,8 +49,9 @@ namespace Interactions {
}
export interface Location extends DataLocation<Interactions, Element> {}
- export function Location(interactions: Interactions, unitA?: Unit, indexA?: Features.FeatureIndex, unitB?: Unit, indexB?: Features.FeatureIndex): Location {
- return DataLocation('interactions', interactions, { unitA: unitA as any, indexA: indexA as any, unitB: unitB as any, indexB: indexB as any });
+ export function Location(interactions: Interactions, structure: Structure, unitA?: Unit, indexA?: Features.FeatureIndex, unitB?: Unit, indexB?: Features.FeatureIndex): Location {
+ return DataLocation('interactions', interactions,
+ { structure: structure as any, unitA: unitA as any, indexA: indexA as any, unitB: unitB as any, indexB: indexB as any });
}
export function isLocation(x: any): x is Location {
@@ -87,7 +89,9 @@ namespace Interactions {
export interface Loci extends DataLoci<StructureInteractions, Element> { }
export function Loci(structure: Structure, interactions: Interactions, elements: ReadonlyArray<Element>): Loci {
- return DataLoci('interactions', { structure, interactions }, elements, (boundingSphere) => getBoundingSphere(interactions, elements, boundingSphere), () => getLabel(interactions, elements));
+ return DataLoci('interactions', { structure, interactions }, elements,
+ (boundingSphere) => getBoundingSphere(interactions, elements, boundingSphere),
+ () => getLabel(structure, interactions, elements));
}
export function isLoci(x: any): x is Loci {
@@ -103,7 +107,7 @@ namespace Interactions {
}, boundingSphere)
}
- export function getLabel(interactions: Interactions, elements: ReadonlyArray<Element>) {
+ export function getLabel(structure: Structure, interactions: Interactions, elements: ReadonlyArray<Element>) {
const element = elements[0]
if (element === undefined) return ''
const { unitA, indexA, unitB, indexB } = element
@@ -116,7 +120,7 @@ namespace Interactions {
}
return [
_label(interactions, element),
- bondLabel(Bond.Location(unitA, mA[oA[indexA]], unitB, mB[oB[indexB]]), options)
+ bondLabel(Bond.Location(structure, unitA, mA[oA[indexA]], structure, unitB, mB[oB[indexB]]), options)
].join('</br>')
}
}
diff --git a/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts b/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
index 8717cb985abc479070db186c5859edb34faca488..a13a95720688fd97ff2f042fa9ad144fb688971e 100644
--- a/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
@@ -21,7 +21,7 @@ import { InteractionsProvider } from '../interactions';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { InteractionFlag } from '../interactions/common';
-const tmpLoc = StructureElement.Location.create()
+const tmpLoc = StructureElement.Location.create(void 0)
function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InteractionsInterUnitParams>, mesh?: Mesh) {
if (!structure.hasAtomic) return Mesh.createEmpty(mesh)
@@ -49,6 +49,7 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
radius: (edgeIndex: number) => {
const b = edges[edgeIndex]
const fA = unitsFeatures.get(b.unitA.id)
+ tmpLoc.structure = structure;
tmpLoc.unit = b.unitA
tmpLoc.element = b.unitA.elements[fA.members[fA.offsets[b.indexA]]]
const sizeA = theme.size.size(tmpLoc)
@@ -100,8 +101,8 @@ function getInteractionLoci(pickingId: PickingId, structure: Structure, id: numb
const interactions = InteractionsProvider.get(structure).value!
const c = interactions.contacts.edges[groupId]
return Interactions.Loci(structure, interactions, [
- { unitA: c.unitA, indexA: c.indexA, unitB: c.unitB, indexB: c.indexB },
- { unitA: c.unitB, indexA: c.indexB, unitB: c.unitA, indexB: c.indexA },
+ { structure, unitA: c.unitA, indexA: c.indexA, unitB: c.unitB, indexB: c.indexB },
+ { structure, unitA: c.unitB, indexA: c.indexB, unitB: c.unitA, indexB: c.indexA },
])
}
return EmptyLoci
@@ -130,7 +131,7 @@ function createInteractionsIterator(structure: Structure): LocationIterator {
const { contacts } = interactions
const groupCount = contacts.edgeCount
const instanceCount = 1
- const location = Interactions.Location(interactions)
+ const location = Interactions.Location(interactions, structure)
const { element } = location
const getLocation = (groupIndex: number) => {
const c = contacts.edges[groupIndex]
diff --git a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts b/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
index 6626f248950e8526023b5aaff2ef1bc10ae73d55..66a03f6ac7ee24d281c2251051e40bbf4e9a22ba 100644
--- a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
@@ -24,7 +24,7 @@ import { InteractionFlag } from '../interactions/common';
async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<InteractionsIntraUnitParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
- const location = StructureElement.Location.create(unit)
+ const location = StructureElement.Location.create(structure, unit)
const interactions = InteractionsProvider.get(structure).value!
const features = interactions.unitsFeatures.get(unit.id)
@@ -97,8 +97,8 @@ function getInteractionLoci(pickingId: PickingId, structureGroup: StructureGroup
const interactions = InteractionsProvider.get(structure).value!
const { a, b } = interactions.unitsContacts.get(unit.id)
return Interactions.Loci(structure, interactions, [
- { unitA: unit, indexA: a[groupId], unitB: unit, indexB: b[groupId] },
- { unitA: unit, indexA: b[groupId], unitB: unit, indexB: a[groupId] },
+ { structure, unitA: unit, indexA: a[groupId], unitB: unit, indexB: b[groupId] },
+ { structure, unitA: unit, indexA: b[groupId], unitB: unit, indexB: a[groupId] },
])
}
return EmptyLoci
@@ -134,7 +134,7 @@ function createInteractionsIterator(structureGroup: StructureGroup): LocationIte
const contacts = interactions.unitsContacts.get(unit.id)
const groupCount = contacts.edgeCount * 2
const instanceCount = group.units.length
- const location = Interactions.Location(interactions)
+ const location = Interactions.Location(interactions, structure)
const { element } = location
const getLocation = (groupIndex: number, instanceIndex: number) => {
const instanceUnit = group.units[instanceIndex]
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index 7b875d34705a5c92c46020ec173b3ffdc526f5df..d80c58b383b9a8725daed90eb9632203986e2f17 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -11,6 +11,8 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Unit } from '../../mol-model/structure/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
+import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
function getSecondaryStructureParams(data?: Structure) {
let defaultType = 'mmcif' as 'mmcif' | 'dssp'
@@ -18,10 +20,10 @@ function getSecondaryStructureParams(data?: Structure) {
defaultType = 'dssp'
for (let i = 0, il = data.models.length; i < il; ++i) {
const m = data.models[i]
- if (m.sourceData.kind === 'mmCIF') {
- if (data.model.sourceData.data.struct_conf.id.isDefined ||
- data.model.sourceData.data.struct_sheet_range.id.isDefined ||
- data.model.sourceData.data.database_2.database_id.isDefined
+ if (MmcifFormat.is(m.sourceData)) {
+ if (m.sourceData.data.db.struct_conf.id.isDefined ||
+ m.sourceData.data.db.struct_sheet_range.id.isDefined ||
+ m.sourceData.data.db.database_2.database_id.isDefined
) {
// if there is any secondary structure definition given or if there is
// an archival model, don't calculate dssp by default
@@ -83,7 +85,10 @@ async function computeMmcif(structure: Structure): Promise<SecondaryStructureVal
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0]
if (Unit.isAtomic(u)) {
- map.set(u.invariantId, u.model.properties.secondaryStructure)
+ const secondaryStructure = ModelSecondaryStructure.Provider.get(u.model)
+ if (secondaryStructure) {
+ map.set(u.invariantId, secondaryStructure)
+ }
}
}
return map
diff --git a/src/mol-model-props/pdbe/preferred-assembly.ts b/src/mol-model-props/pdbe/preferred-assembly.ts
index 9be69ce401bd1bbc4fd2847f97f3af0e7cd321c4..ebc7fb081c24c9e50396450f84618f0a06a09b99 100644
--- a/src/mol-model-props/pdbe/preferred-assembly.ts
+++ b/src/mol-model-props/pdbe/preferred-assembly.ts
@@ -8,13 +8,15 @@ import { Column, Table } from '../../mol-data/db';
import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export namespace PDBePreferredAssembly {
export type Property = string
export function getFirstFromModel(model: Model): Property {
- const asm = model.symmetry.assemblies;
- return asm.length ? asm[0].id : '';
+ const symmetry = ModelSymmetry.Provider.get(model)
+ return symmetry?.assemblies.length ? symmetry.assemblies[0].id : '';
}
export function get(model: Model): Property {
@@ -46,8 +48,8 @@ export namespace PDBePreferredAssembly {
});
function fromCifData(model: Model): string | undefined {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const cat = model.sourceData.frame.categories.pdbe_preferred_assembly;
+ if (!MmcifFormat.is(model.sourceData)) return void 0;
+ const cat = model.sourceData.data.frame.categories.pdbe_preferred_assembly;
if (!cat) return void 0;
return toTable(Schema.pdbe_preferred_assembly, cat).assembly_id.value(0) || getFirstFromModel(model);
}
diff --git a/src/mol-model-props/pdbe/struct-ref-domain.ts b/src/mol-model-props/pdbe/struct-ref-domain.ts
index 54a31131e8e6ecd75134ea49a17227dbda57b06b..db37fee7e8412b3d06e7f5e587aea9822483ebe9 100644
--- a/src/mol-model-props/pdbe/struct-ref-domain.ts
+++ b/src/mol-model-props/pdbe/struct-ref-domain.ts
@@ -9,6 +9,7 @@ import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
import { PropertyWrapper } from '../common/wrapper';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export namespace PDBeStructRefDomain {
export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>
@@ -57,8 +58,8 @@ export namespace PDBeStructRefDomain {
});
function fromCifData(model: Model): Property['data'] {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const cat = model.sourceData.frame.categories.pdbe_struct_ref_domain;
+ if (!MmcifFormat.is(model.sourceData)) return void 0;
+ const cat = model.sourceData.data.frame.categories.pdbe_struct_ref_domain;
if (!cat) return void 0;
return toTable(Schema.pdbe_struct_ref_domain, cat);
}
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index b956250aadcfc613462e4e2b0ce67de22cefc3da..e153de014ba3749c37f0700edb55b9f0a01698b3 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -11,7 +11,7 @@ import { mmCIF_residueId_schema } from '../../mol-io/reader/cif/schema/mmcif-ext
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../mol-model/structure';
import { residueIdFields } from '../../mol-model/structure/export/categories/atom_site';
-import { StructureElement, CifExportContext } from '../../mol-model/structure/structure';
+import { StructureElement, CifExportContext, Structure } from '../../mol-model/structure/structure';
import { CustomPropSymbol } from '../../mol-script/language/symbol';
import Type from '../../mol-script/language/type';
import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
@@ -19,10 +19,15 @@ import { PropertyWrapper } from '../common/wrapper';
import { CustomModelProperty } from '../common/custom-model-property';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { CustomProperty } from '../common/custom-property';
+import { arraySetAdd } from '../../mol-util/array';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export { StructureQualityReport }
-type StructureQualityReport = PropertyWrapper<IndexedCustomProperty.Residue<string[]> | undefined>
+type StructureQualityReport = PropertyWrapper<{
+ issues: IndexedCustomProperty.Residue<string[]>,
+ issueTypes: string[]
+}| undefined>
namespace StructureQualityReport {
export const DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/'
@@ -33,8 +38,8 @@ namespace StructureQualityReport {
export function isApplicable(model?: Model): boolean {
return (
!!model &&
- model.sourceData.kind === 'mmCIF' &&
- (model.sourceData.data.database_2.database_id.isDefined ||
+ MmcifFormat.is(model.sourceData) &&
+ (model.sourceData.data.db.database_2.database_id.isDefined ||
model.entryId.length === 4)
)
}
@@ -88,14 +93,21 @@ namespace StructureQualityReport {
const prop = StructureQualityReportProvider.get(e.unit.model).value;
if (!prop || !prop.data) return _emptyArray;
const rI = e.unit.residueIndex[e.element];
- return prop.data.has(rI) ? prop.data.get(rI)! : _emptyArray;
+ return prop.data.issues.has(rI) ? prop.data.issues.get(rI)! : _emptyArray;
+ }
+
+ export function getIssueTypes(structure?: Structure) {
+ if (!structure) return _emptyArray;
+ const prop = StructureQualityReportProvider.get(structure.models[0]).value;
+ if (!prop || !prop.data) return _emptyArray;
+ return prop.data.issueTypes;
}
function getCifData(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.');
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.');
return {
- residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues),
- groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.frame.categories.pdbe_structure_quality_report_issue_types),
+ residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issues),
+ groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issue_types),
}
}
}
@@ -174,7 +186,7 @@ function createExportContext(ctx: CifExportContext): ReportExportContext {
if (prop) info = prop.info;
if (!prop || !prop.data) continue;
- const { elements, property } = prop.data.getElements(s);
+ const { elements, property } = prop.data.issues.getElements(s);
if (elements.length === 0) continue;
const elementGroupId: number[] = [];
@@ -205,6 +217,8 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
const ret = new Map<ResidueIndex, string[]>();
if (!data.molecules) return;
+ const issueTypes: string[] = [];
+
for (const entity of data.molecules) {
const entity_id = entity.entity_id.toString();
for (const chain of entity.chains) {
@@ -217,12 +231,19 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || '';
const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code);
ret.set(idx, residue.outlier_types);
+
+ for (const t of residue.outlier_types) {
+ arraySetAdd(issueTypes, t);
+ }
}
}
}
}
- return IndexedCustomProperty.fromResidueMap(ret);
+ return {
+ issues: IndexedCustomProperty.fromResidueMap(ret),
+ issueTypes
+ };
}
function createIssueMapFromCif(modelData: Model,
@@ -240,7 +261,17 @@ function createIssueMapFromCif(modelData: Model,
ret.set(idx, groups.get(issue_type_group_id.value(i))!);
}
- return IndexedCustomProperty.fromResidueMap(ret);
+ const issueTypes: string[] = [];
+ groups.forEach(issues => {
+ for (const t of issues) {
+ arraySetAdd(issueTypes, t);
+ }
+ })
+
+ return {
+ issues: IndexedCustomProperty.fromResidueMap(ret),
+ issueTypes
+ };
}
function parseIssueTypes(groupData: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issue_types>): Map<number, string[]> {
diff --git a/src/mol-model-props/pdbe/themes/structure-quality-report.ts b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
index f84a18744b05dc1ca7056b5a02d67999ef2ff035..e3296bab946d7dc478f50b5b20c3cfe05a533ef4 100644
--- a/src/mol-model-props/pdbe/themes/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
@@ -11,6 +11,8 @@ import { ColorTheme, LocationColor } from '../../../mol-theme/color';
import { ThemeDataContext } from '../../../mol-theme/theme';
import { Color } from '../../../mol-util/color';
import { TableLegend } from '../../../mol-util/legend';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { CustomProperty } from '../../common/custom-property';
const ValidationColors = [
Color.fromRgb(170, 170, 170), // not applicable
@@ -28,16 +30,38 @@ const ValidationColorTable: [string, Color][] = [
['Not Applicable', ValidationColors[9]]
]
-export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+export const StructureQualityReportColorThemeParams = {
+ type: PD.MappedStatic('issue-count', {
+ 'issue-count': PD.Group({}),
+ 'specific-issue': PD.Group({
+ kind: PD.Text()
+ })
+ })
+};
+
+type Params = typeof StructureQualityReportColorThemeParams
+
+export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: PD.Values<Params>): ColorTheme<Params> {
let color: LocationColor
if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(StructureQualityReportProvider.descriptor)) {
const getIssues = StructureQualityReport.getIssues;
- color = (location: Location) => {
- if (StructureElement.Location.is(location)) {
- return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+
+ if (props.type.name === 'issue-count') {
+ color = (location: Location) => {
+ if (StructureElement.Location.is(location)) {
+ return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+ }
+ return ValidationColors[0];
+ }
+ } else {
+ const issue = props.type.params.kind;
+ color = (location: Location) => {
+ if (StructureElement.Location.is(location) && getIssues(location).indexOf(issue) >= 0) {
+ return ValidationColors[4];
+ }
+ return ValidationColors[0];
}
- return ValidationColors[0];
}
} else {
color = () => ValidationColors[0];
@@ -48,7 +72,36 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: {
granularity: 'group',
color: color,
props: props,
- description: 'Assigns residue colors according to the number of issues in the PDBe Validation Report.',
+ description: 'Assigns residue colors according to the number of issues or a specific issue in the PDBe Validation Report.',
legend: TableLegend(ValidationColorTable)
}
+}
+
+export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params> = {
+ label: 'PDBe Structure Quality Report',
+ factory: StructureQualityReportColorTheme,
+ getParams: ctx => {
+ const issueTypes = StructureQualityReport.getIssueTypes(ctx.structure);
+ if (issueTypes.length === 0) {
+ return {
+ type: PD.MappedStatic('issue-count', {
+ 'issue-count': PD.Group({})
+ })
+ };
+ }
+
+ return {
+ type: PD.MappedStatic('issue-count', {
+ 'issue-count': PD.Group({}),
+ 'specific-issue': PD.Group({
+ kind: PD.Select(issueTypes[0], PD.arrayToOptions(issueTypes))
+ }, { isFlat: true })
+ })
+ };
+ },
+ defaultValues: PD.getDefaultValues(StructureQualityReportColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
+ ensureCustomProperties: (ctx: CustomProperty.Context, data: ThemeDataContext) => {
+ return data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0]) : Promise.resolve()
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index e4c8c07e2f00ac16de5477a40106ff5a921479ab..6dce3e871e3ebd414256ecc7fb2af5825fe524f6 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -14,6 +14,7 @@ import { GraphQLClient } from '../../mol-util/graphql-client';
import { CustomProperty } from '../common/custom-property';
import { NonNullableArray } from '../../mol-util/type-helpers';
import { CustomStructureProperty } from '../common/custom-structure-property';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
const BiologicalAssemblyNames = new Set([
'author_and_software_defined_assembly',
@@ -25,15 +26,15 @@ const BiologicalAssemblyNames = new Set([
])
export namespace AssemblySymmetry {
- export const DefaultServerUrl = 'http://data-beta.rcsb.org/graphql'
+ export const DefaultServerUrl = 'https://data-beta.rcsb.org/graphql'
export function isApplicable(structure?: Structure): boolean {
// check if structure is from pdb entry
- if (!structure || structure.models.length !== 1 || structure.models[0].sourceData.kind !== 'mmCIF' || (!structure.models[0].sourceData.data.database_2.database_id.isDefined &&
+ if (!structure || structure.models.length !== 1 || !MmcifFormat.is(structure.models[0].sourceData) || (!structure.models[0].sourceData.data.db.database_2.database_id.isDefined &&
structure.models[0].entryId.length !== 4)) return false
// check if assembly is 'biological'
- const mmcif = structure.models[0].sourceData.data
+ const mmcif = structure.models[0].sourceData.data.db
if (!mmcif.pdbx_struct_assembly.details.isDefined) return false
const id = structure.units[0].conformation.operator.assembly.id
const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id)
diff --git a/src/mol-model-props/rcsb/graphql/types.d.ts b/src/mol-model-props/rcsb/graphql/types.ts
similarity index 99%
rename from src/mol-model-props/rcsb/graphql/types.d.ts
rename to src/mol-model-props/rcsb/graphql/types.ts
index 0af39affaf13fc554cf4dfdcfe12c551a42902ad..ac02ff026d544af2de62eed61b9aa8a58a3f52e3 100644
--- a/src/mol-model-props/rcsb/graphql/types.d.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,7 +1,7 @@
/* eslint-disable */
export type Maybe<T> = T | null;
-// Generated in 2020-02-07T10:59:45-08:00
+// Generated in 2020-02-21T15:58:06-08:00
/** All built-in and custom scalars, mapped to their actual values */
export type Scalars = {
@@ -14,7 +14,6 @@ export type Scalars = {
UNREPRESENTABLE: any,
};
-
export type AuditAuthor = {
readonly identifier_ORCID?: Maybe<Scalars['String']>,
readonly name?: Maybe<Scalars['String']>,
@@ -1750,6 +1749,7 @@ export type RcsbEntryContainerIdentifiers = {
readonly emdb_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>,
readonly entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>,
readonly entry_id: Scalars['String'],
+ readonly model_ids?: Maybe<ReadonlyArray<Maybe<Scalars['Int']>>>,
readonly non_polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>,
readonly polymer_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>,
readonly pubmed_id?: Maybe<Scalars['Int']>,
@@ -1921,7 +1921,6 @@ export type RcsbNonpolymerInstanceAnnotationAnnotationLineage = {
export type RcsbNonpolymerInstanceFeature = {
readonly assignment_version?: Maybe<Scalars['String']>,
- readonly auth_seq_id?: Maybe<Scalars['String']>,
readonly comp_id?: Maybe<Scalars['String']>,
readonly description?: Maybe<Scalars['String']>,
readonly feature_id?: Maybe<Scalars['String']>,
@@ -1942,6 +1941,7 @@ export type RcsbNonpolymerInstanceFeatureFeatureValue = {
};
export type RcsbNonpolymerInstanceFeatureSummary = {
+ readonly comp_id?: Maybe<Scalars['String']>,
readonly count?: Maybe<Scalars['Int']>,
readonly maximum_length?: Maybe<Scalars['Int']>,
readonly maximum_value?: Maybe<Scalars['Float']>,
diff --git a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
index 136aea063f014e6d3debddb152a2e1baf0a5b6d0..be69dbcda1645c51fda6b31ec0768f2cc15460c4 100644
--- a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
+++ b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
@@ -91,7 +91,7 @@ function getIntraClashBoundingSphere(unit: Unit.Atomic, clashes: IntraUnitClashe
}, boundingSphere)
}
-function getIntraClashLabel(unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
+function getIntraClashLabel(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
const idx = elements[0]
if (idx === undefined) return ''
const { edgeProps: { id, magnitude, distance } } = clashes
@@ -100,12 +100,14 @@ function getIntraClashLabel(unit: Unit.Atomic, clashes: IntraUnitClashes, elemen
return [
`Clash id: ${id[idx]} | Magnitude: ${mag} \u212B | Distance: ${dist} \u212B`,
- bondLabel(Bond.Location(unit, clashes.a[idx], unit, clashes.b[idx]))
+ bondLabel(Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
].join('</br>')
}
-function IntraClashLoci(unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
- return DataLoci('intra-clashes', { unit, clashes }, elements, (boundingSphere: Sphere3D) => getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere), () => getIntraClashLabel(unit, clashes, elements))
+function IntraClashLoci(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
+ return DataLoci('intra-clashes', { unit, clashes }, elements,
+ (boundingSphere: Sphere3D) => getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
+ () => getIntraClashLabel(structure, unit, clashes, elements))
}
function getIntraClashLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number) {
@@ -115,7 +117,7 @@ function getIntraClashLoci(pickingId: PickingId, structureGroup: StructureGroup,
const unit = group.units[instanceId]
if (Unit.isAtomic(unit)) {
const clashes = ClashesProvider.get(structure).value!.intraUnit.get(unit.id)
- return IntraClashLoci(unit, clashes, [groupId])
+ return IntraClashLoci(structure, unit, clashes, [groupId])
}
}
return EmptyLoci
@@ -134,7 +136,7 @@ function createIntraClashIterator(structureGroup: StructureGroup): LocationItera
const { a } = clashes
const groupCount = clashes.edgeCount * 2
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
@@ -203,7 +205,7 @@ function getInterClashBoundingSphere(clashes: InterUnitClashes, elements: number
}, boundingSphere)
}
-function getInterClashLabel(clashes: InterUnitClashes, elements: number[]) {
+function getInterClashLabel(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
const idx = elements[0]
if (idx === undefined) return ''
const c = clashes.edges[idx]
@@ -212,19 +214,21 @@ function getInterClashLabel(clashes: InterUnitClashes, elements: number[]) {
return [
`Clash id: ${c.props.id} | Magnitude: ${mag} \u212B | Distance: ${dist} \u212B`,
- bondLabel(Bond.Location(c.unitA, c.indexA, c.unitB, c.indexB))
+ bondLabel(Bond.Location(structure, c.unitA, c.indexA, structure, c.unitB, c.indexB))
].join('</br>')
}
-function InterClashLoci(clashes: InterUnitClashes, elements: number[]) {
- return DataLoci('inter-clashes', clashes, elements, (boundingSphere: Sphere3D) => getInterClashBoundingSphere(clashes, elements, boundingSphere), () => getInterClashLabel(clashes, elements))
+function InterClashLoci(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
+ return DataLoci('inter-clashes', clashes, elements,
+ (boundingSphere: Sphere3D) => getInterClashBoundingSphere(clashes, elements, boundingSphere),
+ () => getInterClashLabel(structure, clashes, elements))
}
function getInterClashLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, groupId } = pickingId
if (id === objectId) {
const clashes = ClashesProvider.get(structure).value!.interUnit
- return InterClashLoci(clashes, [groupId])
+ return InterClashLoci(structure, clashes, [groupId])
}
return EmptyLoci
}
@@ -239,7 +243,7 @@ function createInterClashIterator(structure: Structure): LocationIterator {
const clashes = ClashesProvider.get(structure).value!.interUnit
const groupCount = clashes.edgeCount
const instanceCount = 1
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number) => {
const clash = clashes.edges[groupIndex]
location.unit = clash.unitA
diff --git a/src/mol-model-props/rcsb/themes/geometry-quality.ts b/src/mol-model-props/rcsb/themes/geometry-quality.ts
index 201d8fabf73f9b997620431889d104c532cd39da..1f39b8de4b19e47b1765c0c85ae93cbe7ab9c64f 100644
--- a/src/mol-model-props/rcsb/themes/geometry-quality.ts
+++ b/src/mol-model-props/rcsb/themes/geometry-quality.ts
@@ -14,6 +14,7 @@ import { CustomProperty } from '../../common/custom-property';
import { ValidationReportProvider, ValidationReport } from '../validation-report';
import { TableLegend } from '../../../mol-util/legend';
import { PolymerType } from '../../../mol-model/structure/model/types';
+import { SetUtils } from '../../../mol-util/set';
const DefaultColor = Color(0x909090)
@@ -23,13 +24,28 @@ const TwoIssuesColor = Color(0xf46d43)
const ThreeOrMoreIssuesColor = Color(0xa50026)
const ColorLegend = TableLegend([
+ ['Data unavailable', DefaultColor],
['No issues', NoIssuesColor],
['One issue', OneIssueColor],
['Two issues', TwoIssuesColor],
- ['Three or more issues', ThreeOrMoreIssuesColor]
+ ['Three or more issues', ThreeOrMoreIssuesColor],
])
-export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+export function getGeometricQualityColorThemeParams(ctx: ThemeDataContext) {
+ const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]).value
+ const options: [string, string][] = []
+ if (validationReport) {
+ const kinds = new Set<string>()
+ validationReport.geometryIssues.forEach(v => v.forEach(k => kinds.add(k)))
+ kinds.forEach(k => options.push([k, k]))
+ }
+ return {
+ ignore: PD.MultiSelect([] as string[], options)
+ }
+}
+export type GeometricQualityColorThemeParams = ReturnType<typeof getGeometricQualityColorThemeParams>
+
+export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Values<GeometricQualityColorThemeParams>): ColorTheme<GeometricQualityColorThemeParams> {
let color: LocationColor = () => DefaultColor
const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0])
@@ -42,19 +58,26 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: {}): Col
const { geometryIssues, clashes, bondOutliers, angleOutliers } = value
const residueIndex = model.atomicHierarchy.residueAtomSegments.index
const { polymerType } = model.atomicHierarchy.derived.residue
+ const ignore = new Set(props.ignore)
+
color = (location: Location): Color => {
if (StructureElement.Location.is(location) && location.unit.model === model) {
const { element } = location
const rI = residueIndex[element]
- let value = geometryIssues.get(rI)?.size
- if (value !== undefined && polymerType[rI] === PolymerType.NA) {
- value = 0
- if (clashes.getVertexEdgeCount(element) > 0) value += 1
- if (bondOutliers.index.has(element)) value += 1
- if (angleOutliers.index.has(element)) value += 1
+
+ const value = geometryIssues.get(rI)
+ if (value === undefined) return DefaultColor
+
+ let count = SetUtils.differenceSize(value, ignore)
+
+ if (count > 0 && polymerType[rI] === PolymerType.NA) {
+ count = 0
+ if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1
+ if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1
+ if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1
}
- switch (value) {
+ switch (count) {
case undefined: return DefaultColor
case 0: return NoIssuesColor
case 1: return OneIssueColor
@@ -72,16 +95,16 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: {}): Col
color,
props,
contextHash,
- description: 'Assigns residue colors according to the number of geometry issues.',
+ description: 'Assigns residue colors according to the number of (filtered) geometry issues.',
legend: ColorLegend
}
}
-export const GeometryQualityColorThemeProvider: ColorTheme.Provider<{}> = {
+export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQualityColorThemeParams> = {
label: 'RCSB Geometry Quality',
factory: GeometryQualityColorTheme,
- getParams: () => ({}),
- defaultValues: PD.getDefaultValues({}),
+ getParams: getGeometricQualityColorThemeParams,
+ defaultValues: PD.getDefaultValues(getGeometricQualityColorThemeParams({})),
isApplicable: (ctx: ThemeDataContext) => ValidationReport.isApplicable(ctx.structure?.models[0]),
ensureCustomProperties: (ctx: CustomProperty.Context, data: ThemeDataContext) => {
return data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0]) : Promise.resolve()
diff --git a/src/mol-model-props/rcsb/validation-report.ts b/src/mol-model-props/rcsb/validation-report.ts
index c2a2b054f8dab317d739a391fef2823b56658b0f..ada844656b5fd832507d19efae31e330cbe3d98c 100644
--- a/src/mol-model-props/rcsb/validation-report.ts
+++ b/src/mol-model-props/rcsb/validation-report.ts
@@ -18,6 +18,7 @@ import { IntMap, SortedArray } from '../../mol-data/int';
import { arrayMax } from '../../mol-util/array';
import { equalEps } from '../../mol-math/linear-algebra/3d/common';
import { Vec3 } from '../../mol-math/linear-algebra';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export { ValidationReport }
@@ -90,8 +91,8 @@ namespace ValidationReport {
export function isApplicable(model?: Model): boolean {
return (
!!model &&
- model.sourceData.kind === 'mmCIF' &&
- (model.sourceData.data.database_2.database_id.isDefined ||
+ MmcifFormat.is(model.sourceData) &&
+ (model.sourceData.data.db.database_2.database_id.isDefined ||
model.entryId.length === 4)
)
}
diff --git a/src/mol-model/structure/export/categories/modified-residues.ts b/src/mol-model/structure/export/categories/modified-residues.ts
index e19e33636c6c1b7531fbd22876517e517e18686a..51726e8c6b2a1df02b78335e1b9087f7c01b3a33 100644
--- a/src/mol-model/structure/export/categories/modified-residues.ts
+++ b/src/mol-model/structure/export/categories/modified-residues.ts
@@ -35,7 +35,7 @@ function getModifiedResidues({ structures }: CifExportContext): StructureElement
const ret = [];
const prop = P.residue.label_comp_id;
- const loc = StructureElement.Location.create();
+ const loc = StructureElement.Location.create(structure);
for (const unit of structure.units) {
if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
const residues = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
@@ -45,7 +45,7 @@ function getModifiedResidues({ structures }: CifExportContext): StructureElement
loc.element = unit.elements[seg.start];
const name = prop(loc);
if (map.has(name)) {
- ret[ret.length] = StructureElement.Location.create(loc.unit, loc.element);
+ ret[ret.length] = StructureElement.Location.clone(loc);
}
}
}
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index a5bc27ce4b6d9cf74350fd1a705eeef8bcc4c0ff..21d9c13488ac510ddcf6bb5cac5c0c39e378db9b 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -13,6 +13,7 @@ import CifField = CifWriter.Field
import CifCategory = CifWriter.Category
import { Column } from '../../../../mol-data/db';
import { residueIdFields } from './atom_site';
+import { ModelSecondaryStructure } from '../../../../mol-model-formats/structure/property/secondary-structure';
export const _struct_conf: CifCategory<CifExportContext> = {
name: 'struct_conf',
@@ -70,11 +71,14 @@ interface SSElement<T extends SecondaryStructure.Element> {
function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContext, kind: SecondaryStructure.Element['kind']) {
// TODO: encode secondary structure for different models?
- const { key, elements } = ctx.structures[0].model.properties.secondaryStructure;
+ const secondaryStructure = ModelSecondaryStructure.Provider.get(ctx.firstModel)
+ if (!secondaryStructure) return [] as SSElement<T>[]
+ const { key, elements } = secondaryStructure;
const ssElements: SSElement<any>[] = [];
- for (const unit of ctx.structures[0].units) {
+ const structure = ctx.structures[0];
+ for (const unit of structure.units) {
// currently can only support this for "identity" operators.
if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
@@ -100,8 +104,8 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
if (startIdx !== key[current.index]) {
move = false;
ssElements[ssElements.length] = {
- start: StructureElement.Location.create(unit, segs.offsets[start]),
- end: StructureElement.Location.create(unit, segs.offsets[prev]),
+ start: StructureElement.Location.create(structure, unit, segs.offsets[start]),
+ end: StructureElement.Location.create(structure, unit, segs.offsets[prev]),
length: prev - start + 1,
element
}
diff --git a/src/mol-model/structure/export/categories/utils.ts b/src/mol-model/structure/export/categories/utils.ts
index 091e92172dcbfeefa10bb7e069c717103474a05a..4f500efbf56d9dfe93322614ca74b4b1d1958e47 100644
--- a/src/mol-model/structure/export/categories/utils.ts
+++ b/src/mol-model/structure/export/categories/utils.ts
@@ -13,10 +13,11 @@ import { UniqueArray } from '../../../../mol-data/generic';
import { sortArray } from '../../../../mol-data/util';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { CifExportContext } from '../mmcif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
- if (model.sourceData.kind !== 'mmCIF') return;
- return model.sourceData.data[name];
+ if (!MmcifFormat.is(model.sourceData)) return;
+ return model.sourceData.data.db[name];
}
export function getUniqueResidueNamesFromStructures(structures: Structure[]) {
@@ -50,9 +51,9 @@ export function copy_mmCif_category(name: keyof mmCIF_Schema, condition?: (struc
if (condition && !condition(structures[0])) return CifWriter.Category.Empty;
const model = structures[0].model;
- if (model.sourceData.kind !== 'mmCIF') return CifWriter.Category.Empty;
+ if (!MmcifFormat.is(model.sourceData)) return CifWriter.Category.Empty;
- const table = model.sourceData.data[name];
+ const table = model.sourceData.data.db[name];
if (!table || !table._rowCount) return CifWriter.Category.Empty;
return CifWriter.Category.ofTable(table);
}
diff --git a/src/mol-model/structure/model.ts b/src/mol-model/structure/model.ts
index 8a1dccfdebe0bda698574a261203ab9741156036..a1cb4a8bd81a7af47e32eafbc8236632cc61c6d9 100644
--- a/src/mol-model/structure/model.ts
+++ b/src/mol-model/structure/model.ts
@@ -6,9 +6,9 @@
import { Model } from './model/model'
import * as Types from './model/types'
-import { ModelSymmetry } from './model/properties/symmetry'
+import { Symmetry } from './model/properties/symmetry'
import StructureSequence from './model/properties/sequence'
export * from './model/properties/custom/indexed'
export * from './model/indexing'
-export { Model, Types, ModelSymmetry, StructureSequence }
\ No newline at end of file
+export { Model, Types, Symmetry, StructureSequence }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 74cd85af6bf0d1b6652f4e390b654cbef7c67fc2..04dd2a0dd482c28713a5bb4c68686bf244752153 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,11 +8,9 @@
import UUID from '../../../mol-util/uuid';
import StructureSequence from './properties/sequence';
import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
-import { ModelSymmetry } from './properties/symmetry';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
import { CustomProperties } from '../common/custom-property';
-import { SecondaryStructure } from './properties/seconday-structure';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from '../../../mol-model-formats/structure/format';
import { calcModelCenter } from './util';
@@ -20,9 +18,9 @@ import { Vec3 } from '../../../mol-math/linear-algebra';
import { Mutable } from '../../../mol-util/type-helpers';
import { Coordinates } from '../coordinates';
import { Topology } from '../topology';
-import { _parse_mmCif } from '../../../mol-model-formats/structure/mmcif/parser';
import { Task } from '../../../mol-task';
-import { IndexPairBonds } from '../../../mol-model-formats/structure/mmcif/bonds/index-pair';
+import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
+import { createModels } from '../../../mol-model-formats/structure/basic/parser';
/**
* Interface to the "source data" of the molecule.
@@ -47,7 +45,6 @@ export interface Model extends Readonly<{
sourceData: ModelFormat,
- symmetry: ModelSymmetry,
entities: Entities,
sequence: StructureSequence,
@@ -56,8 +53,6 @@ export interface Model extends Readonly<{
atomicRanges: AtomicRanges,
properties: {
- /** secondary structure provided by the input file */
- readonly secondaryStructure: SecondaryStructure,
/** maps modified residue name to its parent */
readonly modifiedResidues: Readonly<{
parentId: ReadonlyMap<string, string>,
@@ -87,7 +82,6 @@ export interface Model extends Readonly<{
} { }
export namespace Model {
- // TODO: is this enough?
export type Trajectory = ReadonlyArray<Model>
export function trajectoryFromModelAndCoordinates(model: Model, coordinates: Coordinates): Trajectory {
@@ -113,12 +107,13 @@ export namespace Model {
export function trajectoryFromTopologyAndCoordinates(topology: Topology, coordinates: Coordinates): Task<Trajectory> {
return Task.create('Create Trajectory', async ctx => {
- const model = (await _parse_mmCif(topology.format, ctx))[0];
+ const model = (await createModels(topology.basic, topology.sourceData, ctx))[0];
if (!model) throw new Error('found no model')
const trajectory = trajectoryFromModelAndCoordinates(model, coordinates)
const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount }
+ const indexPairBonds = IndexPairBonds.fromData(bondData)
for (const m of trajectory) {
- IndexPairBonds.attachFromData(m, bondData)
+ IndexPairBonds.Provider.set(m, indexPairBonds)
}
return trajectory
})
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 5b17b8b4f2e137161191553075bf4b8c41d4ff6a..0f1bee9cd65d589251a2a74fa83f5f4266841d1a 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -50,7 +50,7 @@ export const AtomsSchema = {
};
export type AtomsSchema = typeof AtomsSchema
-export interface Atoms extends Table<AtomsSchema> { }
+export type Atoms = Table<AtomsSchema>
export const ResiduesSchema = {
/**
@@ -83,7 +83,7 @@ export const ResiduesSchema = {
pdbx_PDB_ins_code: mmCIF.atom_site.pdbx_PDB_ins_code,
};
export type ResiduesSchema = typeof ResiduesSchema
-export interface Residues extends Table<ResiduesSchema> { }
+export type Residues = Table<ResiduesSchema>
export const ChainsSchema = {
/**
@@ -102,7 +102,7 @@ export const ChainsSchema = {
label_entity_id: mmCIF.atom_site.label_entity_id
}
export type ChainsSchema = typeof ChainsSchema
-export interface Chains extends Table<ChainsSchema> { }
+export type Chains = Table<ChainsSchema>
export interface AtomicData {
atoms: Atoms,
@@ -139,6 +139,8 @@ export interface AtomicSegments {
export interface AtomicIndex {
/** @returns index or -1 if not present. */
getEntityFromChain(cI: ChainIndex): EntityIndex,
+ /** @returns index or -1 if not present. */
+ findEntity(label_asym_id: string): EntityIndex
/**
* Find chain using label_ mmCIF properties
diff --git a/src/mol-model/structure/model/properties/computed.ts b/src/mol-model/structure/model/properties/computed.ts
deleted file mode 100644
index 39896495fbaa30bcf65f3575e6664b7517a9af68..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/model/properties/computed.ts
+++ /dev/null
@@ -1,22 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// TODO: stuff like "residue type/flags", isRingAtom, rings, bonds??, wrap these in a computation?
-// secondary structure is also a computed property
-
-// import { SecondaryStructureType } from '../constants'
-
-
-// interface SecondaryStructure {
-// ofResidue: ArrayLike<SecondaryStructureType>,
-// // atom segmentation??
-// segments: Segmentation
-// }
-
-// interface Conformation {
-// positions: Conformation,
-// secondaryStructure: SecondaryStructure
-// }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/custom/indexed.ts b/src/mol-model/structure/model/properties/custom/indexed.ts
index 4e8aa7ef39895112531941eee44bbab9b52cd24f..de239f33f5ed8a6708ce12a8d670e87ad45ce97e 100644
--- a/src/mol-model/structure/model/properties/custom/indexed.ts
+++ b/src/mol-model/structure/model/properties/custom/indexed.ts
@@ -109,7 +109,7 @@ class SegmentedMappedIndexedCustomProperty<Idx extends IndexedCustomProperty.Ind
const seg = chains.move();
if (!this.has(seg.index) || seenIndices.has(seg.index)) continue;
seenIndices.add(seg.index);
- loci[loci.length] = StructureElement.Location.create(unit, unit.elements[seg.start]);
+ loci[loci.length] = StructureElement.Location.create(structure, unit, unit.elements[seg.start]);
}
}
@@ -154,7 +154,7 @@ class ElementMappedCustomProperty<T = any> implements IndexedCustomProperty<Elem
const e = elements[i];
if (!this.has(e) || seenIndices.has(e)) continue;
seenIndices.add(elements[i]);
- loci[loci.length] = StructureElement.Location.create(unit, e);
+ loci[loci.length] = StructureElement.Location.create(structure, unit, e);
}
}
@@ -202,7 +202,7 @@ class EntityMappedCustomProperty<T = any> implements IndexedCustomProperty<Entit
const eI = index.getEntityFromChain(seg.index);
if (!this.has(eI) || seenIndices.has(eI)) continue;
seenIndices.add(eI);
- loci[loci.length] = StructureElement.Location.create(unit, unit.elements[seg.start]);
+ loci[loci.length] = StructureElement.Location.create(structure, unit, unit.elements[seg.start]);
}
}
diff --git a/src/mol-model/structure/model/properties/symmetry.ts b/src/mol-model/structure/model/properties/symmetry.ts
index 38b9e5e12642ac80ad7c8e5ae1daa661bd6334a9..a25aa43a4d55541e6e9f40fffd990b4b71a938ea 100644
--- a/src/mol-model/structure/model/properties/symmetry.ts
+++ b/src/mol-model/structure/model/properties/symmetry.ts
@@ -10,6 +10,7 @@ import { StructureQuery } from '../../query'
import { Model } from '../../model'
import { Spacegroup } from '../../../../mol-math/geometry';
import { Vec3 } from '../../../../mol-math/linear-algebra';
+import { ModelSymmetry } from '../../../../mol-model-formats/structure/property/symmetry';
/** Determine an atom set and a list of operators that should be applied to that set */
export interface OperatorGroup {
@@ -42,7 +43,7 @@ export namespace Assembly {
}
}
-interface ModelSymmetry {
+interface Symmetry {
readonly assemblies: ReadonlyArray<Assembly>,
readonly spacegroup: Spacegroup,
readonly isNonStandardCrytalFrame: boolean,
@@ -58,13 +59,14 @@ interface ModelSymmetry {
}
}
-namespace ModelSymmetry {
- export const Default: ModelSymmetry = { assemblies: [], spacegroup: Spacegroup.ZeroP1, isNonStandardCrytalFrame: false };
+namespace Symmetry {
+ export const Default: Symmetry = { assemblies: [], spacegroup: Spacegroup.ZeroP1, isNonStandardCrytalFrame: false };
export function findAssembly(model: Model, id: string): Assembly | undefined {
const _id = id.toLocaleLowerCase();
- return arrayFind(model.symmetry.assemblies, a => a.id.toLowerCase() === _id);
+ const symmetry = ModelSymmetry.Provider.get(model)
+ return symmetry ? arrayFind(symmetry.assemblies, a => a.id.toLowerCase() === _id) : undefined;
}
}
-export { ModelSymmetry }
\ No newline at end of file
+export { Symmetry }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/atomic-index.ts b/src/mol-model/structure/model/properties/utils/atomic-index.ts
index f35949c1cd71eb26c540f809e2e22ffc6219caec..b16cbb5289ee2b1dfead9b7a32b2fdb2453a0f6b 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -51,7 +51,9 @@ interface Mapping {
chain_index_label_seq_id: Map<ChainIndex, Map<string | number, ResidueIndex>>,
auth_asym_id_auth_seq_id: Map<string, Map<number, ChainIndex>>,
- chain_index_auth_seq_id: Map<ChainIndex, Map<string | number, ResidueIndex>>
+ chain_index_auth_seq_id: Map<ChainIndex, Map<string | number, ResidueIndex>>,
+
+ label_asym_id: Map<string, EntityIndex>,
}
function createMapping(entities: Entities, data: AtomicData, segments: AtomicSegments): Mapping {
@@ -67,6 +69,7 @@ function createMapping(entities: Entities, data: AtomicData, segments: AtomicSeg
chain_index_label_seq_id: new Map(),
auth_asym_id_auth_seq_id: new Map(),
chain_index_auth_seq_id: new Map(),
+ label_asym_id: new Map(),
};
}
@@ -79,6 +82,11 @@ class Index implements AtomicIndex {
return this.map.chain_index_entity_index[cI];
}
+ findEntity(label_asym_id: string): EntityIndex {
+ const entityIndex = this.map.label_asym_id.get(label_asym_id)
+ return entityIndex !== undefined ? entityIndex : -1 as EntityIndex
+ }
+
findChainLabel(key: AtomicIndex.ChainLabelKey): ChainIndex {
const eI = this.entityIndex(key.label_entity_id);
if (eI < 0 || !this.map.entity_index_label_asym_id.has(eI)) return -1 as ChainIndex;
@@ -216,7 +224,9 @@ export function getAtomicIndex(data: AtomicData, entities: Entities, segments: A
map.auth_asym_id_auth_seq_id.set(authAsymId, auth_asym_id_auth_seq_id)
}
- updateMapMapIndex(map.entity_index_label_asym_id, entityIndex, label_asym_id.value(chainIndex), chainIndex);
+ const labelAsymId = label_asym_id.value(chainIndex)
+ if (!map.label_asym_id.has(labelAsymId)) map.label_asym_id.set(labelAsymId, entityIndex);
+ updateMapMapIndex(map.entity_index_label_asym_id, entityIndex, labelAsymId, chainIndex);
const chain_index_label_seq_id = new Map<string | number, ResidueIndex>();
const chain_index_auth_seq_id = new Map<string | number, ResidueIndex>();
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index d9f083413db7634beb079693f418b50d18ebeaa9..95a1e8e41d6b9688c79b8316186748eb08501001 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -221,6 +221,7 @@ export const WaterNames = new Set([
export const AminoAcidNamesL = new Set([
'HIS', 'ARG', 'LYS', 'ILE', 'PHE', 'LEU', 'TRP', 'ALA', 'MET', 'PRO', 'CYS',
'ASN', 'VAL', 'GLY', 'SER', 'GLN', 'TYR', 'ASP', 'GLU', 'THR', 'SEC', 'PYL',
+ 'UNK' // unknown amino acid from CCD
])
export const AminoAcidNamesD = new Set([
'DAL', // D-ALANINE
@@ -247,8 +248,14 @@ export const AminoAcidNamesD = new Set([
])
export const AminoAcidNames = SetUtils.unionMany(AminoAcidNamesL, AminoAcidNamesD)
-export const RnaBaseNames = new Set([ 'A', 'C', 'T', 'G', 'I', 'U' ])
-export const DnaBaseNames = new Set([ 'DA', 'DC', 'DT', 'DG', 'DI', 'DU' ])
+export const RnaBaseNames = new Set([
+ 'A', 'C', 'T', 'G', 'I', 'U',
+ 'N' // unknown RNA base from CCD
+])
+export const DnaBaseNames = new Set([
+ 'DA', 'DC', 'DT', 'DG', 'DI', 'DU',
+ 'DN' // unknown DNA base from CCD
+])
export const PeptideBaseNames = new Set([ 'APN', 'CPN', 'TPN', 'GPN' ])
export const PurineBaseNames = new Set([ 'A', 'G', 'DA', 'DG', 'DI', 'APN', 'GPN' ])
export const PyrimidineBaseNames = new Set([ 'C', 'T', 'U', 'DC', 'DT', 'DU', 'CPN', 'TPN' ])
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index d73e9f1a4026f1a7062c87ab65a36f6c97ce8cc1..43b2538b98ba727032ab231948c203283e123f61 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -6,13 +6,12 @@
import { Structure, StructureElement, Unit } from '../structure';
import { now } from '../../../mol-util/now';
-import { ElementIndex } from '../model';
import { BondType } from '../model/types';
import { StructureSelection } from './selection';
import { defaultBondTest } from './queries/internal';
export interface QueryContextView {
- readonly element: StructureElement.Location;
+ readonly element: Readonly<StructureElement.Location>;
readonly currentStructure: Structure;
}
@@ -28,7 +27,7 @@ export class QueryContext implements QueryContextView {
readonly inputStructure: Structure;
/** Current element */
- readonly element = StructureElement.Location.create();
+ readonly element: StructureElement.Location = StructureElement.Location.create(void 0);
currentStructure: Structure = void 0 as any;
/** Current bond between atoms */
@@ -37,14 +36,9 @@ export class QueryContext implements QueryContextView {
/** Supply this from the outside. Used by the internal.generator.current symbol */
currentSelection: StructureSelection | undefined = void 0;
- setElement(unit: Unit, e: ElementIndex) {
- this.element.unit = unit;
- this.element.element = e;
- }
-
pushCurrentElement(): StructureElement.Location {
this.currentElementStack[this.currentElementStack.length] = this.element;
- (this.element as StructureElement.Location) = StructureElement.Location.create();
+ (this.element as StructureElement.Location) = StructureElement.Location.create(void 0);
return this.element;
}
@@ -112,16 +106,21 @@ export interface QueryContextOptions {
export interface QueryPredicate { (ctx: QueryContext): boolean }
export interface QueryFn<T = any> { (ctx: QueryContext): T }
-export class QueryContextBondInfo<U extends Unit = Unit> {
- a: StructureElement.Location<U> = StructureElement.Location.create();
+class QueryContextBondInfo<U extends Unit = Unit> {
+ a: StructureElement.Location<U> = StructureElement.Location.create(void 0);
aIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
- b: StructureElement.Location<U> = StructureElement.Location.create();
+ b: StructureElement.Location<U> = StructureElement.Location.create(void 0);
bIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
type: BondType = BondType.Flag.None;
order: number = 0;
private testFn: QueryPredicate = defaultBondTest;
+ setStructure(s: Structure) {
+ this.a.structure = s;
+ this.b.structure = s;
+ }
+
setTestFn(fn?: QueryPredicate) {
this.testFn = fn || defaultBondTest;
}
@@ -136,6 +135,10 @@ export class QueryContextBondInfo<U extends Unit = Unit> {
}
private swap() {
+ // const sA = this.a.structure;
+ // this.a.structure = this.b.structure;
+ // this.b.structure = sA;
+
const idxA = this.aIndex;
this.aIndex = this.bIndex;
this.bIndex = idxA;
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index aff78800bc31595d98513243e04d6771a132d0c6..3b689246c33f2db5e22062ab22e426d75c4a7737 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -56,6 +56,7 @@ export function getCurrentStructureProperties(ctx: QueryContext, props: UnitType
const { units } = ctx.currentStructure;
const l = ctx.pushCurrentElement();
+ l.structure = ctx.currentStructure;
for (const unit of units) {
l.unit = unit;
const elements = unit.elements;
@@ -239,6 +240,9 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
const atomicBond = queryCtx.atomicBond;
const interBonds = input.interUnitBonds;
+
+ atomicBond.setStructure(input);
+
for (const unit of structure.units) {
if (!Unit.isAtomic(unit)) continue;
@@ -248,8 +252,6 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
const bondedUnits = interBonds.getConnectedUnits(unit);
const buCount = bondedUnits.length;
- atomicBond.a.unit = inputUnit;
-
const srcElements = unit.elements;
const inputElements = inputUnit.elements;
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index 646f67dfc7f60cba98cf1facc4314fa58a014c48..afac8b988674b8fe329eab0bf1fca5f2a5ea83e9 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -64,6 +64,7 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
const l = ctx.pushCurrentElement();
const builder = inputStructure.subsetBuilder(true);
+ l.structure = inputStructure;
for (const unit of units) {
l.unit = unit;
const elements = unit.elements;
@@ -89,6 +90,7 @@ function atomGroupsSegmented({ unitTest, entityTest, chainTest, residueTest, ato
const l = ctx.pushCurrentElement();
const builder = inputStructure.subsetBuilder(true);
+ l.structure = inputStructure;
for (const unit of units) {
l.unit = unit;
if (!unitTest(ctx)) continue;
@@ -158,6 +160,7 @@ function atomGroupsGrouped({ unitTest, entityTest, chainTest, residueTest, atomT
const l = ctx.pushCurrentElement();
const builder = new LinearGroupingBuilder(inputStructure);
+ l.structure = inputStructure;
for (const unit of units) {
l.unit = unit;
if (!unitTest(ctx)) continue;
@@ -295,6 +298,8 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
const atomicBond = ctx.atomicBond;
atomicBond.setTestFn(bondTest);
+ atomicBond.setStructure(structure);
+
// Process intra unit bonds
for (const unit of structure.units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
diff --git a/src/mol-model/structure/query/queries/internal.ts b/src/mol-model/structure/query/queries/internal.ts
index c0258e58d901e769fe51dd787c9b9625b5da0fd0..68ce9e555818ad41443e00864fef4dd21670f8ab 100644
--- a/src/mol-model/structure/query/queries/internal.ts
+++ b/src/mol-model/structure/query/queries/internal.ts
@@ -22,7 +22,7 @@ export function defaultBondTest(ctx: QueryContext) {
export function atomicSequence(): StructureQuery {
return function query_atomicSequence(ctx) {
const { inputStructure } = ctx;
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(inputStructure);
const units: Unit[] = [];
for (const unit of inputStructure.units) {
@@ -50,7 +50,7 @@ export function atomicSequence(): StructureQuery {
export function water(): StructureQuery {
return function query_water(ctx) {
const { inputStructure } = ctx;
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(inputStructure);
const units: Unit[] = [];
for (const unit of inputStructure.units) {
@@ -69,7 +69,7 @@ export function water(): StructureQuery {
export function atomicHet(): StructureQuery {
return function query_atomicHet(ctx) {
const { inputStructure } = ctx;
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(inputStructure);
const units: Unit[] = [];
for (const unit of inputStructure.units) {
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index 8f38b20430e72dc66118da04056af4639d2f69aa..6c7fd7319cbf17b7bbc3d34cb9cc0e7e532b4a24 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -94,6 +94,7 @@ function getIncludeSurroundingsWithRadius(ctx: QueryContext, source: Structure,
const { elementRadius, elementRadiusClosure, sourceMaxRadius, radius } = params;
ctx.pushCurrentElement();
+ ctx.element.structure = structure;
for (const unit of structure.units) {
ctx.element.unit = unit;
const { x, y, z } = unit.conformation;
@@ -115,6 +116,7 @@ function getIncludeSurroundingsWithRadius(ctx: QueryContext, source: Structure,
function createElementRadiusFn(ctx: QueryContext, eRadius: QueryFn<number>): StructureElement.Property<number> {
return e => {
+ ctx.element.structure = e.structure;
ctx.element.unit = e.unit;
ctx.element.element = e.element;
return eRadius(ctx);
@@ -123,6 +125,7 @@ function createElementRadiusFn(ctx: QueryContext, eRadius: QueryFn<number>): Str
function findStructureRadius(ctx: QueryContext, eRadius: QueryFn<number>) {
let r = 0;
+ ctx.element.structure = ctx.inputStructure;
for (const unit of ctx.inputStructure.units) {
ctx.element.unit = unit;
const elements = unit.elements;
@@ -252,6 +255,7 @@ export function expandProperty(query: StructureQuery, property: QueryFn): Struct
const builders: StructureSubsetBuilder[] = [];
ctx.pushCurrentElement();
StructureSelection.forEach(src, (s, sI) => {
+ ctx.element.structure = s;
for (const unit of s.units) {
ctx.element.unit = unit;
const elements = unit.elements;
@@ -272,6 +276,7 @@ export function expandProperty(query: StructureQuery, property: QueryFn): Struct
if (sI % 10 === 0) ctx.throwIfTimedOut();
});
+ ctx.element.structure = ctx.inputStructure;
for (const unit of ctx.inputStructure.units) {
ctx.element.unit = unit;
const elements = unit.elements;
@@ -355,6 +360,8 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
const inputUnitA = inputStructure.unitMap.get(unit.id) as Unit.Atomic;
const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order } } = inputUnitA.bonds;
+ atomicBond.setStructure(inputStructure);
+
// Process intra unit bonds
atomicBond.a.unit = inputUnitA;
atomicBond.b.unit = inputUnitA;
diff --git a/src/mol-model/structure/query/utils/builders.ts b/src/mol-model/structure/query/utils/builders.ts
index c7d0c6ceeff8abcecbc2aa94e138a1df320e19c7..add4742dd95b13e7fbaeca60c12be03c8264a60c 100644
--- a/src/mol-model/structure/query/utils/builders.ts
+++ b/src/mol-model/structure/query/utils/builders.ts
@@ -56,7 +56,7 @@ export class LinearGroupingBuilder {
private singletonSelection(): StructureSelection {
const builder = this.source.subsetBuilder(true);
- const loc = StructureElement.Location.create();
+ const loc = StructureElement.Location.create(this.source);
for (let i = 0, _i = this.builders.length; i < _i; i++) {
this.builders[i].setSingletonLocation(loc);
builder.addToUnit(loc.unit.id, loc.element);
diff --git a/src/mol-model/structure/query/utils/structure-distance.ts b/src/mol-model/structure/query/utils/structure-distance.ts
index f05ca7cb1fe2e87e464fa281ed68f97c5020ee0a..bdea7bfe1089c874d003b9786ae161b5673fafab 100644
--- a/src/mol-model/structure/query/utils/structure-distance.ts
+++ b/src/mol-model/structure/query/utils/structure-distance.ts
@@ -61,12 +61,14 @@ namespace MinMaxDist {
const { units } = a;
let withinRange = false;
+ ctx.element.structure = a;
for (let i = 0, _i = units.length; i < _i; i++) {
const unit = units[i];
const { elements, conformation: { position } } = unit;
+ ctx.element.unit = unit;
for (let i = 0, _i = elements.length; i < _i; i++) {
const e = elements[i];
- ctx.setElement(unit, e);
+ ctx.element.element = e;
const tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
if (tp === Result.BelowMin) return Result.BelowMin;
if (tp === Result.WithinMax) withinRange = true;
@@ -102,12 +104,14 @@ namespace MaxRadiusDist {
if (a.elementCount === 0 || b.elementCount === 0) return 0;
const { units } = a;
+ ctx.element.structure = a;
for (let i = 0, _i = units.length; i < _i; i++) {
const unit = units[i];
+ ctx.element.unit = unit;
const { elements, conformation: { position } } = unit;
for (let i = 0, _i = elements.length; i < _i; i++) {
const e = elements[i];
- ctx.setElement(unit, e);
+ ctx.element.element = e;
if (toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), maxDist, elementRadius)) return true;
}
}
diff --git a/src/mol-model/structure/structure/element/location.ts b/src/mol-model/structure/structure/element/location.ts
index c0d745b23633d308a425b7c8312ca9bfa541f6da..ec5f970e4a17f64c08a5d6775cb68505260b3c30 100644
--- a/src/mol-model/structure/structure/element/location.ts
+++ b/src/mol-model/structure/structure/element/location.ts
@@ -8,22 +8,34 @@
import { ElementIndex } from '../../model';
import Unit from '../unit';
import { Vec3 } from '../../../../mol-math/linear-algebra';
+import Structure from '../structure';
export { Location }
interface Location<U = Unit> {
readonly kind: 'element-location',
+ structure: Structure,
unit: U,
/** Index into element (atomic/coarse) properties of unit.model */
element: ElementIndex
}
namespace Location {
- export function create<U extends Unit>(unit?: U, element?: ElementIndex): Location<U> {
- return { kind: 'element-location', unit: unit!, element: element || (0 as ElementIndex) };
+ export function create<U extends Unit>(structure: Structure | undefined, unit?: U, element?: ElementIndex): Location<U> {
+ return {
+ kind: 'element-location',
+ structure: structure as any,
+ unit: unit as any,
+ element: element || (0 as ElementIndex)
+ };
}
- export function set(a: Location, unit?: Unit, element?: ElementIndex): Location {
+ export function clone<U extends Unit>(l: Location<U>): Location<U> {
+ return create(l.structure, l.unit, l.element);
+ }
+
+ export function set(a: Location, structure?: Structure, unit?: Unit, element?: ElementIndex): Location {
+ if (structure) a.structure = structure;
if (unit) a.unit = unit
if (element !== undefined) a.element = element
return a;
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 4523f631ae8f423215188430a64f006a2d1968dd..76746ddb8b49af4dcda61173166e9c1c6d6df908 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -90,11 +90,12 @@ export namespace Loci {
const unit = loci.elements[0].unit;
const element = unit.elements[OrderedSet.getAt(loci.elements[0].indices, 0)];
if (e) {
+ e.structure = loci.structure;
e.unit = loci.elements[0].unit;
e.element = element;
return e;
}
- return Location.create(unit, element);
+ return Location.create(loci.structure, unit, element);
}
export function toStructure(loci: Loci): Structure {
@@ -365,7 +366,7 @@ export namespace Loci {
export function extendToWholeEntities(loci: Loci): Loci {
const elements: Loci['elements'][0][] = []
- const l = Location.create()
+ const l = Location.create(loci.structure)
const entities = new Set<string>()
const { units } = loci.structure
diff --git a/src/mol-model/structure/structure/element/stats.ts b/src/mol-model/structure/structure/element/stats.ts
index fea5bc4198831c24457a31530aa641b1d9b44f7c..ac9f6e2854b4946c60c278af1a5a93e45338108d 100644
--- a/src/mol-model/structure/structure/element/stats.ts
+++ b/src/mol-model/structure/structure/element/stats.ts
@@ -10,6 +10,7 @@ import Unit from '../unit';
import { Loci } from './loci';
import { Location } from './location';
import { ChainIndex } from '../../model/indexing';
+import Structure from '../structure';
export interface Stats {
elementCount: number
@@ -37,12 +38,12 @@ export namespace Stats {
unitCount: 0,
structureCount: 0,
- firstElementLoc: Location.create(),
- firstConformationLoc: Location.create(),
- firstResidueLoc: Location.create(),
- firstChainLoc: Location.create(),
- firstUnitLoc: Location.create(),
- firstStructureLoc: Location.create(),
+ firstElementLoc: Location.create(void 0),
+ firstConformationLoc: Location.create(void 0),
+ firstResidueLoc: Location.create(void 0),
+ firstChainLoc: Location.create(void 0),
+ firstUnitLoc: Location.create(void 0),
+ firstStructureLoc: Location.create(void 0),
}
}
@@ -51,7 +52,7 @@ export namespace Stats {
map.set(key, count + inc)
}
- function handleElement(stats: Stats, element: Loci['elements'][0]) {
+ function handleElement(stats: Stats, structure: Structure, element: Loci['elements'][0]) {
const { indices, unit } = element
const { elements } = unit
const size = OrderedSet.size(indices)
@@ -60,19 +61,19 @@ export namespace Stats {
const residueAltIdCounts = new Map<string, number>()
if (size > 0) {
- Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+ Location.set(stats.firstElementLoc, structure, unit, elements[OrderedSet.start(indices)])
}
// count single element unit as unit not element
if (size === elements.length) {
stats.unitCount += 1
if (stats.unitCount === 1) {
- Location.set(stats.firstUnitLoc, unit, elements[OrderedSet.start(indices)])
+ Location.set(stats.firstUnitLoc, structure, unit, elements[OrderedSet.start(indices)])
}
} else if (size === 1) {
stats.elementCount += 1
if (stats.elementCount === 1) {
- Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+ Location.set(stats.firstElementLoc, structure, unit, elements[OrderedSet.start(indices)])
}
} else {
if (Unit.isAtomic(unit)) {
@@ -99,7 +100,7 @@ export namespace Stats {
// full residue
stats.residueCount += 1
if (stats.residueCount === 1) {
- Location.set(stats.firstResidueLoc, unit, offsets[rI])
+ Location.set(stats.firstResidueLoc, structure, unit, offsets[rI])
}
} else {
// partial residue
@@ -116,7 +117,7 @@ export namespace Stats {
if (stats.conformationCount === 1) {
for (let l = offsets[rI], _l = offsets[rI + 1]; l < _l; ++l) {
if (k === label_alt_id.value(l)) {
- Location.set(stats.firstConformationLoc, unit, l)
+ Location.set(stats.firstConformationLoc, structure, unit, l)
break
}
}
@@ -131,13 +132,13 @@ export namespace Stats {
} else {
stats.elementCount += size
if (stats.elementCount === 1) {
- Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+ Location.set(stats.firstElementLoc, structure, unit, elements[OrderedSet.start(indices)])
}
}
}
}
- function handleUnitChainsSimple(stats: Stats, element: Loci['elements'][0]) {
+ function handleUnitChainsSimple(stats: Stats, structure: Structure, element: Loci['elements'][0]) {
const { indices, unit } = element;
const size = OrderedSet.size(indices);
if (size === 0) return;
@@ -148,7 +149,7 @@ export namespace Stats {
if (size === elements.length) {
stats.chainCount += 1;
if (stats.chainCount === 1) {
- Location.set(stats.firstChainLoc, unit, elements[OrderedSet.start(indices)]);
+ Location.set(stats.firstChainLoc, structure, unit, elements[OrderedSet.start(indices)]);
}
}
return;
@@ -186,13 +187,13 @@ export namespace Stats {
// full chain
stats.chainCount += 1;
if (stats.chainCount === 1) {
- Location.set(stats.firstChainLoc, unit, offsets[cI]);
+ Location.set(stats.firstChainLoc, structure, unit, offsets[cI]);
}
}
}
}
- function handleUnitChainsPartitioned(stats: Stats, lociElements: Loci['elements'], start: number, end: number) {
+ function handleUnitChainsPartitioned(stats: Stats, structure: Structure, lociElements: Loci['elements'], start: number, end: number) {
let element = lociElements[start];
// all the elements have the same model since they are part of the same group so this is ok.
@@ -273,7 +274,7 @@ export namespace Stats {
const eI = elements[OrderedSet.getAt(indices, i)];
const cI = index[eI];
if (cI === firstCI) {
- Location.set(stats.firstChainLoc, unit, eI);
+ Location.set(stats.firstChainLoc, structure, unit, eI);
return;
}
}
@@ -289,13 +290,13 @@ export namespace Stats {
stats.structureCount += 1
if (stats.structureCount === 1) {
const { unit, indices } = loci.elements[0]
- Location.set(stats.firstStructureLoc, unit, unit.elements[OrderedSet.min(indices)])
+ Location.set(stats.firstStructureLoc, loci.structure, unit, unit.elements[OrderedSet.min(indices)])
}
} else {
for (const e of loci.elements) {
- handleElement(stats, e)
+ handleElement(stats, loci.structure, e)
if (!Unit.Traits.is(e.unit.traits, Unit.Trait.Partitioned)) {
- handleUnitChainsSimple(stats, e);
+ handleUnitChainsSimple(stats, loci.structure, e);
} else {
hasPartitions = true;
}
@@ -314,9 +315,9 @@ export namespace Stats {
const end = i;
i--;
if (end - start === 1) {
- handleUnitChainsSimple(stats, e);
+ handleUnitChainsSimple(stats, loci.structure, e);
} else {
- handleUnitChainsPartitioned(stats, loci.elements, start, end);
+ handleUnitChainsPartitioned(stats, loci.structure, loci.elements, start, end);
}
}
}
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 1b11bc22c9f8c627dd19c34f62f520a70eaade1d..48ab835a516d3c50613ad4e5004389db0f6d53a8 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -7,6 +7,8 @@
import StructureElement from './element'
import Unit from './unit'
import { VdwRadius } from '../model/properties/atomic';
+import { ModelSecondaryStructure } from '../../../mol-model-formats/structure/property/secondary-structure';
+import { SecondaryStructureType } from '../model/types';
function p<T>(p: StructureElement.Property<T>) { return p; }
@@ -60,7 +62,7 @@ function _compId(l: StructureElement.Location) {
function compId(l: StructureElement.Location) {
if (!Unit.isAtomic(l.unit)) notAtomic()
if (!hasMicroheterogeneity(l)) return _compId(l)
- return l.unit.model.sourceData.data.atom_site.label_comp_id.value(l.element)
+ return l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])
}
function seqId(l: StructureElement.Location) {
@@ -103,8 +105,20 @@ const residue = {
isNonStandard: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.mon_nstd_flag[0] !== 'y'),
hasMicroheterogeneity: p(hasMicroheterogeneity),
microheterogeneityCompIds: p(microheterogeneityCompIds),
- secondary_structure_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
- secondary_structure_key: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
+ // TODO implement as symbol in SecondaryStructureProvider (not ModelSecondaryStructure.Provider)
+ secondary_structure_type: p(l => {
+ if (!Unit.isAtomic(l.unit)) notAtomic()
+ const secondaryStructure = ModelSecondaryStructure.Provider.get(l.unit.model)
+ if (secondaryStructure) return secondaryStructure.type[l.unit.residueIndex[l.element]]
+ else return SecondaryStructureType.Flag.NA
+ }),
+ // TODO implement as symbol in SecondaryStructureProvider (not ModelSecondaryStructure.Provider)
+ secondary_structure_key: p(l => {
+ if (!Unit.isAtomic(l.unit)) notAtomic()
+ const secondaryStructure = ModelSecondaryStructure.Provider.get(l.unit.model)
+ if (secondaryStructure) return secondaryStructure.key[l.unit.residueIndex[l.element]]
+ else return -1
+ }),
chem_comp_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.type),
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index aae04aa3c2f8fb64156168329e1069e68a3a1af8..c03a2a97b212e350f5bcf609fc421b98bb2036d1 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -401,7 +401,7 @@ function getModels(s: Structure) {
function getUniqueResidueNames(s: Structure) {
const prop = StructureProperties.residue.label_comp_id;
const names = new Set<string>();
- const loc = StructureElement.Location.create();
+ const loc = StructureElement.Location.create(s);
for (const unit of s.units) {
// TODO: support coarse unit?
if (!Unit.isAtomic(unit)) continue;
@@ -418,7 +418,7 @@ function getUniqueResidueNames(s: Structure) {
function getEntityIndices(structure: Structure): ReadonlyArray<EntityIndex> {
const { units } = structure;
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
const keys = UniqueArray.create<number, EntityIndex>();
for (const unit of units) {
@@ -871,7 +871,7 @@ namespace Structure {
}
export class ElementLocationIterator implements Iterator<StructureElement.Location> {
- private current = StructureElement.Location.create();
+ private current: StructureElement.Location;
private unitIndex = 0;
private elements: StructureElement.Set;
private maxIdx = 0;
@@ -905,6 +905,7 @@ namespace Structure {
}
constructor(private structure: Structure) {
+ this.current = StructureElement.Location.create(structure);
this.hasNext = structure.elementCount > 0;
if (this.hasNext) {
this.elements = structure.units[0].elements;
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 6568f9cb4f41af97513ea1d51376dd958f85f628..e6c5bae4673f2379bfaeb1b2296f905b74613b70 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -10,10 +10,11 @@ import { EquivalenceClasses } from '../../../mol-data/util';
import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry';
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { RuntimeContext, Task } from '../../../mol-task';
-import { ModelSymmetry, Model } from '../model';
+import { Symmetry, Model } from '../model';
import { QueryContext, StructureSelection } from '../query';
import Structure from './structure';
import Unit from './unit';
+import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
namespace StructureSymmetry {
export function buildAssembly(structure: Structure, asmName: string) {
@@ -21,7 +22,7 @@ namespace StructureSymmetry {
const models = structure.models;
if (models.length !== 1) throw new Error('Can only build assemblies from structures based on 1 model.');
- const assembly = ModelSymmetry.findAssembly(models[0], asmName);
+ const assembly = Symmetry.findAssembly(models[0], asmName);
if (!assembly) throw new Error(`Assembly '${asmName}' is not defined.`);
const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { id: assembly.id, operList: [] })
@@ -95,7 +96,7 @@ namespace StructureSymmetry {
}
}
-function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3, modelCenter: Vec3) {
+function getOperators(symmetry: Symmetry, ijkMin: Vec3, ijkMax: Vec3, modelCenter: Vec3) {
const { spacegroup, ncsOperators } = symmetry;
const ncsCount = (ncsOperators && ncsOperators.length) || 0
const operators: SymmetryOperator[] = [];
@@ -135,7 +136,7 @@ function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3, model
return operators;
}
-function getOperatorsCached333(symmetry: ModelSymmetry, ref: Vec3) {
+function getOperatorsCached333(symmetry: Symmetry, ref: Vec3) {
if (symmetry._operators_333 && Vec3.equals(ref, symmetry._operators_333.ref)) {
return symmetry._operators_333.operators;
}
@@ -161,7 +162,10 @@ async function _buildNCS(ctx: RuntimeContext, structure: Structure) {
const models = structure.models;
if (models.length !== 1) throw new Error('Can only build NCS from structures based on 1 model.');
- const operators = models[0].symmetry.ncsOperators;
+ const symmetry = ModelSymmetry.Provider.get(models[0])
+ if (!symmetry) return structure
+
+ const operators = symmetry.ncsOperators;
if (!operators || !operators.length) return structure;
return assembleOperators(structure, operators);
}
@@ -170,11 +174,14 @@ async function findSymmetryRange(ctx: RuntimeContext, structure: Structure, ijkM
const models = structure.models;
if (models.length !== 1) throw new Error('Can only build symmetries from structures based on 1 model.');
- const { spacegroup } = models[0].symmetry;
+ const symmetry = ModelSymmetry.Provider.get(models[0])
+ if (!symmetry) return structure
+
+ const { spacegroup } = symmetry;
if (SpacegroupCell.isZero(spacegroup.cell)) return structure;
const modelCenter = Model.getCenter(models[0])
- const operators = getOperators(models[0].symmetry, ijkMin, ijkMax, modelCenter);
+ const operators = getOperators(symmetry, ijkMin, ijkMax, modelCenter);
return assembleOperators(structure, operators);
}
@@ -182,7 +189,9 @@ async function findMatesRadius(ctx: RuntimeContext, structure: Structure, radius
const models = structure.models;
if (models.length !== 1) throw new Error('Can only build symmetries from structures based on 1 model.');
- const symmetry = models[0].symmetry;
+ const symmetry = ModelSymmetry.Provider.get(models[0])
+ if (!symmetry) return structure
+
const { spacegroup } = symmetry;
if (SpacegroupCell.isZero(spacegroup.cell)) return structure;
diff --git a/src/mol-model/structure/structure/unit/bonds.ts b/src/mol-model/structure/structure/unit/bonds.ts
index 698677153f4ef231f917ec2d3627ccec99c1da3d..2cc0c7b298e04d449f22f65a800c6441a6dcd520 100644
--- a/src/mol-model/structure/structure/unit/bonds.ts
+++ b/src/mol-model/structure/structure/unit/bonds.ts
@@ -19,16 +19,28 @@ export * from './bonds/inter-compute'
namespace Bond {
export interface Location<U extends Unit = Unit> {
readonly kind: 'bond-location',
+
+ aStructure: Structure,
aUnit: U,
/** Index into aUnit.elements */
aIndex: StructureElement.UnitIndex,
+
+ bStructure: Structure,
bUnit: U,
/** Index into bUnit.elements */
bIndex: StructureElement.UnitIndex,
}
- export function Location(aUnit?: Unit, aIndex?: StructureElement.UnitIndex, bUnit?: Unit, bIndex?: StructureElement.UnitIndex): Location {
- return { kind: 'bond-location', aUnit: aUnit as any, aIndex: aIndex as any, bUnit: bUnit as any, bIndex: bIndex as any };
+ export function Location(aStructure?: Structure, aUnit?: Unit, aIndex?: StructureElement.UnitIndex, bStructure?: Structure, bUnit?: Unit, bIndex?: StructureElement.UnitIndex): Location {
+ return {
+ kind: 'bond-location',
+ aStructure: aStructure as any,
+ aUnit: aUnit as any,
+ aIndex: aIndex as any,
+ bStructure: bStructure as any,
+ bUnit: bUnit as any,
+ bIndex: bIndex as any
+ };
}
export function isLocation(x: any): x is Location {
@@ -37,6 +49,7 @@ namespace Bond {
export function areLocationsEqual(locA: Location, locB: Location) {
return (
+ locA.aStructure.label === locB.aStructure.label && locA.bStructure.label === locB.bStructure.label &&
locA.aIndex === locB.aIndex && locA.bIndex === locB.bIndex &&
locA.aUnit.id === locB.aUnit.id && locA.bUnit.id === locB.bUnit.id
)
@@ -86,7 +99,7 @@ namespace Bond {
const indexB = SortedArray.indexOf(unitB.elements, elementB) as StructureElement.UnitIndex | -1
if (indexB === -1) return
- bonds.push(Location(unitA, indexA, unitB, indexB))
+ bonds.push(Location(loci.structure, unitA, indexA, loci.structure, unitB, indexB))
});
return Loci(structure, bonds);
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index 2b3d68e415233d0ef4177355f1ed9f2d07aa4f52..053bf322f1b7efa5a96cf9463ae25980555df551 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -13,11 +13,11 @@ import { InterUnitBonds, InterUnitEdgeProps } from './data';
import { SortedArray } from '../../../../../mol-data/int';
import { Vec3, Mat4 } from '../../../../../mol-math/linear-algebra';
import StructureElement from '../../element';
-import { StructConn } from '../../../../../mol-model-formats/structure/mmcif/bonds';
import { ElementIndex } from '../../../model/indexing';
import { getInterBondOrderFromTable } from '../../../model/properties/atomic/bonds';
-import { IndexPairBonds } from '../../../../../mol-model-formats/structure/mmcif/bonds/index-pair';
+import { IndexPairBonds } from '../../../../../mol-model-formats/structure/property/bonds/index-pair';
import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
+import { StructConn } from '../../../../../mol-model-formats/structure/property/bonds/struct_conn';
const MAX_RADIUS = 4;
@@ -46,8 +46,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const { occupancy: occupancyB } = unitB.model.atomicConformation;
const { lookup3d } = unitB;
- const structConn = unitA.model === unitB.model && unitA.model.sourceData.kind === 'mmCIF' ? StructConn.get(unitA.model) : void 0;
- const indexPairs = unitA.model === unitB.model ? IndexPairBonds.get(unitA.model) : void 0;
+ const structConn = unitA.model === unitB.model && StructConn.Provider.get(unitA.model)
+ const indexPairs = unitA.model === unitB.model && IndexPairBonds.Provider.get(unitA.model)
// the lookup queries need to happen in the "unitB space".
// that means imageA = inverseOperB(operA(aI))
@@ -75,18 +75,20 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
continue // assume `indexPairs` supplies all bonds
}
- const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
+ const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
if (structConnEntries && structConnEntries.length) {
let added = false;
for (const se of structConnEntries) {
- for (const p of se.partners) {
- const _bI = SortedArray.indexOf(unitB.elements, p.atomIndex) as StructureElement.UnitIndex;
- if (_bI < 0 || _aI === _bI) continue;
- // check if the bond is within MAX_RADIUS for this pair of units
- if (getDistance(unitA, aI, unitB, p.atomIndex) > MAX_RADIUS) continue;
- builder.add(_aI, _bI, { order: se.order, flag: se.flags });
- added = true;
- }
+ const { partnerA, partnerB } = se
+ const p = partnerA.atomIndex === aI ? partnerB : partnerA
+ const _bI = SortedArray.indexOf(unitB.elements, p.atomIndex) as StructureElement.UnitIndex;
+ if (_bI < 0) continue;
+
+ // check if the bond is within MAX_RADIUS for this pair of units
+ if (getDistance(unitA, aI, unitB, p.atomIndex) > MAX_RADIUS) continue;
+
+ builder.add(_aI, _bI, { order: se.order, flag: se.flags });
+ added = true;
}
// assume, for an atom, that if any inter unit bond is given
// all are given and thus we don't need to compute any other
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 10327a44a84dbe743128edecb7501666093dd5e4..1ba15206b2a9a0e6ddad536477760e9b792140ca 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,10 +11,11 @@ import Unit from '../../unit'
import { IntAdjacencyGraph } from '../../../../../mol-math/graph';
import { BondComputationProps, getElementIdx, MetalsSet, getElementThreshold, isHydrogen, getElementPairThreshold, DefaultBondComputationProps } from './common';
import { SortedArray } from '../../../../../mol-data/int';
-import { StructConn, ComponentBond } from '../../../../../mol-model-formats/structure/mmcif/bonds';
import { getIntraBondOrderFromTable } from '../../../model/properties/atomic/bonds';
import StructureElement from '../../element';
-import { IndexPairBonds } from '../../../../../mol-model-formats/structure/mmcif/bonds/index-pair';
+import { IndexPairBonds } from '../../../../../mol-model-formats/structure/property/bonds/index-pair';
+import { ComponentBond } from '../../../../../mol-model-formats/structure/property/bonds/comp';
+import { StructConn } from '../../../../../mol-model-formats/structure/property/bonds/struct_conn';
function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], atomCount: number): IntraUnitBonds {
const builder = new IntAdjacencyGraph.EdgeBuilder(atomCount, atomA, atomB);
@@ -29,6 +30,8 @@ function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.U
return builder.createGraph({ flags, order });
}
+const __structConnAdded = new Set<StructureElement.UnitIndex>();
+
function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBonds {
const MAX_RADIUS = 4;
@@ -39,9 +42,9 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
const { label_comp_id } = unit.model.atomicHierarchy.residues;
const query3d = unit.lookup3d;
- const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.get(unit.model) : void 0;
- const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBond.get(unit.model) : void 0;
- const indexPairs = IndexPairBonds.get(unit.model)
+ const structConn = StructConn.Provider.get(unit.model)
+ const component = ComponentBond.Provider.get(unit.model)
+ const indexPairs = IndexPairBonds.Provider.get(unit.model)
const atomA: StructureElement.UnitIndex[] = [];
const atomB: StructureElement.UnitIndex[] = [];
@@ -51,6 +54,8 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
let lastResidue = -1;
let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+ const structConnAdded = __structConnAdded;
+
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atoms[_aI];
@@ -66,19 +71,26 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
continue // assume `indexPairs` supplies all bonds
}
- const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
- const structConnAdded = new Set<StructureElement.UnitIndex>()
+ const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
+ let hasStructConn = false;
if (structConnEntries) {
for (const se of structConnEntries) {
- for (const p of se.partners) {
- const _bI = SortedArray.indexOf(unit.elements, p.atomIndex) as StructureElement.UnitIndex;
- if (_bI < 0 || _aI === _bI) continue;
- atomA[atomA.length] = _aI;
- atomB[atomB.length] = _bI;
- flags[flags.length] = se.flags;
- order[order.length] = se.order;
- structConnAdded.add(_bI)
- }
+ const { partnerA, partnerB } = se
+ // symmetry must be the same for intra-unit bonds
+ if (partnerA.symmetry !== partnerB.symmetry) continue
+
+ const p = partnerA.atomIndex === aI ? partnerB : partnerA
+ const _bI = SortedArray.indexOf(unit.elements, p.atomIndex) as StructureElement.UnitIndex;
+ if (_bI < 0) continue;
+
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ flags[flags.length] = se.flags;
+ order[order.length] = se.order;
+
+ if (!hasStructConn) structConnAdded.clear();
+ hasStructConn = true;
+ structConnAdded.add(_bI);
}
}
@@ -106,7 +118,7 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
for (let ni = 0; ni < count; ni++) {
const _bI = indices[ni];
- if (structConnAdded.has(_bI)) continue;
+ if (hasStructConn && structConnAdded.has(_bI)) continue;
const bI = atoms[_bI];
if (bI <= aI) continue;
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
index 2cddb0e9c5cfd3ce0d972f1ba3f681c91b993d1e..0b98c288cd7e44f5409655d1919e232a726fdb0b 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
@@ -8,9 +8,9 @@ import Unit from '../../unit';
import Structure from '../../structure';
import { PairRestraints, CrossLinkRestraint } from './data';
import { StructureElement } from '../../../structure';
-import { IHMCrossLinkRestraint } from '../../../../../mol-model-formats/structure/mmcif/pair-restraint';
+import { ModelCrossLinkRestraint } from '../../../../../mol-model-formats/structure/property/pair-restraints/cross-links';
-function _addRestraints(map: Map<number, number>, unit: Unit, restraints: IHMCrossLinkRestraint) {
+function _addRestraints(map: Map<number, number>, unit: Unit, restraints: ModelCrossLinkRestraint) {
const { elements } = unit;
const elementCount = elements.length;
const kind = unit.kind
@@ -25,7 +25,7 @@ function extractInter(pairs: CrossLinkRestraint[], unitA: Unit, unitB: Unit) {
if (unitA.model !== unitB.model) return
if (unitA.model.sourceData.kind !== 'mmCIF') return
- const restraints = IHMCrossLinkRestraint.fromModel(unitA.model)
+ const restraints = ModelCrossLinkRestraint.Provider.get(unitA.model)
if (!restraints) return
const rA = new Map<number, StructureElement.UnitIndex>();
@@ -47,7 +47,7 @@ function extractInter(pairs: CrossLinkRestraint[], unitA: Unit, unitB: Unit) {
function extractIntra(pairs: CrossLinkRestraint[], unit: Unit) {
if (unit.model.sourceData.kind !== 'mmCIF') return
- const restraints = IHMCrossLinkRestraint.fromModel(unit.model)
+ const restraints = ModelCrossLinkRestraint.Provider.get(unit.model)
if (!restraints) return
const { elements } = unit;
@@ -75,7 +75,7 @@ function extractIntra(pairs: CrossLinkRestraint[], unit: Unit) {
})
}
-function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: IHMCrossLinkRestraint, row: number): CrossLinkRestraint {
+function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: ModelCrossLinkRestraint, row: number): CrossLinkRestraint {
return {
unitA, indexA, unitB, indexB,
@@ -89,7 +89,7 @@ function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitInde
function extractCrossLinkRestraints(structure: Structure): PairRestraints<CrossLinkRestraint> {
const pairs: CrossLinkRestraint[] = []
- if (!structure.models.some(m => IHMCrossLinkRestraint.fromModel(m))) {
+ if (!structure.models.some(m => ModelCrossLinkRestraint.Provider.get(m))) {
return new PairRestraints(pairs)
}
diff --git a/src/mol-model/structure/structure/util/lookup3d.ts b/src/mol-model/structure/structure/util/lookup3d.ts
index c10e03095960cdbd6e8044158a7802c700419d6e..e3ac9d7dbc713d32db378d5e11ac223c350b28d4 100644
--- a/src/mol-model/structure/structure/util/lookup3d.ts
+++ b/src/mol-model/structure/structure/util/lookup3d.ts
@@ -100,7 +100,7 @@ export class StructureLookup3D {
const closeUnits = this.unitLookup.find(x, y, z, radius);
if (closeUnits.count === 0) return;
- const se = StructureElement.Location.create();
+ const se = StructureElement.Location.create(this.structure);
const queryRadius = pivotR + maxRadius + radius;
for (let t = 0, _t = closeUnits.count; t < _t; t++) {
diff --git a/src/mol-model/structure/structure/util/unit-transforms.ts b/src/mol-model/structure/structure/util/unit-transforms.ts
index 9a7be99d81c87d0dd07069336db9b7cda6782416..f2de9309b2d0d65654b581b2d3e772dcc1d4c609 100644
--- a/src/mol-model/structure/structure/util/unit-transforms.ts
+++ b/src/mol-model/structure/structure/util/unit-transforms.ts
@@ -18,8 +18,10 @@ export class StructureUnitTransforms {
private unitOffsetMap = IntMap.Mutable<number>();
private groupIndexMap = IntMap.Mutable<number>();
private size: number;
-
+
private _isIdentity: boolean | undefined = undefined;
+
+ version = 0;
constructor(readonly structure: Structure) {
this.unitTransforms = new Float32Array(structure.units.length * 16)
@@ -39,6 +41,7 @@ export class StructureUnitTransforms {
}
reset() {
+ this.version = 0;
fillIdentityTransform(this.unitTransforms, this.size);
this._isIdentity = true
}
@@ -58,6 +61,7 @@ export class StructureUnitTransforms {
}
setTransform(matrix: Mat4, unit: Unit) {
+ this.version = (this.version + 1) % 0x7fffffff;
Mat4.toArray(matrix, this.unitTransforms, this.unitOffsetMap.get(unit.id))
this._isIdentity = undefined
}
diff --git a/src/mol-model/structure/topology/topology.ts b/src/mol-model/structure/topology/topology.ts
index d5e6dbac27cde544ce95dc6784bbb880a2eeab67..6ef843f72f937e518baaa489571ca361759bc377 100644
--- a/src/mol-model/structure/topology/topology.ts
+++ b/src/mol-model/structure/topology/topology.ts
@@ -1,11 +1,12 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { UUID } from '../../../mol-util';
import { Column } from '../../../mol-data/db';
+import { BasicData } from '../../../mol-model-formats/structure/basic/schema';
import { ModelFormat } from '../../../mol-model-formats/structure/format';
export { Topology }
@@ -14,7 +15,8 @@ interface Topology {
readonly id: UUID
readonly label: string
- readonly format: ModelFormat
+ readonly basic: BasicData
+ readonly sourceData: ModelFormat
readonly bonds: {
readonly indexA: Column<number>,
@@ -47,11 +49,12 @@ interface Topology {
}
namespace Topology {
- export function create(label: string, format: ModelFormat, bonds: Topology['bonds']): Topology {
+ export function create(label: string, basic: BasicData, bonds: Topology['bonds'], format: ModelFormat): Topology {
return {
id: UUID.create22(),
label,
- format,
+ basic,
+ sourceData: format,
bonds
}
}
diff --git a/src/mol-plugin-ui/controls/parameters.tsx b/src/mol-plugin-ui/controls/parameters.tsx
index a942c12439df0d7fdcc595e26d000c8ea361e3fc..49363d5cd68a1fa21a03855f4ffe426dd887a1a4 100644
--- a/src/mol-plugin-ui/controls/parameters.tsx
+++ b/src/mol-plugin-ui/controls/parameters.tsx
@@ -59,6 +59,7 @@ function controlFor(param: PD.Any): ParamControl | undefined {
case 'color-list': return ColorListControl;
case 'vec3': return Vec3Control;
case 'file': return FileControl;
+ case 'file-list': return FileListControl;
case 'select': return SelectControl;
case 'text': return TextControl;
case 'interval': return typeof param.min !== 'undefined' && typeof param.max !== 'undefined'
@@ -436,7 +437,6 @@ export class Vec3Control extends React.PureComponent<ParamProps<PD.Vec3>, { isEx
}
}
-
export class FileControl extends React.PureComponent<ParamProps<PD.FileParam>> {
change(value: File) {
this.props.onChange({ name: this.props.name, param: this.props.param, value });
@@ -449,13 +449,40 @@ export class FileControl extends React.PureComponent<ParamProps<PD.FileParam>> {
render() {
const value = this.props.value;
- // return <input disabled={this.props.isDisabled} value={void 0} type='file' multiple={false} />
return <div className='msp-btn msp-btn-block msp-btn-action msp-loader-msp-btn-file' style={{ marginTop: '1px' }}>
{value ? value.name : 'Select a file...'} <input disabled={this.props.isDisabled} onChange={this.onChangeFile} type='file' multiple={false} accept={this.props.param.accept} />
</div>
}
}
+export class FileListControl extends React.PureComponent<ParamProps<PD.FileListParam>> {
+ change(value: FileList) {
+ this.props.onChange({ name: this.props.name, param: this.props.param, value });
+ }
+
+ onChangeFileList = (e: React.ChangeEvent<HTMLInputElement>) => {
+ this.change(e.target.files!);
+ }
+
+ render() {
+ const value = this.props.value;
+
+ const names: string[] = []
+ if (value) {
+ for (let i = 0, il = value.length; i < il; ++i) {
+ names.push(value[i].name)
+ }
+ }
+ const label = names.length === 0
+ ? 'Select files...' : names.length === 1
+ ? names[0] : `${names.length} files selected`
+
+ return <div className='msp-btn msp-btn-block msp-btn-action msp-loader-msp-btn-file' style={{ marginTop: '1px' }}>
+ {label} <input disabled={this.props.isDisabled} onChange={this.onChangeFileList} type='file' multiple={true} accept={this.props.param.accept} />
+ </div>
+ }
+}
+
export class MultiSelectControl extends React.PureComponent<ParamProps<PD.MultiSelect<any>>, { isExpanded: boolean }> {
state = { isExpanded: false }
diff --git a/src/mol-plugin-ui/sequence.tsx b/src/mol-plugin-ui/sequence.tsx
index 1ab7f214fdab49c0aa8b6955fa40b0ba797c2fd9..f89f119ee02447590f1c133c4654f8fad497bba9 100644
--- a/src/mol-plugin-ui/sequence.tsx
+++ b/src/mol-plugin-ui/sequence.tsx
@@ -39,13 +39,13 @@ function splitModelEntityId(modelEntityId: string) {
function getSequenceWrapper(state: SequenceViewState, structureSelection: StructureElementSelectionManager): SequenceWrapper.Any | string {
const { structure, modelEntityId, chainGroupId, operatorKey } = state
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
const [ modelIdx, entityId ] = splitModelEntityId(modelEntityId)
const units: Unit[] = []
for (const unit of structure.units) {
- StructureElement.Location.set(l, unit, unit.elements[0])
+ StructureElement.Location.set(l, structure, unit, unit.elements[0])
if (structure.getModelIndex(unit.model) !== modelIdx) continue
if (SP.entity.id(l) !== entityId) continue
if (unit.chainGroupId !== chainGroupId) continue
@@ -60,7 +60,7 @@ function getSequenceWrapper(state: SequenceViewState, structureSelection: Struct
let sw: SequenceWrapper<any>
if (unit.polymerElements.length) {
- const l = StructureElement.Location.create(unit, unit.elements[0])
+ const l = StructureElement.Location.create(structure, unit, unit.elements[0])
const entitySeq = unit.model.sequence.byEntityKey[SP.entity.key(l)]
// check if entity sequence is available
if (entitySeq && entitySeq.sequence.length <= MaxDisplaySequenceLength) {
@@ -92,11 +92,11 @@ function getSequenceWrapper(state: SequenceViewState, structureSelection: Struct
function getModelEntityOptions(structure: Structure) {
const options: [string, string][] = []
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
const seen = new Set<string>()
for (const unit of structure.units) {
- StructureElement.Location.set(l, unit, unit.elements[0])
+ StructureElement.Location.set(l, structure, unit, unit.elements[0])
const id = SP.entity.id(l)
const modelIdx = structure.getModelIndex(unit.model)
const key = `${modelIdx}|${id}`
@@ -121,12 +121,12 @@ function getModelEntityOptions(structure: Structure) {
function getChainOptions(structure: Structure, modelEntityId: string) {
const options: [number, string][] = []
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
const seen = new Set<number>()
const [ modelIdx, entityId ] = splitModelEntityId(modelEntityId)
for (const unit of structure.units) {
- StructureElement.Location.set(l, unit, unit.elements[0])
+ StructureElement.Location.set(l, structure, unit, unit.elements[0])
if (structure.getModelIndex(unit.model) !== modelIdx) continue
if (SP.entity.id(l) !== entityId) continue
@@ -147,12 +147,12 @@ function getChainOptions(structure: Structure, modelEntityId: string) {
function getOperatorOptions(structure: Structure, modelEntityId: string, chainGroupId: number) {
const options: [string, string][] = []
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
const seen = new Set<string>()
const [ modelIdx, entityId ] = splitModelEntityId(modelEntityId)
for (const unit of structure.units) {
- StructureElement.Location.set(l, unit, unit.elements[0])
+ StructureElement.Location.set(l, structure, unit, unit.elements[0])
if (structure.getModelIndex(unit.model) !== modelIdx) continue
if (SP.entity.id(l) !== entityId) continue
if (unit.chainGroupId !== chainGroupId) continue
diff --git a/src/mol-plugin-ui/sequence/chain.ts b/src/mol-plugin-ui/sequence/chain.ts
index b3e53700e3263f3dd3ed84a57a46962300ba4999..e15f691ec47f4f00861965eaaa6816e579f1c1b5 100644
--- a/src/mol-plugin-ui/sequence/chain.ts
+++ b/src/mol-plugin-ui/sequence/chain.ts
@@ -54,14 +54,14 @@ export class ChainSequenceWrapper extends SequenceWrapper<StructureUnit> {
let residueCount = 0
let elementCount = 0
const counts: string[] = []
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(data.structure)
const unitIndices = new Map<number, Interval<StructureElement.UnitIndex>>()
const lociElements: StructureElement.Loci['elements'][0][] = []
for (let i = 0, il = data.units.length; i < il; ++i) {
const unit = data.units[i]
- StructureElement.Location.set(l, unit, unit.elements[0])
+ StructureElement.Location.set(l, data.structure, unit, unit.elements[0])
const entitySeq = unit.model.sequence.byEntityKey[StructureProperties.entity.key(l)]
if (entitySeq) residueCount += entitySeq.sequence.length
elementCount += unit.elements.length
diff --git a/src/mol-plugin-ui/sequence/polymer.ts b/src/mol-plugin-ui/sequence/polymer.ts
index 1402a8888735197aeb3f8d9b972a826a58142838..2073dd4bb284c9d726457bac65348a3adb86bb2c 100644
--- a/src/mol-plugin-ui/sequence/polymer.ts
+++ b/src/mol-plugin-ui/sequence/polymer.ts
@@ -66,7 +66,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
}
constructor(data: StructureUnit) {
- const l = StructureElement.Location.create(data.units[0], data.units[0].elements[0])
+ const l = StructureElement.Location.create(data.structure, data.units[0], data.units[0].elements[0])
const entitySeq = data.units[0].model.sequence.byEntityKey[SP.entity.key(l)]
const length = entitySeq.sequence.length
diff --git a/src/mol-plugin-ui/sequence/sequence.tsx b/src/mol-plugin-ui/sequence/sequence.tsx
index f1ef4b5ffbf1ac949c9b014479c349e5ae725ba2..3ff18fdcefbbfa270195d2cc2cb1a4059e0ca239 100644
--- a/src/mol-plugin-ui/sequence/sequence.tsx
+++ b/src/mol-plugin-ui/sequence/sequence.tsx
@@ -176,7 +176,7 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
return classList.join(' ')
}
- private location = StructureElement.Location.create();
+ private location = StructureElement.Location.create(void 0);
private getSequenceNumber(seqIdx: number) {
let seqNum = ''
const loci = this.props.sequenceWrapper.getLoci(seqIdx)
diff --git a/src/mol-plugin-ui/viewport/simple-settings.tsx b/src/mol-plugin-ui/viewport/simple-settings.tsx
index 699c7c484d49c87f962ce8c3c57540b2c920ef65..387e0154319e1b650725ccdc27eeaecbc10c2596 100644
--- a/src/mol-plugin-ui/viewport/simple-settings.tsx
+++ b/src/mol-plugin-ui/viewport/simple-settings.tsx
@@ -21,7 +21,7 @@ const SimpleSettingsParams = {
'transparent': PD.EmptyGroup(),
'opaque': PD.Group({ color: PD.Color(Color(0xFCFBF9), { description: 'Custom background color' }) }, { isFlat: true })
}, { description: 'Background of the 3D canvas' }),
- renderStyle: PD.Select('glossy', [['toon', 'Toon'], ['matte', 'Matte'], ['glossy', 'Glossy'], ['metallic', 'Metallic']], { description: 'Style in which the 3D scene is rendered' }),
+ renderStyle: PD.Select('glossy', [['flat', 'Flat'], ['matte', 'Matte'], ['glossy', 'Glossy'], ['metallic', 'Metallic']], { description: 'Style in which the 3D scene is rendered' }),
occlusion: PD.Boolean(false, { description: 'Darken occluded crevices with the ambient occlusion effect' }),
outline: PD.Boolean(false, { description: 'Draw outline around 3D objects' }),
fog: PD.Boolean(false, { description: 'Show fog in the distance' }),
@@ -49,7 +49,7 @@ export class SimpleSettingsControl extends PluginUIComponent {
if (!this.plugin.canvas3d) return;
const renderer = this.plugin.canvas3d.props.renderer;
- if (p.value === 'toon') {
+ if (p.value === 'flat') {
PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
renderer: { ...renderer, lightIntensity: 0, ambientIntensity: 1, roughness: 0.4, metalness: 0 }
} });
@@ -80,7 +80,7 @@ export class SimpleSettingsControl extends PluginUIComponent {
} });
} else if (p.name === 'fog') {;
PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- cameraFog: p.value ? 50 : 1,
+ cameraFog: p.value ? 50 : 0,
} });
} else if (p.name === 'clipFar') {;
PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
@@ -97,7 +97,7 @@ export class SimpleSettingsControl extends PluginUIComponent {
if (renderer) {
if (renderer.lightIntensity === 0 && renderer.ambientIntensity === 1 && renderer.roughness === 0.4 && renderer.metalness === 0) {
- renderStyle = 'toon'
+ renderStyle = 'flat'
} else if (renderer.lightIntensity === 0.6 && renderer.ambientIntensity === 0.4) {
if (renderer.roughness === 1 && renderer.metalness === 0) {
renderStyle = 'matte'
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
index 2c35e078ea35a00d2b138ed09085be460b7ab257..69742b2992896625fd383526de1a7e8183c90520 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
@@ -6,13 +6,11 @@
import { OrderedSet } from '../../../../../mol-data/int';
import { StructureQualityReport, StructureQualityReportProvider } from '../../../../../mol-model-props/pdbe/structure-quality-report';
-import { StructureQualityReportColorTheme } from '../../../../../mol-model-props/pdbe/themes/structure-quality-report';
+import { StructureQualityReportColorThemeProvider } from '../../../../../mol-model-props/pdbe/themes/structure-quality-report';
import { Loci } from '../../../../../mol-model/loci';
import { StructureElement } from '../../../../../mol-model/structure';
import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
import { PluginBehavior } from '../../../behavior';
-import { ThemeDataContext } from '../../../../../mol-theme/theme';
-import { CustomProperty } from '../../../../../mol-model-props/common/custom-property';
export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'pdbe-structure-quality-report-prop',
@@ -32,7 +30,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
const u = e.unit;
if (!u.model.customProperties.has(StructureQualityReportProvider.descriptor)) return void 0;
- const se = StructureElement.Location.create(u, u.elements[OrderedSet.getAt(e.indices, 0)]);
+ const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
const issues = StructureQualityReport.getIssues(se);
if (issues.length === 0) return 'PDBe Validation: No Issues';
return `PDBe Validation: ${issues.join(', ')}`;
@@ -45,16 +43,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
this.ctx.customModelProperties.register(this.provider, false);
this.ctx.lociLabels.addProvider(this.labelPDBeValidation);
- this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('pdbe-structure-quality-report', {
- label: 'PDBe Structure Quality Report',
- factory: StructureQualityReportColorTheme,
- getParams: () => ({}),
- defaultValues: {},
- isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
- ensureCustomProperties: (ctx: CustomProperty.Context, data: ThemeDataContext) => {
- return data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0]) : Promise.resolve()
- }
- })
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('pdbe-structure-quality-report', StructureQualityReportColorThemeProvider)
}
update(p: { autoAttach: boolean, showTooltip: boolean }) {
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index 9f3a48c3ae6a0795b89798f77d1685aca4d19c54..e945aeab6b78486381c78f4802c5f1a95e117b8e 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -45,7 +45,7 @@ export const HighlightLoci = PluginBehavior.create({
}
register() {
this.subscribeObservable(this.ctx.behaviors.interaction.hover, ({ current, buttons, modifiers }) => {
- if (!this.ctx.canvas3d) return
+ if (!this.ctx.canvas3d || this.ctx.isBusy) return
let matched = false
if (Binding.match(this.params.bindings.hoverHighlightOnly, buttons, modifiers)) {
@@ -132,7 +132,7 @@ export const SelectLoci = PluginBehavior.create({
})
this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
- if (!this.ctx.canvas3d) return
+ if (!this.ctx.canvas3d || this.ctx.isBusy) return;
// only trigger the 1st action that matches
for (const [binding, action, condition] of actions) {
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
index ea703fe3691773819183ba7f215374de547d1af7..0f1d5ecca749050a9ef7e3f7e0aa388d53e21dd5 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -9,30 +9,31 @@ import { Structure, Model } from '../../../../mol-model/structure';
import { VolumeServerInfo } from './model';
import { PluginContext } from '../../../../mol-plugin/context';
import { RuntimeContext } from '../../../../mol-task';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
if (!s) return defaultKind;
const model = s.models[0];
- if (model.sourceData.kind !== 'mmCIF') return defaultKind;
+ if (!MmcifFormat.is(model.sourceData)) return defaultKind;
- const { data } = model.sourceData;
+ const { db } = model.sourceData.data;
// prefer EMDB entries over structure-factors (SF) e.g. for 'ELECTRON CRYSTALLOGRAPHY' entries
// like 6axz or 6kj3 for which EMDB entries are available but map calculation from SF is hard
- for (let i = 0, il = data.pdbx_database_related._rowCount; i < il; ++i) {
- if (data.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
+ for (let i = 0, il = db.pdbx_database_related._rowCount; i < il; ++i) {
+ if (db.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
return 'em'
}
}
- if (data.pdbx_database_status.status_code_sf.isDefined && data.pdbx_database_status.status_code_sf.value(0) === 'REL') {
+ if (db.pdbx_database_status.status_code_sf.isDefined && db.pdbx_database_status.status_code_sf.value(0) === 'REL') {
return 'x-ray'
}
// fallbacks
- for (let i = 0; i < data.exptl.method.rowCount; i++) {
- const v = data.exptl.method.value(i).toUpperCase();
+ for (let i = 0; i < db.exptl.method.rowCount; i++) {
+ const v = db.exptl.method.value(i).toUpperCase();
if (v.indexOf('MICROSCOPY') >= 0) return 'em';
}
return defaultKind;
@@ -41,9 +42,9 @@ export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.
/** Returns EMD ID when available, otherwise falls back to PDB ID */
export function getEmIds(model: Model): string[] {
const ids: string[] = []
- if (model.sourceData.kind !== 'mmCIF') return [ model.entryId ]
+ if (!MmcifFormat.is(model.sourceData)) return [ model.entryId ]
- const { db_id, db_name, content_type } = model.sourceData.data.pdbx_database_related
+ const { db_id, db_name, content_type } = model.sourceData.data.db.pdbx_database_related
if (!db_name.isDefined) return [ model.entryId ]
for (let i = 0, il = db_name.rowCount; i < il; ++i) {
diff --git a/src/mol-plugin/behavior/static/camera.ts b/src/mol-plugin/behavior/static/camera.ts
index 0fc627654b28bab00b8a4c7b1cfafdcc114c6f70..32971d8edc6ae922e406d40e21293f20c74290a0 100644
--- a/src/mol-plugin/behavior/static/camera.ts
+++ b/src/mol-plugin/behavior/static/camera.ts
@@ -16,7 +16,7 @@ export function registerDefault(ctx: PluginContext) {
export function Reset(ctx: PluginContext) {
PluginCommands.Camera.Reset.subscribe(ctx, () => {
- ctx.canvas3d?.resetCamera();
+ ctx.canvas3d?.requestCameraReset();
})
}
diff --git a/src/mol-plugin/behavior/static/representation.ts b/src/mol-plugin/behavior/static/representation.ts
index 8cdbe6ad31c5e7fc7e2b02dc6060a070e0e81885..4bc083eda3a22c68e928bb84fa804efd53a08c81 100644
--- a/src/mol-plugin/behavior/static/representation.ts
+++ b/src/mol-plugin/behavior/static/representation.ts
@@ -20,7 +20,7 @@ export function SyncRepresentationToCanvas(ctx: PluginContext) {
ctx.events.canvas3d.initialized.subscribe(() => {
ctx.canvas3d?.reprCount.subscribe(v => {
- if (reprCount === 0) ctx.canvas3d?.resetCamera();
+ if (reprCount === 0) ctx.canvas3d?.requestCameraReset();
reprCount = v;
});
})
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 591d9763e840dc14302bc7ed3bf9c1d0da2e16db..802a6ad2c8aa0697b026055c97056bdf04209d00 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -192,6 +192,11 @@ export class PluginContext {
*/
readonly fetch = ajaxGet
+ /** return true is animating or updating */
+ get isBusy() {
+ return this.behaviors.state.isAnimating.value || this.behaviors.state.isUpdating.value;
+ }
+
runTask<T>(task: Task<T>) {
return this.tasks.run(task);
}
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 51a4ee96fc85fecbf830c482b3d4c0cf108e71d9..9c43953cd18827be185aeac38a5988635e214bc9 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -25,7 +25,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateActions.Structure.DownloadStructure),
PluginSpec.Action(StateActions.Structure.AddTrajectory),
PluginSpec.Action(StateActions.Volume.DownloadDensity),
- PluginSpec.Action(StateActions.DataFormat.OpenFile),
+ PluginSpec.Action(StateActions.DataFormat.OpenFiles),
PluginSpec.Action(StateActions.Structure.Create3DRepresentationPreset),
PluginSpec.Action(StateActions.Structure.Remove3DRepresentationPreset),
PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
diff --git a/src/mol-plugin/state/actions/data-format.ts b/src/mol-plugin/state/actions/data-format.ts
index 75ae09650b465dcce5012b5bbac8cd058b7a3c5b..a759f94eb6f85cbffa670868f29e62318eb5ab2b 100644
--- a/src/mol-plugin/state/actions/data-format.ts
+++ b/src/mol-plugin/state/actions/data-format.ts
@@ -119,36 +119,35 @@ export interface DataFormatProvider<D extends PluginStateObject.Data.Binary | Pl
//
-export const OpenFile = StateAction.build({
- display: { name: 'Open File', description: 'Load a file and optionally create its default visuals' },
+export const OpenFiles = StateAction.build({
+ display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
from: PluginStateObject.Root,
params: (a, ctx: PluginContext) => {
const { extensions, options } = ctx.dataFormat.registry
return {
- file: PD.File({ accept: Array.from(extensions.values()).map(e => `.${e}`).join(',') + ',.gz,.zip' }),
+ files: PD.FileList({ accept: Array.from(extensions.values()).map(e => `.${e}`).join(',') + ',.gz,.zip', multiple: true }),
format: PD.Select('auto', options),
visuals: PD.Boolean(true, { description: 'Add default visuals' }),
}
}
-})(({ params, state }, ctx: PluginContext) => Task.create('Open File', async taskCtx => {
- const info = getFileInfo(params.file)
- const data = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: ctx.dataFormat.registry.binaryExtensions.has(info.ext) });
- const dataStateObject = await state.updateTree(data).runInContext(taskCtx);
-
- // Alternative for more complex states where the builder is not a simple StateBuilder.To<>:
- /*
- const dataRef = dataTree.ref;
- await state.updateTree(dataTree).runInContext(taskCtx);
- const dataCell = state.select(dataRef)[0];
- */
-
- // const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: /\.bcif$/i.test(params.file.name) });
-
- const provider = params.format === 'auto' ? ctx.dataFormat.registry.auto(info, dataStateObject) : ctx.dataFormat.registry.get(params.format)
- const b = state.build().to(data.ref);
- const options = { visuals: params.visuals }
- // need to await the 2nd update the so that the enclosing Task finishes after the update is done.
- await provider.getDefaultBuilder(ctx, b, options, state).runInContext(taskCtx)
+})(({ params, state }, ctx: PluginContext) => Task.create('Open Files', async taskCtx => {
+ for (let i = 0, il = params.files.length; i < il; ++i) {
+ try {
+ const file = params.files[i]
+ const info = getFileInfo(file)
+ const isBinary = ctx.dataFormat.registry.binaryExtensions.has(info.ext)
+ const data = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file, isBinary });
+ const dataStateObject = await state.updateTree(data).runInContext(taskCtx);
+ const provider = params.format === 'auto'
+ ? ctx.dataFormat.registry.auto(info, dataStateObject)
+ : ctx.dataFormat.registry.get(params.format)
+ const b = state.build().to(data.ref);
+ // need to await so that the enclosing Task finishes after the update is done.
+ await provider.getDefaultBuilder(ctx, b, { visuals: params.visuals }, state).runInContext(taskCtx)
+ } catch (e) {
+ ctx.log.error(e)
+ }
+ }
}));
//
diff --git a/src/mol-plugin/state/representation/model.ts b/src/mol-plugin/state/representation/model.ts
index 143d8ce61c0504cbb6153ed239bd62f4ce5ed3e5..47abb3649f33ac19334f3edca6fddc52675692c9 100644
--- a/src/mol-plugin/state/representation/model.ts
+++ b/src/mol-plugin/state/representation/model.ts
@@ -11,13 +11,16 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { RuntimeContext } from '../../../mol-task';
import { PluginContext } from '../../context';
-import { Assembly, ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry';
+import { Assembly, Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
import { PluginStateObject as SO } from '../objects';
+import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
export namespace ModelStructureRepresentation {
export function getParams(model?: Model, defaultValue?: 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates') {
- const assemblyIds = model ? model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : [];
- const showSymm = !model ? true : !SpacegroupCell.isZero(model.symmetry.spacegroup.cell);
+ const symmetry = model && ModelSymmetry.Provider.get(model)
+
+ const assemblyIds = symmetry ? symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : [];
+ const showSymm = !symmetry ? true : !SpacegroupCell.isZero(symmetry.spacegroup.cell);
const modes = {
deposited: PD.EmptyGroup(),
@@ -58,17 +61,19 @@ export namespace ModelStructureRepresentation {
async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string) {
let asm: Assembly | undefined = void 0;
+ const symmetry = ModelSymmetry.Provider.get(model)
+
// if no id is specified, use the 1st assembly.
- if (!id && model.symmetry.assemblies.length !== 0) {
- id = model.symmetry.assemblies[0].id;
+ if (!id && symmetry && symmetry.assemblies.length !== 0) {
+ id = symmetry.assemblies[0].id;
}
- if (model.symmetry.assemblies.length === 0) {
+ if (!symmetry || symmetry.assemblies.length === 0) {
if (id !== 'deposited') {
plugin.log.warn(`Model '${model.entryId}' has no assembly, returning deposited structure.`);
}
} else {
- asm = ModelSymmetry.findAssembly(model, id || '');
+ asm = Symmetry.findAssembly(model, id || '');
if (!asm) {
plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning deposited structure.`);
}
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 77a364905ab46d5199b7455d6d0942c4477dd3d1..d593a97b01f8ae8f2aa79c5d5577ee468e0eee94 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -32,6 +32,7 @@ import { parseDcd } from '../../../mol-io/reader/dcd/parser';
import { coordinatesFromDcd } from '../../../mol-model-formats/structure/dcd';
import { topologyFromPsf } from '../../../mol-model-formats/structure/psf';
import { deepEqual } from '../../../mol-util';
+import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
export { CoordinatesFromDcd };
export { TopologyFromPsf };
@@ -300,8 +301,8 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
if (!a) {
return { id: PD.Optional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. Value \'deposited\' can be used to specify deposited asymmetric unit.' })) };
}
- const model = a.data;
- const ids = model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
+ const assemblies = ModelSymmetry.Provider.get(a.data)?.assemblies || []
+ const ids = assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
ids.push(['deposited', 'Deposited']);
return {
id: PD.Optional(PD.Select(ids[0][0], ids, { label: 'Asm Id', description: 'Assembly Id' }))
@@ -713,12 +714,13 @@ const CustomModelProperties = PluginStateTransform.BuiltIn({
});
}
});
-async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: RuntimeContext, params: PD.Values<PD.Params>) {
+async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: RuntimeContext, params: ReturnType<CustomModelProperties['createDefaultParams']>) {
const propertyCtx = { runtime: taskCtx, fetch: ctx.fetch }
- for (const name of Object.keys(params)) {
+ const { autoAttach, properties } = params
+ for (const name of Object.keys(properties)) {
const property = ctx.customModelProperties.get(name)
const props = params[name as keyof typeof params]
- if (props.autoAttach) {
+ if (autoAttach.includes(name)) {
try {
await property.attach(propertyCtx, model, props)
} catch (e) {
@@ -747,12 +749,13 @@ const CustomStructureProperties = PluginStateTransform.BuiltIn({
});
}
});
-async function attachStructureProps(structure: Structure, ctx: PluginContext, taskCtx: RuntimeContext, params: PD.Values<PD.Params>) {
+async function attachStructureProps(structure: Structure, ctx: PluginContext, taskCtx: RuntimeContext, params: ReturnType<CustomStructureProperties['createDefaultParams']>) {
const propertyCtx = { runtime: taskCtx, fetch: ctx.fetch }
- for (const name of Object.keys(params)) {
+ const { autoAttach, properties } = params
+ for (const name of Object.keys(properties)) {
const property = ctx.customStructureProperties.get(name)
const props = params[name as keyof typeof params]
- if (props.autoAttach) {
+ if (autoAttach.includes(name)) {
try {
await property.attach(propertyCtx, structure, props)
} catch (e) {
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index f4c9956b90c2ce42c13e091a49f5ab83a3a73c2a..611d19c55790844b5bd6f68bb60c8121f857f134 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -13,7 +13,7 @@ import { BuiltInStructureRepresentationsName } from '../../../mol-repr/structure
import { StructureParams } from '../../../mol-repr/structure/representation';
import { BuiltInVolumeRepresentationsName } from '../../../mol-repr/volume/registry';
import { VolumeParams } from '../../../mol-repr/volume/representation';
-import { StateTransformer } from '../../../mol-state';
+import { StateTransformer, StateObject } from '../../../mol-state';
import { Task } from '../../../mol-task';
import { BuiltInColorThemeName, ColorTheme, BuiltInColorThemes } from '../../../mol-theme/color';
import { BuiltInSizeThemeName, SizeTheme } from '../../../mol-theme/size';
@@ -36,6 +36,7 @@ import { LabelParams, LabelRepresentation } from '../../../mol-repr/shape/loci/l
import { OrientationRepresentation, OrientationParams } from '../../../mol-repr/shape/loci/orientation';
import { AngleParams, AngleRepresentation } from '../../../mol-repr/shape/loci/angle';
import { DihedralParams, DihedralRepresentation } from '../../../mol-repr/shape/loci/dihedral';
+import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
export { StructureRepresentation3D }
export { StructureRepresentation3DHelpers }
@@ -649,13 +650,16 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
...UnitcellParams,
}
})({
+ isApplicable: a => !!ModelSymmetry.Provider.get(a.data),
canAutoUpdate({ oldParams, newParams }) {
return true;
},
apply({ a, params }) {
return Task.create('Model Unitcell', async ctx => {
+ const symmetry = ModelSymmetry.Provider.get(a.data)
+ if (!symmetry) return StateObject.Null
const repr = await getUnitcellRepresentation(ctx, a.data, params);
- return new SO.Shape.Representation3D({ repr, source: a }, { label: `Unitcell`, description: a.data.symmetry.spacegroup.name });
+ return new SO.Shape.Representation3D({ repr, source: a }, { label: `Unitcell`, description: symmetry.spacegroup.name });
});
},
update({ a, b, newParams }) {
diff --git a/src/mol-plugin/util/model-unitcell.ts b/src/mol-plugin/util/model-unitcell.ts
index def1a033b60a822e853d63967424ae78d81ff547..7ea961e9dbd12bd53edf1a804038ecc9e4ec99ba 100644
--- a/src/mol-plugin/util/model-unitcell.ts
+++ b/src/mol-plugin/util/model-unitcell.ts
@@ -1,10 +1,10 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Model, ModelSymmetry } from '../../mol-model/structure';
+import { Model, Symmetry } from '../../mol-model/structure';
import { ShapeRepresentation } from '../../mol-repr/shape/representation';
import { Shape } from '../../mol-model/shape';
import { ColorNames } from '../../mol-util/color/names';
@@ -16,6 +16,7 @@ import { BoxCage } from '../../mol-geo/primitive/box';
import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
import { transformCage, cloneCage } from '../../mol-geo/primitive/cage';
import { radToDeg } from '../../mol-math/misc';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
const translate05 = Mat4.fromTranslation(Mat4(), Vec3.create(0.5, 0.5, 0.5))
const unitCage = transformCage(cloneCage(BoxCage()), translate05)
@@ -24,7 +25,7 @@ const tmpRef = Vec3()
const tmpTranslate = Mat4()
interface UnitcellData {
- symmetry: ModelSymmetry
+ symmetry: Symmetry
ref: Vec3
}
@@ -54,11 +55,14 @@ function getUnitcellMesh(data: UnitcellData, props: UnitcellProps, mesh?: Mesh)
export async function getUnitcellRepresentation(ctx: RuntimeContext, model: Model, params: UnitcellProps, prev?: ShapeRepresentation<UnitcellData, Mesh, Mesh.Params>) {
const repr = prev || ShapeRepresentation(getUnitcellShape, Mesh.Utils);
- const data = {
- symmetry: model.symmetry,
- ref: Vec3.transformMat4(Vec3(), Model.getCenter(model), model.symmetry.spacegroup.cell.toFractional)
+ const symmetry = ModelSymmetry.Provider.get(model)
+ if (symmetry) {
+ const data = {
+ symmetry,
+ ref: Vec3.transformMat4(Vec3(), Model.getCenter(model), symmetry.spacegroup.cell.toFractional)
+ }
+ await repr.createOrUpdate(params, data).runInContext(ctx);
}
- await repr.createOrUpdate(params, data).runInContext(ctx);
return repr;
}
diff --git a/src/mol-repr/structure/representation.ts b/src/mol-repr/structure/representation.ts
index a5cc1224e74b2591708ef7346c3502d4f6c162fb..a01d70ab45d288d9054a15a7832c37eae3170bb6 100644
--- a/src/mol-repr/structure/representation.ts
+++ b/src/mol-repr/structure/representation.ts
@@ -19,13 +19,15 @@ import { TextureMesh } from '../../mol-geo/geometry/texture-mesh/texture-mesh';
import { Text } from '../../mol-geo/geometry/text/text';
export interface StructureRepresentationState extends Representation.State {
- unitTransforms: StructureUnitTransforms | null
+ unitTransforms: StructureUnitTransforms | null,
+ unitTransformsVersion: number
}
export const StructureRepresentationStateBuilder: Representation.StateBuilder<StructureRepresentationState> = {
create: () => {
return {
...Representation.createState(),
- unitTransforms: null
+ unitTransforms: null,
+ unitTransformsVersion: -1
}
},
update: (state: StructureRepresentationState, update: Partial<StructureRepresentationState>) => {
diff --git a/src/mol-repr/structure/representation/ellipsoid.ts b/src/mol-repr/structure/representation/ellipsoid.ts
index 2fd4c05a3485e76df1baa23178c4cc5156ba8b70..9d8f9cf10bedc2f8764f4c40b33ad0520b3d9e2d 100644
--- a/src/mol-repr/structure/representation/ellipsoid.ts
+++ b/src/mol-repr/structure/representation/ellipsoid.ts
@@ -11,7 +11,7 @@ import { Structure } from '../../../mol-model/structure';
import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { EllipsoidMeshParams, EllipsoidMeshVisual } from '../visual/ellipsoid-mesh';
import { UnitKind, UnitKindOptions } from '../../../mol-repr/structure/visual/util/common';
-import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/mmcif/anisotropic';
+import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic';
import { IntraUnitBondParams, IntraUnitBondVisual } from '../visual/bond-intra-unit-cylinder';
import { InterUnitBondParams, InterUnitBondVisual } from '../visual/bond-inter-unit-cylinder';
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 478f1762aa1e76be703e10be9e9ebab241c30674..8ce3568ece2c05d3b2d1bd1aed2866229ae09fd7 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -18,10 +18,11 @@ import { Theme } from '../../mol-theme/theme';
import { Task } from '../../mol-task';
import { PickingId } from '../../mol-geo/geometry/picking';
import { Loci, EmptyLoci, isEmptyLoci, isEveryLoci, isDataLoci } from '../../mol-model/loci';
-import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
+import { MarkerAction, MarkerActions, applyMarkerAction } from '../../mol-util/marker-action';
import { Overpaint } from '../../mol-theme/overpaint';
import { Transparency } from '../../mol-theme/transparency';
import { Mat4, EPSILON } from '../../mol-math/linear-algebra';
+import { Interval } from '../../mol-data/int';
export const UnitsParams = {
...StructureParams,
@@ -88,6 +89,13 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
if (promise) await promise
visuals.set(group.hashCode, { visual, group })
oldVisuals.delete(group.hashCode)
+
+ // Remove highlight
+ // TODO: remove selection too??
+ if (visual.renderObject) {
+ const arr = visual.renderObject.values.tMarker.ref.value.array;
+ applyMarkerAction(arr, Interval.ofBounds(0, arr.length), MarkerAction.RemoveHighlight);
+ }
} else {
// console.log(label, 'not found visualGroup to reuse, creating new')
// newGroups.push(group)
@@ -223,9 +231,13 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
if (transparency !== undefined && !Transparency.areEqual(transparency, _state.transparency)) {
newState.transparency = transparency
}
- if (transform !== undefined && !Mat4.areEqual(transform, _state.transform, EPSILON)) { newState.transform = transform
+ if (transform !== undefined && !Mat4.areEqual(transform, _state.transform, EPSILON)) {
+ newState.transform = transform
+ }
+ if (unitTransforms !== _state.unitTransforms || unitTransforms?.version !== state.unitTransformsVersion) {
+ newState.unitTransforms = unitTransforms
+ _state.unitTransformsVersion = unitTransforms ? unitTransforms?.version : -1
}
- if (unitTransforms !== _state.unitTransforms) newState.unitTransforms = unitTransforms
if (syncManually !== _state.syncManually) newState.syncManually = syncManually
if (markerActions !== _state.markerActions) newState.markerActions = markerActions
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
index 4a998a09ae0661a1682ecd8e570546a25570d4aa..6ab12e6477d19023cef0e4d2351736dbbc8dae51 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -33,7 +33,7 @@ function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, inde
}
const tmpRef = Vec3()
-const tmpLoc = StructureElement.Location.create()
+const tmpLoc = StructureElement.Location.create(void 0)
function createInterUnitBondCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitBondParams>, mesh?: Mesh) {
const bonds = structure.interUnitBonds
@@ -90,6 +90,7 @@ function createInterUnitBondCylinderMesh(ctx: VisualContext, structure: Structur
},
radius: (edgeIndex: number) => {
const b = edges[edgeIndex]
+ tmpLoc.structure = structure
tmpLoc.unit = b.unitA
tmpLoc.element = b.unitA.elements[b.indexA]
const sizeA = theme.size.size(tmpLoc)
@@ -142,12 +143,12 @@ function getBondLoci(pickingId: PickingId, structure: Structure, id: number) {
const bond = structure.interUnitBonds.edges[groupId]
return Bond.Loci(structure, [
Bond.Location(
- bond.unitA, bond.indexA as StructureElement.UnitIndex,
- bond.unitB, bond.indexB as StructureElement.UnitIndex
+ structure, bond.unitA, bond.indexA as StructureElement.UnitIndex,
+ structure, bond.unitB, bond.indexB as StructureElement.UnitIndex
),
Bond.Location(
- bond.unitB, bond.indexB as StructureElement.UnitIndex,
- bond.unitA, bond.indexA as StructureElement.UnitIndex
+ structure, bond.unitB, bond.indexB as StructureElement.UnitIndex,
+ structure, bond.unitA, bond.indexA as StructureElement.UnitIndex
)
])
}
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index 622603ae1daf724817766cb85ded366dcf604898..7283e794ab2381f67cf335efab01a61af03dbf52 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -25,7 +25,7 @@ import { ignoreBondType, BondCylinderParams, BondIterator } from './util/bond';
function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitBondParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
- const location = StructureElement.Location.create(unit)
+ const location = StructureElement.Location.create(structure, unit)
const elements = unit.elements;
const bonds = unit.bonds
@@ -135,12 +135,12 @@ function getBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: n
if (Unit.isAtomic(unit)) {
return Bond.Loci(structure, [
Bond.Location(
- unit, unit.bonds.a[groupId] as StructureElement.UnitIndex,
- unit, unit.bonds.b[groupId] as StructureElement.UnitIndex
+ structure, unit, unit.bonds.a[groupId] as StructureElement.UnitIndex,
+ structure, unit, unit.bonds.b[groupId] as StructureElement.UnitIndex
),
Bond.Location(
- unit, unit.bonds.b[groupId] as StructureElement.UnitIndex,
- unit, unit.bonds.a[groupId] as StructureElement.UnitIndex
+ structure, unit, unit.bonds.b[groupId] as StructureElement.UnitIndex,
+ structure, unit, unit.bonds.a[groupId] as StructureElement.UnitIndex
)
])
}
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index 3fd7397e53e585a6a7b00196fe3c26c2a8b78e32..0379023e9fdd0dcab6580e3d723dda028ad17fea 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -24,7 +24,7 @@ function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Struc
const { links, elements } = structure.carbohydrates
const { linkSizeFactor } = props
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const builderProps = {
linkCount: links.length,
@@ -74,7 +74,7 @@ function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
const { elements, links } = structure.carbohydrates
const groupCount = links.length
const instanceCount = 1
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number) => {
const link = links[groupIndex]
const carbA = elements[link.carbohydrateIndexA]
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index a266989792f17ada44312b13b21dc0f0f107df60..39ab381b91a15002eb6187e22dafa319d0fc98b2 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -53,7 +53,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
const carbohydrates = structure.carbohydrates
const n = carbohydrates.elements.length
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
for (let i = 0; i < n; ++i) {
const c = carbohydrates.elements[i];
@@ -187,7 +187,7 @@ function CarbohydrateElementIterator(structure: Structure): LocationIterator {
const carbElements = structure.carbohydrates.elements
const groupCount = carbElements.length * 2
const instanceCount = 1
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
function getLocation (groupIndex: number, instanceIndex: number) {
const carb = carbElements[Math.floor(groupIndex / 2)]
const ring = carb.unit.rings.all[carb.ringIndex]
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index bc661bde59560ffa46768ddb7d5888f57cf95071..1b176e4b3065c257d7b6760ada6e503fd2707837 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -25,7 +25,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structur
const { terminalLinks, elements } = structure.carbohydrates
const { terminalLinkSizeFactor } = props
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const builderProps = {
linkCount: terminalLinks.length,
@@ -91,7 +91,7 @@ function CarbohydrateTerminalLinkIterator(structure: Structure): LocationIterato
const { elements, terminalLinks } = structure.carbohydrates
const groupCount = terminalLinks.length
const instanceCount = 1
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number) => {
const terminalLink = terminalLinks[groupIndex]
if (terminalLink.fromCarbohydrate) {
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
index 06e78634061a48264db601159b9d76e7d7f29c2f..db047214479a432ea8d0e84dc57c3f5d9b3fd0d1 100644
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
@@ -24,7 +24,7 @@ function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Str
if (!crossLinks.count) return Mesh.createEmpty(mesh)
const { sizeFactor } = props
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const builderProps = {
linkCount: crossLinks.count,
@@ -76,8 +76,10 @@ function CrossLinkRestraintIterator(structure: Structure): LocationIterator {
const location = Bond.Location()
const getLocation = (groupIndex: number) => {
const pair = pairs[groupIndex]
+ location.aStructure = structure
location.aUnit = pair.unitA
location.aIndex = pair.indexA
+ location.bStructure = structure
location.bUnit = pair.unitB
location.bIndex = pair.indexB
return location
@@ -91,8 +93,8 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
const pair = structure.crossLinkRestraints.pairs[groupId]
if (pair) {
return Bond.Loci(structure, [
- Bond.Location(pair.unitA, pair.indexA, pair.unitB, pair.indexB),
- Bond.Location(pair.unitB, pair.indexB, pair.unitA, pair.indexA)
+ Bond.Location(structure, pair.unitA, pair.indexA, structure, pair.unitB, pair.indexB),
+ Bond.Location(structure, pair.unitB, pair.indexB, structure, pair.unitA, pair.indexA)
])
}
}
diff --git a/src/mol-repr/structure/visual/ellipsoid-mesh.ts b/src/mol-repr/structure/visual/ellipsoid-mesh.ts
index e812c2098799de3123955c0afc733417532b7b22..1496651807b0186b284d40b29c466cc986db747a 100644
--- a/src/mol-repr/structure/visual/ellipsoid-mesh.ts
+++ b/src/mol-repr/structure/visual/ellipsoid-mesh.ts
@@ -17,7 +17,7 @@ import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Vec3, Mat3, Tensor, EPSILON } from '../../../mol-math/linear-algebra';
import { isHydrogen } from '../../../mol-repr/structure/visual/util/common';
import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
-import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/mmcif/anisotropic'
+import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic'
import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
@@ -62,7 +62,7 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
const vertexCount = elementCount * sphereVertexCount(detail)
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh)
- const atomSiteAnisotrop = AtomSiteAnisotrop.get(model)
+ const atomSiteAnisotrop = AtomSiteAnisotrop.Provider.get(model)
if (!atomSiteAnisotrop) return Mesh.createEmpty(mesh)
const v = Vec3()
@@ -74,7 +74,7 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
const { U } = data
const space = data._schema.U.space
const pos = unit.conformation.invariantPosition
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
l.unit = unit
for (let i = 0; i < elementCount; i++) {
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 22c939e38816cee1b2c91518aa31ab56586be6b9..d52d00a8b31ab34fcec773514dc74f94bca0159c 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -38,7 +38,7 @@ export function getGaussianSurfaceVisual(webgl?: WebGLContext) {
async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props
- const { transform, field, idField } = await computeUnitGaussianDensity(unit, props, ctx.webgl).runInContext(ctx.runtime)
+ const { transform, field, idField } = await computeUnitGaussianDensity(structure, unit, props, ctx.webgl).runInContext(ctx.runtime)
const params = {
isoLevel: Math.exp(-smoothness),
@@ -119,7 +119,7 @@ async function createGaussianSurfaceTextureMesh(ctx: VisualContext, unit: Unit,
if (!ctx.webgl) throw new Error('webgl context required to create gaussian surface texture-mesh')
const isoLevel = Math.exp(-props.smoothness)
- const densityTextureData = await computeUnitGaussianDensityTexture2d(unit, props, ctx.webgl).runInContext(ctx.runtime)
+ const densityTextureData = await computeUnitGaussianDensityTexture2d(structure, unit, props, ctx.webgl).runInContext(ctx.runtime)
// console.log(densityTextureData)
// console.log('vertexGroupTexture', readTexture(ctx.webgl, densityTextureData.texture))
// ctx.webgl.waitForGpuCommandsCompleteSync()
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index 04bd8c7f54c4beba04875370728705120547926c..c0410641e47220cfb54ed4a9d584c0462c2a119d 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -17,7 +17,7 @@ import { VisualUpdateState } from '../../util';
async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
const { smoothness } = props
- const { transform, field, idField } = await computeUnitGaussianDensity(unit, props, ctx.webgl).runInContext(ctx.runtime)
+ const { transform, field, idField } = await computeUnitGaussianDensity(structure, unit, props, ctx.webgl).runInContext(ctx.runtime)
const params = {
isoLevel: Math.exp(-smoothness),
diff --git a/src/mol-repr/structure/visual/label-text.ts b/src/mol-repr/structure/visual/label-text.ts
index a2511e993ed5c9a4cf9c2651c4d9c89d0ee8cdca..696f64fb3db59946bd23df3d226afe56eaf77ac8 100644
--- a/src/mol-repr/structure/visual/label-text.ts
+++ b/src/mol-repr/structure/visual/label-text.ts
@@ -67,8 +67,7 @@ const tmpVec = Vec3();
const boundaryHelper = new BoundaryHelper();
function createChainText(ctx: VisualContext, structure: Structure, theme: Theme, props: LabelTextProps, text?: Text): Text {
-
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
const { units, serialMapping } = structure;
const { auth_asym_id, label_asym_id } = StructureProperties.chain;
const { cumulativeUnitElementCount } = serialMapping
@@ -93,8 +92,7 @@ function createChainText(ctx: VisualContext, structure: Structure, theme: Theme,
}
function createResidueText(ctx: VisualContext, structure: Structure, theme: Theme, props: LabelTextProps, text?: Text): Text {
-
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
const { units, serialMapping } = structure;
const { auth_seq_id, label_comp_id } = StructureProperties.residue;
const { cumulativeUnitElementCount } = serialMapping
@@ -145,8 +143,7 @@ function createResidueText(ctx: VisualContext, structure: Structure, theme: Them
}
function createElementText(ctx: VisualContext, structure: Structure, theme: Theme, props: LabelTextProps, text?: Text): Text {
-
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
const { units, serialMapping } = structure;
const { label_atom_id, label_alt_id } = StructureProperties.atom;
const { cumulativeUnitElementCount } = serialMapping
diff --git a/src/mol-repr/structure/visual/molecular-surface-mesh.ts b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
index 0971b4a11ff202d6e421abb96ba75c438de39271..ac17068a8d4371e7331f440719234ae3fbf3c4b3 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -27,7 +27,7 @@ export type MolecularSurfaceMeshParams = typeof MolecularSurfaceMeshParams
async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceProps, mesh?: Mesh): Promise<Mesh> {
- const { transform, field, idField } = await computeUnitMolecularSurface(unit, props).runInContext(ctx.runtime)
+ const { transform, field, idField } = await computeUnitMolecularSurface(structure, unit, props).runInContext(ctx.runtime)
const params = {
isoLevel: props.probeRadius,
scalarField: field,
diff --git a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
index b7b809b61b2a9c31154e8028a0ead2657e0d58c8..964857397e3458cdc7ec5196ffe7c07679157f24 100644
--- a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
@@ -28,7 +28,7 @@ export type MolecularSurfaceWireframeParams = typeof MolecularSurfaceWireframePa
async function createMolecularSurfaceWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceProps, lines?: Lines): Promise<Lines> {
- const { transform, field, idField } = await computeUnitMolecularSurface(unit, props).runInContext(ctx.runtime)
+ const { transform, field, idField } = await computeUnitMolecularSurface(structure, unit, props).runInContext(ctx.runtime)
const params = {
isoLevel: props.probeRadius,
scalarField: field,
diff --git a/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts b/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
index df4ffead22d6a9600eace70d6a45b056f5564e94..fadec4c0f7b0b20c89da7429ce89ba536bc93285 100644
--- a/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
+++ b/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
@@ -88,10 +88,10 @@ export function createOrientationEllipsoidMesh(ctx: VisualContext, unit: Unit, s
//
function UnitIterator(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const groupCount = 1
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
diff --git a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
index 73da6a17de41b4753927ac618c336d294b2cfd00..84d8ac7e3d6481e69357bb80f8106574351c0d86 100644
--- a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
@@ -42,7 +42,7 @@ function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, struc
const pB = Vec3.zero()
const cylinderProps: CylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments }
- const polymerBackboneIt = PolymerBackboneIterator(unit)
+ const polymerBackboneIt = PolymerBackboneIterator(structure, unit)
while (polymerBackboneIt.hasNext) {
const { centerA, centerB } = polymerBackboneIt.move()
pos(centerA.element, pA)
diff --git a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
index 074c190839214a03c04bcb88b18773a520c5304c..78b7aba9e0fe950b95b8226053a20767d1188b4d 100644
--- a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
@@ -48,7 +48,7 @@ function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure:
}
let i = 0
- const polymerGapIt = PolymerGapIterator(unit)
+ const polymerGapIt = PolymerGapIterator(structure, unit)
while (polymerGapIt.hasNext) {
const { centerA, centerB } = polymerGapIt.move()
if (centerA.element === centerB.element) {
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index b21b11ccb50d6b7824d58e26329ada568fd29a13..1b05d5e840b9fcd865fd146157d940e909e29828 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -25,11 +25,11 @@ export function ignoreBondType(include: BondType.Flag, exclude: BondType.Flag, f
export namespace BondIterator {
export function fromGroup(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const unit = group.units[0]
const groupCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
@@ -42,7 +42,7 @@ export namespace BondIterator {
export function fromStructure(structure: Structure): LocationIterator {
const groupCount = structure.interUnitBonds.edgeCount
const instanceCount = 1
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number) => {
const bond = structure.interUnitBonds.edges[groupIndex]
location.unit = bond.unitA
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index eeee2ceea5f5a6dca2dc20c2073f1430602b1c04..855b37efd01fff324aa46681098c72e0249028ea 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -105,7 +105,7 @@ export function getConformation(unit: Unit) {
}
}
-export function getUnitConformationAndRadius(unit: Unit, ignoreHydrogens = false) {
+export function getUnitConformationAndRadius(structure: Structure, unit: Unit, ignoreHydrogens = false) {
const conformation = getConformation(unit)
const { elements } = unit
@@ -135,7 +135,7 @@ export function getUnitConformationAndRadius(unit: Unit, ignoreHydrogens = false
id
}
- const l = StructureElement.Location.create(unit)
+ const l = StructureElement.Location.create(structure, unit)
const sizeTheme = PhysicalSizeTheme({}, {})
const radius = (index: number) => {
l.element = index as ElementIndex
@@ -146,7 +146,7 @@ export function getUnitConformationAndRadius(unit: Unit, ignoreHydrogens = false
}
export function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens = false) {
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
const sizeTheme = PhysicalSizeTheme({}, {})
let xs: ArrayLike<number>
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index 82bdedfb1a94ed641157765f537c7650c7efff44..daa69d87e0d1d8a8e51fa3fac80c0e9fff83308c 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -38,7 +38,7 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
const v = Vec3.zero()
const pos = unit.conformation.invariantPosition
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(structure)
l.unit = unit
for (let i = 0; i < elementCount; i++) {
@@ -159,10 +159,10 @@ export function getSerialElementLoci(pickingId: PickingId, structure: Structure,
export namespace ElementIterator {
export function fromGroup(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const groupCount = group.elements.length
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
@@ -177,7 +177,7 @@ export namespace ElementIterator {
const groupCount = elementCount
const instanceCount = 1
const { unitIndices, elementIndices } = structure.serialMapping
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number) => {
location.unit = units[unitIndices[groupIndex]]
location.element = elementIndices[groupIndex]
diff --git a/src/mol-repr/structure/visual/util/gaussian.ts b/src/mol-repr/structure/visual/util/gaussian.ts
index fb850975919ee193613eb1527a5e5e324eb05d7b..b836de2c6f443a7dd974df803564ba842cbebe64 100644
--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/src/mol-repr/structure/visual/util/gaussian.ts
@@ -34,22 +34,22 @@ export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTexturePr
//
-export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
- const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
+export function computeUnitGaussianDensity(structure: Structure, unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
+ const { position, radius } = getUnitConformationAndRadius(structure, unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props, webgl);
});
}
-export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
+export function computeUnitGaussianDensityTexture(structure: Structure, unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
+ const { position, radius } = getUnitConformationAndRadius(structure, unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return GaussianDensityTexture(webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
});
}
-export function computeUnitGaussianDensityTexture2d(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
+export function computeUnitGaussianDensityTexture2d(structure: Structure, unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
+ const { position, radius } = getUnitConformationAndRadius(structure, unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return GaussianDensityTexture2d(webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
});
diff --git a/src/mol-repr/structure/visual/util/molecular-surface.ts b/src/mol-repr/structure/visual/util/molecular-surface.ts
index 5d3fd7491289151b590c1d4f8a8c681cc2926f27..550e99fadee2694046d461363a96e096d7dce2a0 100644
--- a/src/mol-repr/structure/visual/util/molecular-surface.ts
+++ b/src/mol-repr/structure/visual/util/molecular-surface.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from '../../../../mol-model/structure';
+import { Unit, Structure } from '../../../../mol-model/structure';
import { Task, RuntimeContext } from '../../../../mol-task';
import { getUnitConformationAndRadius } from './common';
import { PositionData, DensityData } from '../../../../mol-math/geometry';
@@ -15,9 +15,9 @@ export type MolecularSurfaceProps = MolecularSurfaceCalculationProps & {
ignoreHydrogens: boolean
}
-function getPositionDataAndMaxRadius(unit: Unit, props: MolecularSurfaceProps) {
+function getPositionDataAndMaxRadius(structure: Structure, unit: Unit, props: MolecularSurfaceProps) {
const { probeRadius, ignoreHydrogens } = props
- const { position, radius } = getUnitConformationAndRadius(unit, ignoreHydrogens)
+ const { position, radius } = getUnitConformationAndRadius(structure, unit, ignoreHydrogens)
const { indices } = position
const n = OrderedSet.size(indices)
const radii = new Float32Array(OrderedSet.end(indices))
@@ -33,8 +33,8 @@ function getPositionDataAndMaxRadius(unit: Unit, props: MolecularSurfaceProps) {
return { position: { ...position, radius: radii }, maxRadius }
}
-export function computeUnitMolecularSurface(unit: Unit, props: MolecularSurfaceProps) {
- const { position, maxRadius } = getPositionDataAndMaxRadius(unit, props)
+export function computeUnitMolecularSurface(structure: Structure, unit: Unit, props: MolecularSurfaceProps) {
+ const { position, maxRadius } = getPositionDataAndMaxRadius(structure, unit, props)
return Task.create('Molecular Surface', async ctx => {
return await MolecularSurface(ctx, position, maxRadius, props);
});
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index 41c744a168f3667f074ec9154a8ff66ffd35f6c6..6b54f3bb1648f8ea6a004502689eed80ec00a373 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -15,12 +15,12 @@ import { eachAtomicUnitTracedElement } from './polymer';
export namespace NucleotideLocationIterator {
export function fromGroup(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const u = group.units[0]
const nucleotideElementIndices = Unit.isAtomic(u) ? u.nucleotideElements : []
const groupCount = nucleotideElementIndices.length
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index d40bdbebb4d11ca1bcc521a3e9b1067520827c51..dc868b4587a62883b04b11d9c4c54e8b1c02da2d 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -43,11 +43,11 @@ export function getGapRanges(unit: Unit): SortedRanges<ElementIndex> {
export namespace PolymerLocationIterator {
export function fromGroup(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const polymerElements = group.units[0].polymerElements
const groupCount = polymerElements.length
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
@@ -60,11 +60,11 @@ export namespace PolymerLocationIterator {
export namespace PolymerGapLocationIterator {
export function fromGroup(structureGroup: StructureGroup): LocationIterator {
- const { group } = structureGroup
+ const { group, structure } = structureGroup
const gapElements = group.units[0].gapElements
const groupCount = gapElements.length
const instanceCount = group.units.length
- const location = StructureElement.Location.create()
+ const location = StructureElement.Location.create(structure)
const getLocation = (groupIndex: number, instanceIndex: number) => {
const unit = group.units[instanceIndex]
location.unit = unit
@@ -214,8 +214,8 @@ export function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: S
const unitIndexB = OrderedSet.indexOf(unit.elements, unit.gapElements[groupId % 2 ? groupId - 1 : groupId + 1]) as StructureElement.UnitIndex
if (unitIndexA !== -1 && unitIndexB !== -1) {
return Bond.Loci(structure, [
- Bond.Location(unit, unitIndexA, unit, unitIndexB),
- Bond.Location(unit, unitIndexB, unit, unitIndexA)
+ Bond.Location(structure, unit, unitIndexA, structure, unit, unitIndexB),
+ Bond.Location(structure, unit, unitIndexB, structure, unit, unitIndexA)
])
}
}
diff --git a/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts b/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
index 82155734d9d95f0cbe9ab739ddd7989e4a50a83a..c8bb7f68173506b6879a8a197e076833e08c88d4 100644
--- a/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/backbone-iterator.ts
@@ -4,19 +4,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, ElementIndex, ResidueIndex } from '../../../../../mol-model/structure';
+import { Unit, Structure, StructureElement, ElementIndex, ResidueIndex } from '../../../../../mol-model/structure';
import { Segmentation } from '../../../../../mol-data/int';
import Iterator from '../../../../../mol-data/iterator';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
import { getPolymerRanges } from '../polymer';
/** Iterates over consecutive pairs of residues/coarse elements in polymers */
-export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
+export function PolymerBackboneIterator(structure: Structure, unit: Unit): Iterator<PolymerBackbonePair> {
switch (unit.kind) {
- case Unit.Kind.Atomic: return new AtomicPolymerBackboneIterator(unit)
+ case Unit.Kind.Atomic: return new AtomicPolymerBackboneIterator(structure, unit)
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
- return new CoarsePolymerBackboneIterator(unit)
+ return new CoarsePolymerBackboneIterator(structure, unit)
}
}
@@ -25,10 +25,10 @@ interface PolymerBackbonePair {
centerB: StructureElement.Location
}
-function createPolymerBackbonePair (unit: Unit) {
+function createPolymerBackbonePair (structure: Structure, unit: Unit) {
return {
- centerA: StructureElement.Location.create(unit),
- centerB: StructureElement.Location.create(unit),
+ centerA: StructureElement.Location.create(structure, unit),
+ centerB: StructureElement.Location.create(structure, unit),
}
}
@@ -80,11 +80,11 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
return this.value;
}
- constructor(private unit: Unit.Atomic) {
+ constructor(structure: Structure, private unit: Unit.Atomic) {
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements)
- this.value = createPolymerBackbonePair(unit)
+ this.value = createPolymerBackbonePair(structure, unit)
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
}
}
@@ -126,9 +126,9 @@ export class CoarsePolymerBackboneIterator implements Iterator<PolymerBackbonePa
return this.value;
}
- constructor(private unit: Unit.Spheres | Unit.Gaussians) {
+ constructor(structure: Structure, private unit: Unit.Spheres | Unit.Gaussians) {
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
- this.value = createPolymerBackbonePair(unit)
+ this.value = createPolymerBackbonePair(structure, unit)
this.hasNext = this.polymerIt.hasNext
}
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/polymer/gap-iterator.ts b/src/mol-repr/structure/visual/util/polymer/gap-iterator.ts
index 5b8208f57bc07ebae58b2ea0ab4610d89279ad2a..0da71df3904149025a867a7a0421dc3ffb2f7152 100644
--- a/src/mol-repr/structure/visual/util/polymer/gap-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/gap-iterator.ts
@@ -4,18 +4,18 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, ElementIndex, ResidueIndex } from '../../../../../mol-model/structure';
+import { Unit, StructureElement, ElementIndex, ResidueIndex, Structure } from '../../../../../mol-model/structure';
import Iterator from '../../../../../mol-data/iterator';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
import { getGapRanges } from '../polymer';
/** Iterates over gaps, i.e. the stem residues/coarse elements adjacent to gaps */
-export function PolymerGapIterator(unit: Unit): Iterator<PolymerGapPair> {
+export function PolymerGapIterator(structure: Structure, unit: Unit): Iterator<PolymerGapPair> {
switch (unit.kind) {
- case Unit.Kind.Atomic: return new AtomicPolymerGapIterator(unit)
+ case Unit.Kind.Atomic: return new AtomicPolymerGapIterator(structure, unit)
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
- return new CoarsePolymerGapIterator(unit)
+ return new CoarsePolymerGapIterator(structure, unit)
}
}
@@ -24,10 +24,10 @@ interface PolymerGapPair {
centerB: StructureElement.Location
}
-function createPolymerGapPair (unit: Unit) {
+function createPolymerGapPair (structure: Structure, unit: Unit) {
return {
- centerA: StructureElement.Location.create(unit),
- centerB: StructureElement.Location.create(unit),
+ centerA: StructureElement.Location.create(structure, unit),
+ centerB: StructureElement.Location.create(structure, unit),
}
}
@@ -46,10 +46,10 @@ export class AtomicPolymerGapIterator implements Iterator<PolymerGapPair> {
return this.value;
}
- constructor(private unit: Unit.Atomic) {
+ constructor(structure: Structure, private unit: Unit.Atomic) {
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
this.gapIt = SortedRanges.transientSegments(getGapRanges(unit), unit.elements);
- this.value = createPolymerGapPair(unit)
+ this.value = createPolymerGapPair(structure, unit)
this.hasNext = this.gapIt.hasNext
}
}
@@ -67,9 +67,9 @@ export class CoarsePolymerGapIterator implements Iterator<PolymerGapPair> {
return this.value;
}
- constructor(private unit: Unit.Spheres | Unit.Gaussians) {
+ constructor(structure: Structure, private unit: Unit.Spheres | Unit.Gaussians) {
this.gapIt = SortedRanges.transientSegments(getGapRanges(unit), unit.elements);
- this.value = createPolymerGapPair(unit)
+ this.value = createPolymerGapPair(structure, unit)
this.hasNext = this.gapIt.hasNext
}
}
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index f0b405a0fcb31bc15362cb015cb36f965606858a..2631d7588926625f383c0ade64cd016cbbc1f7af 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -47,11 +47,11 @@ interface PolymerTraceElement {
const SecStrucTypeNA = SecondaryStructureType.create(SecondaryStructureType.Flag.NA)
-function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
+function createPolymerTraceElement (structure: Structure, unit: Unit): PolymerTraceElement {
return {
- center: StructureElement.Location.create(unit),
- centerPrev: StructureElement.Location.create(unit),
- centerNext: StructureElement.Location.create(unit),
+ center: StructureElement.Location.create(structure, unit),
+ centerPrev: StructureElement.Location.create(structure, unit),
+ centerNext: StructureElement.Location.create(structure, unit),
first: false, last: false,
initial: false, final: false,
secStrucFirst: false, secStrucLast: false,
@@ -302,7 +302,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.cyclicPolymerMap = unit.model.atomicRanges.cyclicPolymerMap
this.polymerIt = SortedRanges.transientSegments(this.polymerRanges, unit.elements)
this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
- this.value = createPolymerTraceElement(unit)
+ this.value = createPolymerTraceElement(structure, unit)
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
const secondaryStructure = SecondaryStructureProvider.get(structure).value?.get(unit.invariantId)
@@ -397,7 +397,7 @@ export class CoarsePolymerTraceIterator implements Iterator<PolymerTraceElement>
constructor(private unit: Unit.Spheres | Unit.Gaussians, structure: Structure) {
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
- this.value = createPolymerTraceElement(unit)
+ this.value = createPolymerTraceElement(structure, unit)
Vec3.set(this.value.d12, 1, 0, 0)
Vec3.set(this.value.d23, 1, 0, 0)
switch (unit.kind) {
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index ef8b1f00daef96e0c5d5fbfe09587e178566f86b..16c072ff40491cae1f2c181df6d4eef3194fe1fa 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -81,7 +81,7 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(ctx.structure)
const asymIdSerialMap = getAsymIdSerialMap(ctx.structure.root)
const labelTable = Array.from(asymIdSerialMap.keys())
diff --git a/src/mol-theme/color/entity-source.ts b/src/mol-theme/color/entity-source.ts
index c38d9f14a2776eaf61953b61bc99816856bed500..a8ac312bfe1693d8be1637d780f1709702303b5d 100644
--- a/src/mol-theme/color/entity-source.ts
+++ b/src/mol-theme/color/entity-source.ts
@@ -16,6 +16,7 @@ import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend, ScaleLegend } from '../../mol-util/legend';
import { isInteger } from '../../mol-util/number';
import { ColorLists } from '../../mol-util/color/lists';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
const DefaultList = 'dark-2'
const DefaultColor = Color(0xFAFAFA)
@@ -100,8 +101,8 @@ function getMaps(models: ReadonlyArray<Model>) {
for (let i = 0, il = models.length; i <il; ++i) {
const m = models[i]
- if (m.sourceData.kind !== 'mmCIF') continue
- const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
+ if (!MmcifFormat.is(m.sourceData)) continue
+ const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data.db
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_scientific_name, entity_src_gen.plasmid_name, entity_src_gen.pdbx_gene_src_gene)
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat, entity_src_nat.pdbx_organism_scientific, entity_src_nat.pdbx_plasmid_name)
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn, pdbx_entity_src_syn.organism_scientific)
@@ -125,7 +126,7 @@ export function EntitySourceColorTheme(ctx: ThemeDataContext, props: PD.Values<E
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(ctx.structure)
const { models } = ctx.structure.root
const { seqToSrcByModelEntity, srcKeySerialMap } = getMaps(models)
diff --git a/src/mol-theme/color/polymer-id.ts b/src/mol-theme/color/polymer-id.ts
index 18f0e76541605b271f10de8c4bd6bd096ba69aa4..46955e905c48bad6d951683869e8c9f3fb5f94ee 100644
--- a/src/mol-theme/color/polymer-id.ts
+++ b/src/mol-theme/color/polymer-id.ts
@@ -90,7 +90,7 @@ export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Poly
let legend: ScaleLegend | TableLegend | undefined
if (ctx.structure) {
- const l = StructureElement.Location.create()
+ const l = StructureElement.Location.create(ctx.structure)
const polymerAsymIdSerialMap = getPolymerAsymIdSerialMap(ctx.structure.root)
const labelTable = Array.from(polymerAsymIdSerialMap.keys())
diff --git a/src/mol-theme/color/uncertainty.ts b/src/mol-theme/color/uncertainty.ts
index b715369f10fb8db503a5c89c3745a07b8382e44d..d7511cb0533f6554bf50d9d92797ef1b0df223f5 100644
--- a/src/mol-theme/color/uncertainty.ts
+++ b/src/mol-theme/color/uncertainty.ts
@@ -67,5 +67,5 @@ export const UncertaintyColorThemeProvider: ColorTheme.Provider<UncertaintyColor
factory: UncertaintyColorTheme,
getParams: getUncertaintyColorThemeParams,
defaultValues: PD.getDefaultValues(UncertaintyColorThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.sourceData.data.ihm_sphere_obj_site.rmsf.isDefined)
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
}
\ No newline at end of file
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index cc58137b48249a7806c84a2d0ee367569d1e2fdd..a903862f28ade44b66a725717f671d1ff53a2f4c 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -112,8 +112,8 @@ function _structureElementStatsLabel(stats: StructureElement.Stats, countsOnly =
export function bondLabel(bond: Bond.Location, options: Partial<LabelOptions> = {}): string {
const o = { ...DefaultLabelOptions, ...options }
- const locA = StructureElement.Location.create(bond.aUnit, bond.aUnit.elements[bond.aIndex])
- const locB = StructureElement.Location.create(bond.bUnit, bond.bUnit.elements[bond.bIndex])
+ const locA = StructureElement.Location.create(bond.aStructure, bond.aUnit, bond.aUnit.elements[bond.aIndex])
+ const locB = StructureElement.Location.create(bond.bStructure, bond.bUnit, bond.bUnit.elements[bond.bIndex])
const labelA = _elementLabel(locA, o.granularity, o.hidePrefix)
const labelB = _elementLabel(locB, o.granularity, o.hidePrefix)
let offset = 0
@@ -137,7 +137,7 @@ export function bundleLabel(bundle: Loci.Bundle<any>, options: Partial<LabelOpti
const o = { ...DefaultLabelOptions, ...options }
const locations = (bundle.loci as StructureElement.Loci[]).map(l => {
const { unit, indices } = l.elements[0]
- return StructureElement.Location.create(unit, unit.elements[OrderedSet.start(indices)])
+ return StructureElement.Location.create(l.structure, unit, unit.elements[OrderedSet.start(indices)])
})
const labels = locations.map(l => _elementLabel(l, o.granularity, o.hidePrefix))
diff --git a/src/mol-theme/size/uncertainty.ts b/src/mol-theme/size/uncertainty.ts
index 78e4dc41c8d915d8904b8c3c4d6bb47696dfe122..5f9da065b4b8331ac620db16e6e4b806446ac176 100644
--- a/src/mol-theme/size/uncertainty.ts
+++ b/src/mol-theme/size/uncertainty.ts
@@ -57,5 +57,5 @@ export const UncertaintySizeThemeProvider: SizeTheme.Provider<UncertaintySizeThe
factory: UncertaintySizeTheme,
getParams: getUncertaintySizeThemeParams,
defaultValues: PD.getDefaultValues(UncertaintySizeThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.sourceData.data.ihm_sphere_obj_site.rmsf.isDefined)
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
}
\ No newline at end of file
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index 4ba2901d7190e73786769c9d9e8de16e175e834e..edcf9300c4635fb1ac00869978d8f9457f58906c 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -119,15 +119,25 @@ export namespace ParamDefinition {
}
export interface FileParam extends Base<File> {
- type: 'file',
+ type: 'file'
accept?: string
}
- export function File(info?: Info & { accept?: string }): FileParam {
+ export function File(info?: Info & { accept?: string, multiple?: boolean }): FileParam {
const ret = setInfo<FileParam>({ type: 'file', defaultValue: void 0 as any }, info);
if (info && info.accept) ret.accept = info.accept;
return ret;
}
+ export interface FileListParam extends Base<FileList> {
+ type: 'file-list'
+ accept?: string
+ }
+ export function FileList(info?: Info & { accept?: string, multiple?: boolean }): FileListParam {
+ const ret = setInfo<FileListParam>({ type: 'file-list', defaultValue: void 0 as any }, info);
+ if (info && info.accept) ret.accept = info.accept;
+ return ret;
+ }
+
export interface Range {
/** If given treat as a range. */
min?: number
@@ -256,7 +266,7 @@ export namespace ParamDefinition {
}
export type Any =
- | Value<any> | Select<any> | MultiSelect<any> | BooleanParam | Text | Color | Vec3 | Numeric | FileParam | Interval | LineGraph
+ | Value<any> | Select<any> | MultiSelect<any> | BooleanParam | Text | Color | Vec3 | Numeric | FileParam | FileListParam | Interval | LineGraph
| ColorList<any> | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any> | Script | ObjectList
export type Params = { [k: string]: Any }
diff --git a/src/mol-util/set.ts b/src/mol-util/set.ts
index 25114f787f1df08d836f969726272cc95d4f13e0..af02d56a3cab789b73612da9c24a48d43c4c461f 100644
--- a/src/mol-util/set.ts
+++ b/src/mol-util/set.ts
@@ -67,6 +67,14 @@ export namespace SetUtils {
return flag;
}
+ export function intersectionSize<T>(setA: ReadonlySet<T>, setB: ReadonlySet<T>): number {
+ let count = 0
+ setB.forEach(elem => {
+ if (setA.has(elem)) count += 1;
+ })
+ return count;
+ }
+
/** Create set containing elements of set a that are not in set b. */
export function difference<T>(setA: ReadonlySet<T>, setB: ReadonlySet<T>): Set<T> {
const difference = new Set(setA);
@@ -74,6 +82,15 @@ export namespace SetUtils {
return difference;
}
+ /** Number of elements that are in set a but not in set b. */
+ export function differenceSize<T>(setA: ReadonlySet<T>, setB: ReadonlySet<T>): number {
+ let count = setA.size;
+ setA.forEach(elem => {
+ if (setB.has(elem)) count -= 1
+ })
+ return count;
+ }
+
/** Test if set a and b contain the same elements. */
export function areEqual<T>(setA: ReadonlySet<T>, setB: ReadonlySet<T>) {
if (setA.size !== setB.size) return false
diff --git a/src/mol-util/uuid.ts b/src/mol-util/uuid.ts
index c5f5b508dbe5f70aba21116b8e4ea6da1356fce8..541489a5f5f57d439bff87bdee88381c9eb5cc6e 100644
--- a/src/mol-util/uuid.ts
+++ b/src/mol-util/uuid.ts
@@ -6,13 +6,14 @@
import { now } from '../mol-util/now';
+/** A UUID, either standard 36 characters or 22 characters base64 encoded. */
type UUID = string & { '@type': 'uuid' }
namespace UUID {
const _btoa = typeof btoa !== 'undefined' ? btoa : (s: string) => Buffer.from(s).toString('base64')
const chars: string[] = [];
- /** Creates 22 characted "base64" UUID */
+ /** Creates a 22 characters 'base64' encoded UUID */
export function create22(): UUID {
let d = (+new Date()) + now();
for (let i = 0; i < 16; i++) {
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 8df122b3e8f708a35d22e50f4ddf8ce927e34a9d..c4f7c19b319e039d08a2220ef925fc05b1cab758 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -7,7 +7,7 @@ import { Structure } from '../mol-model/structure'
import { GridLookup3D } from '../mol-math/geometry';
// import { sortArray } from 'mol-data/util';
import { OrderedSet } from '../mol-data/int';
-import { trajectoryFromMmCIF } from '../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure/mmcif';
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
@@ -35,14 +35,14 @@ export async function readCIF(path: string) {
const models = await trajectoryFromMmCIF(parsed.result.blocks[0]).run();
const structures = models.map(Structure.ofModel);
- return { mmcif: models[0].sourceData.data, models, structures };
+ return { mmcif: models[0].sourceData.data as MmcifFormat.Data, models, structures };
}
export async function test() {
const { mmcif, structures } = await readCIF('e:/test/quick/1tqn_updated.cif');
- const lookup = GridLookup3D({ x: mmcif.atom_site.Cartn_x.toArray(), y: mmcif.atom_site.Cartn_y.toArray(), z: mmcif.atom_site.Cartn_z.toArray(),
- indices: OrderedSet.ofBounds(0, mmcif.atom_site._rowCount),
+ const lookup = GridLookup3D({ x: mmcif.db.atom_site.Cartn_x.toArray(), y: mmcif.db.atom_site.Cartn_y.toArray(), z: mmcif.db.atom_site.Cartn_z.toArray(),
+ indices: OrderedSet.ofBounds(0, mmcif.db.atom_site._rowCount),
// radius: [1, 1, 1, 1]
// indices: [1]
});
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 8f7d1ac4e6cd3db684566a39004a2e485c5ed0c5..989e29c7f4df5bb9cef0ab3567fafd6d5390c99c 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -16,7 +16,7 @@ import { Structure, Model, Queries as Q, StructureElement, StructureSelection, S
import to_mmCIF from '../mol-model/structure/export/mmcif'
import { Vec3 } from '../mol-math/linear-algebra';
-import { trajectoryFromMmCIF } from '../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure/mmcif';
// import { printUnits } from '../apps/structure-info/model';
// import { EquivalenceClasses } from '../mol-data/util';
@@ -106,8 +106,8 @@ export async function getBcif(pdbId: string) {
export namespace PropertyAccess {
function baseline(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') throw new Error('Model must be mmCIF');
- const atom_site = model.sourceData.data.atom_site;
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('Model must be mmCIF');
+ const atom_site = model.sourceData.data.db.atom_site;
const id = atom_site.id.value;
let s = 0;
for (let i = 0, _i = atom_site._rowCount; i < _i; i++) {
@@ -117,7 +117,7 @@ export namespace PropertyAccess {
}
function sumProperty(structure: Structure, p: StructureElement.Property<number>) {
- const l = StructureElement.Location.create();
+ const l = StructureElement.Location.create(structure);
let s = 0;
for (const unit of structure.units) {
diff --git a/src/servers/model/properties/providers/wwpdb.ts b/src/servers/model/properties/providers/wwpdb.ts
index 773bbbff39ca5f6df1ba867b8680e31b8bbf4152..c35f991be4998bd07dfcabaee8434f8b2ae3d483 100644
--- a/src/servers/model/properties/providers/wwpdb.ts
+++ b/src/servers/model/properties/providers/wwpdb.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -9,15 +9,17 @@ import * as util from 'util'
import { AttachModelProperty } from '../../property-provider';
import { CIF } from '../../../../mol-io/reader/cif';
import { getParam } from '../../../common/util';
-import { ComponentBond } from '../../../../mol-model-formats/structure/mmcif/bonds';
import { mmCIF_Database, mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { ComponentBond } from '../../../../mol-model-formats/structure/property/bonds/comp';
require('util.promisify').shim()
const readFile = util.promisify(fs.readFile)
export const wwPDB_chemCompBond: AttachModelProperty = async ({ model, params }) => {
const table = await getChemCompBondTable(getTablePath(params))
- return ComponentBond.attachFromExternalData(model, table, true)
+ const data = ComponentBond.chemCompBondFromTable(model, table)
+ const entries = ComponentBond.getEntriesFromChemCompBond(data)
+ return ComponentBond.Provider.set(model, { entries, data })
}
async function read(path: string) {
diff --git a/src/tests/browser/marching-cubes.ts b/src/tests/browser/marching-cubes.ts
index 4f8e8335b34dfd2ae04c720e74c64a49e43b667c..66fa5d3fe59d5d021fc6cacee278e8507d783288 100644
--- a/src/tests/browser/marching-cubes.ts
+++ b/src/tests/browser/marching-cubes.ts
@@ -114,7 +114,7 @@ async function init() {
const mcIsoSurfaceRepr = Representation.fromRenderObject('texture-mesh', mcIsoSurfaceRenderObject)
canvas3d.add(mcIsoSurfaceRepr)
- canvas3d.resetCamera()
+ canvas3d.requestCameraReset()
//
@@ -141,7 +141,7 @@ async function init() {
const meshRepr = Representation.fromRenderObject('mesh', meshRenderObject)
canvas3d.add(meshRepr)
- canvas3d.resetCamera()
+ canvas3d.requestCameraReset()
}
init()
\ No newline at end of file
diff --git a/src/tests/browser/render-lines.ts b/src/tests/browser/render-lines.ts
index 4cecd427cb4e85e4b061bafd95ab948ad6c99408..d782b92aa7540d53169f57741fcebf8b7767ca3a 100644
--- a/src/tests/browser/render-lines.ts
+++ b/src/tests/browser/render-lines.ts
@@ -41,4 +41,4 @@ function linesRepr() {
}
canvas3d.add(linesRepr())
-canvas3d.resetCamera()
\ No newline at end of file
+canvas3d.requestCameraReset()
\ No newline at end of file
diff --git a/src/tests/browser/render-mesh.ts b/src/tests/browser/render-mesh.ts
index ca5ee131a4db0b7c7875d1a419bea8a099420bb2..f5358bf9f6d54ff5d208a854a8b5dd34a8939cd2 100644
--- a/src/tests/browser/render-mesh.ts
+++ b/src/tests/browser/render-mesh.ts
@@ -47,4 +47,4 @@ function meshRepr() {
}
canvas3d.add(meshRepr())
-canvas3d.resetCamera()
\ No newline at end of file
+canvas3d.requestCameraReset()
\ No newline at end of file
diff --git a/src/tests/browser/render-shape.ts b/src/tests/browser/render-shape.ts
index ac2153ce5d55f3069be39ccb5cb08700833dc2d0..cf7b748b6eeaa7d18605fc207aed8c578611909e 100644
--- a/src/tests/browser/render-shape.ts
+++ b/src/tests/browser/render-shape.ts
@@ -112,7 +112,7 @@ export async function init() {
// Create shape from myData and add to canvas3d
await repr.createOrUpdate({}, myData).run((p: Progress) => console.log(Progress.format(p)))
canvas3d.add(repr)
- canvas3d.resetCamera()
+ canvas3d.requestCameraReset()
// Change color after 1s
setTimeout(async () => {
diff --git a/src/tests/browser/render-spheres.ts b/src/tests/browser/render-spheres.ts
index 020b5795906cc42f4c06b8790aebc4571dabe337..094e48585b429ddcee036a1ad64fe65b1239532b 100644
--- a/src/tests/browser/render-spheres.ts
+++ b/src/tests/browser/render-spheres.ts
@@ -40,4 +40,4 @@ function spheresRepr() {
}
canvas3d.add(spheresRepr())
-canvas3d.resetCamera()
\ No newline at end of file
+canvas3d.requestCameraReset()
\ No newline at end of file
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 36e284c5448ed8f3743d3d182ba2ababade6fc24..e19dbb44e12c0505c21816c5173bd05893396f3c 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -195,7 +195,7 @@ async function init() {
if (show.ballAndStick) canvas3d.add(ballAndStickRepr)
if (show.molecularSurface) canvas3d.add(molecularSurfaceRepr)
if (show.gaussianSurface) canvas3d.add(gaussianSurfaceRepr)
- canvas3d.resetCamera()
+ canvas3d.requestCameraReset()
// canvas3d.setProps({ trackball: { ...canvas3d.props.trackball, spin: true } })
}
diff --git a/src/tests/browser/render-text.ts b/src/tests/browser/render-text.ts
index 692e1e4a28a299bfbf5143df4ccbd22448106936..0c11067311cc7733651a443cf00cb2921df955ed 100644
--- a/src/tests/browser/render-text.ts
+++ b/src/tests/browser/render-text.ts
@@ -74,4 +74,4 @@ function spheresRepr() {
canvas3d.add(textRepr())
canvas3d.add(spheresRepr())
-canvas3d.resetCamera()
\ No newline at end of file
+canvas3d.requestCameraReset()
\ No newline at end of file