diff --git a/package-lock.json b/package-lock.json
index 5cd5ce9e9f5b8b0c6b8e3a51e9cbd0b25dd54a4d..24f29c7ffd17e68037eca304abde828732480165 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index a376d66ec660ecd0a6d414d448da20af92c989c0..6b9d3e8cdacb2caa9d0de392f8eba63daebb36b7 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "0.5.1",
+ "version": "0.5.5",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -72,9 +72,8 @@
"@graphql-codegen/typescript-graphql-request": "^1.12.2",
"@graphql-codegen/typescript-operations": "^1.12.2",
"@types/cors": "^2.8.6",
- "@typescript-eslint/eslint-plugin": "^2.20.0",
- "@typescript-eslint/eslint-plugin-tslint": "^2.20.0",
- "@typescript-eslint/parser": "^2.20.0",
+ "@typescript-eslint/eslint-plugin": "^2.21.0",
+ "@typescript-eslint/parser": "^2.21.0",
"benchmark": "^2.1.4",
"circular-dependency-plugin": "^5.2.0",
"concurrently": "^5.1.0",
@@ -96,7 +95,7 @@
"simple-git": "^1.131.0",
"style-loader": "^1.1.3",
"ts-jest": "^25.2.1",
- "typescript": "^3.8.2",
+ "typescript": "^3.8.3",
"webpack": "^4.41.6",
"webpack-cli": "^3.3.11"
},
@@ -106,9 +105,9 @@
"@types/compression": "1.7.0",
"@types/express": "^4.17.2",
"@types/jest": "^25.1.3",
- "@types/node": "^13.7.4",
- "@types/node-fetch": "^2.5.4",
- "@types/react": "^16.9.22",
+ "@types/node": "^13.7.7",
+ "@types/node-fetch": "^2.5.5",
+ "@types/react": "^16.9.23",
"@types/react-dom": "^16.9.5",
"@types/swagger-ui-dist": "3.0.5",
"argparse": "^1.0.10",
@@ -117,10 +116,11 @@
"cors": "^2.8.5",
"express": "^4.17.1",
"graphql": "^14.6.0",
+ "immer": "^5.3.6",
"immutable": "^3.8.2",
"node-fetch": "^2.6.0",
- "react": "^16.12.0",
- "react-dom": "^16.12.0",
+ "react": "^16.13.0",
+ "react-dom": "^16.13.0",
"rxjs": "^6.5.4",
"swagger-ui-dist": "^3.25.0",
"util.promisify": "^1.0.1",
diff --git a/src/apps/basic-wrapper/helpers.ts b/src/apps/basic-wrapper/helpers.ts
index aefcb26e4fd6b4f2fdd7fe211407f549ce82e208..c26cb3eb4b274478620222f333a88f7eea3c05a2 100644
--- a/src/apps/basic-wrapper/helpers.ts
+++ b/src/apps/basic-wrapper/helpers.ts
@@ -67,7 +67,13 @@ export namespace StateHelper {
}
export function assemble(b: StateBuilder.To<PSO.Molecule.Model>, id?: string) {
- return b.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: id || 'deposited' }, { tags: 'asm' })
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: id || 'deposited' }
+ }
+ }
+ return b.apply(StateTransforms.Model.StructureFromModel, props, { tags: 'asm' })
}
export function visual(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index 79c65460b2a7fb765db156c3f5e0804b2feeb805..1d77c47c9186bf19616a3a6a9cd4c33d317ad62f 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -61,10 +61,16 @@ class BasicWrapper {
? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
: b.apply(StateTransforms.Model.TrajectoryFromPDB);
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: assemblyId || 'deposited' }
+ }
+ }
return parsed
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
.apply(StateTransforms.Model.CustomModelProperties, { autoAttach: [StripedResidues.propertyProvider.descriptor.name], properties: {} }, { ref: 'props', state: { isGhost: false } })
- .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
+ .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
}
private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
@@ -101,8 +107,15 @@ class BasicWrapper {
tree = state.build();
this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
} else {
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: assemblyId || 'deposited' }
+ }
+ }
+
tree = state.build();
- tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
+ tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
}
await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
diff --git a/src/apps/demos/lighting/index.ts b/src/apps/demos/lighting/index.ts
index f54e0eb8eea59ecec5bb3ff27ee87c3a711194e3..dab86f4637c955aee04d9b6ace4e3f36486aaeb0 100644
--- a/src/apps/demos/lighting/index.ts
+++ b/src/apps/demos/lighting/index.ts
@@ -120,9 +120,15 @@ class LightingDemo {
? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
: b.apply(StateTransforms.Model.TrajectoryFromPDB);
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: assemblyId || 'deposited' }
+ }
+ }
return parsed
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
+ .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'asm' });
}
private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
@@ -153,8 +159,14 @@ class LightingDemo {
tree = state.build();
this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
} else {
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: assemblyId || 'deposited' }
+ }
+ }
tree = state.build();
- tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
+ tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
}
await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
diff --git a/src/apps/state-docs/pd-to-md.ts b/src/apps/state-docs/pd-to-md.ts
index f0df30519f9e4e18dfd3cd60509d6b45baf244f0..f725105b4028af9d934d5361e1a20198ea15c1ca 100644
--- a/src/apps/state-docs/pd-to-md.ts
+++ b/src/apps/state-docs/pd-to-md.ts
@@ -39,7 +39,7 @@ function paramInfo(param: PD.Any, offset: number): string {
}
}
-function oToS(options: readonly (readonly [string, string])[]) {
+function oToS(options: readonly (readonly [string, string] | readonly [string, string, string])[]) {
return options.map(o => `'${o[0]}'`).join(', ');
}
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 507ef7a19c151e9e7dfbb02c55540c4fbcfd25b5..d0498beff3601b1444116c301229b81fed5da37d 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -123,18 +123,6 @@ export function printSequence(model: Model) {
console.log();
}
-export function printModRes(model: Model) {
- console.log('\nModified Residues\n=============');
- const map = model.properties.modifiedResidues.parentId;
- const { label_comp_id, _rowCount } = model.atomicHierarchy.residues;
- for (let i = 0; i < _rowCount; i++) {
- const comp_id = label_comp_id.value(i);
- if (!map.has(comp_id)) continue;
- console.log(`[${i}] ${map.get(comp_id)} -> ${comp_id}`);
- }
- console.log();
-}
-
export function printRings(structure: Structure) {
console.log('\nRings\n=============');
for (const unit of structure.units) {
@@ -221,7 +209,6 @@ async function run(frame: CifFrame, args: Args) {
if (args.rings) printRings(structure);
if (args.intraBonds) printBonds(structure, true, false);
if (args.interBonds) printBonds(structure, false, true);
- if (args.mod) printModRes(models[0]);
if (args.sec) printSecStructure(models[0]);
}
diff --git a/src/examples/proteopedia-wrapper/coloring.ts b/src/examples/proteopedia-wrapper/coloring.ts
index 0f7bc4b3a5f423f5ccabcdb4f5cb38ca521508fb..3b25496365d11cc143d1c182c1e8a273286a171b 100644
--- a/src/examples/proteopedia-wrapper/coloring.ts
+++ b/src/examples/proteopedia-wrapper/coloring.ts
@@ -96,6 +96,7 @@ export function createProteopediaCustomTheme(colors: number[]) {
const ProteopediaCustomColorThemeProvider: ColorTheme.Provider<ProteopediaCustomColorThemeParams> = {
label: 'Proteopedia Custom',
+ category: 'Custom',
factory: ProteopediaCustomColorTheme,
getParams: getChainIdColorThemeParams,
defaultValues: PD.getDefaultValues(ProteopediaCustomColorThemeParams),
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index 8611b4ba02d43c5e12770e9935159e4a7520e08f..4efdd23612fc34cc2acb51da55f333be23516716 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -7,7 +7,7 @@
import { ResidueIndex, Model } from '../../mol-model/structure';
import { BuiltInStructureRepresentationsName } from '../../mol-repr/structure/registry';
import { BuiltInColorThemeName } from '../../mol-theme/color';
-import { AminoAcidNames } from '../../mol-model/structure/model/types';
+import { PolymerType } from '../../mol-model/structure/model/types';
import { PluginContext } from '../../mol-plugin/context';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
@@ -54,15 +54,14 @@ export namespace ModelInfo {
const hetMap = new Map<string, ModelInfo['hetResidues'][0]>();
for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
- const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
- if (AminoAcidNames.has(comp_id)) continue;
- const mod_parent = model.properties.modifiedResidues.parentId.get(comp_id);
- if (mod_parent && AminoAcidNames.has(mod_parent)) continue;
+ if (model.atomicHierarchy.derived.residue.polymerType[rI] !== PolymerType.NA) continue;
const cI = chainIndex[residueOffsets[rI]];
const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
if (model.entities.data.type.value(eI) === 'water') continue;
+ const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
+
let lig = hetMap.get(comp_id);
if (!lig) {
lig = { name: comp_id, indices: [] };
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 7254ea8b8727546c2c030bd517a0879cec262d2d..2ecd40ac6a54e4d3f43cb5d3ff2785735b06b1bc 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -92,10 +92,16 @@ class MolStarProteopediaWrapper {
private structure(assemblyId: string) {
const model = this.state.build().to(StateElements.Model);
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: assemblyId || 'deposited' }
+ }
+ }
const s = model
.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 });
+ .apply(StateTransforms.Model.StructureFromModel, props, { ref: StateElements.Assembly });
s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: StateElements.Sequence });
s.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' }, { ref: StateElements.Het });
@@ -213,7 +219,13 @@ class MolStarProteopediaWrapper {
const tree = state.build();
const info = await this.doInfo(true);
const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
- tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: asmId }));
+ const props = {
+ type: {
+ name: 'assembly' as const,
+ params: { id: asmId || 'deposited' }
+ }
+ }
+ tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
await this.applyState(tree);
}
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index a00217f4b7b7aed0e509e252a7fd5ffcd6483c66..5d91550849344da4735be84e2ef6ff116d597e65 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -77,7 +77,7 @@ interface Canvas3D {
handleResize(): void
/** Focuses camera on scene's bounding sphere, centered and zoomed. */
- requestCameraReset(durationMs?: number): void
+ requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
readonly camera: Camera
readonly boundingSphere: Readonly<Sphere3D>
downloadScreenshot(): void
@@ -191,6 +191,7 @@ namespace Canvas3D {
let drawPending = false
let cameraResetRequested = false
let nextCameraResetDuration: number | undefined = void 0
+ let nextCameraResetSnapshot: Partial<Camera.Snapshot> | undefined = void 0
function getLoci(pickingId: PickingId) {
let loci: Loci = EmptyLoci
@@ -290,9 +291,15 @@ namespace Canvas3D {
function resolveCameraReset() {
if (!cameraResetRequested) return;
const { center, radius } = scene.boundingSphere;
- const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration
- camera.focus(center, radius, radius, duration);
+ if (radius > 0) {
+ const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration
+ const focus = camera.getFocus(center, radius, radius);
+ const snapshot = nextCameraResetSnapshot ? { ...focus, ...nextCameraResetSnapshot } : focus;
+ camera.setState(snapshot, duration);
+ }
+
nextCameraResetDuration = void 0;
+ nextCameraResetSnapshot = void 0;
cameraResetRequested = false;
}
@@ -388,8 +395,9 @@ namespace Canvas3D {
getLoci,
handleResize,
- requestCameraReset: (durationMs) => {
- nextCameraResetDuration = durationMs;
+ requestCameraReset: options => {
+ nextCameraResetDuration = options?.durationMs;
+ nextCameraResetSnapshot = options?.snapshot;
cameraResetRequested = true;
},
camera,
diff --git a/src/mol-geo/geometry/base.ts b/src/mol-geo/geometry/base.ts
index 5cce347e24baa25b2e09a91c197d8728f68d4834..f726d3447da2dc8c9d01cc144c0e3c452ce1f863 100644
--- a/src/mol-geo/geometry/base.ts
+++ b/src/mol-geo/geometry/base.ts
@@ -28,8 +28,8 @@ export const VisualQualityInfo = {
'lowest': {},
}
export type VisualQuality = keyof typeof VisualQualityInfo
-export const VisualQualityNames = Object.keys(VisualQualityInfo)
-export const VisualQualityOptions = VisualQualityNames.map(n => [n, n] as [VisualQuality, string])
+export const VisualQualityNames = Object.keys(VisualQualityInfo) as VisualQuality[]
+export const VisualQualityOptions = PD.arrayToOptions(VisualQualityNames)
//
diff --git a/src/mol-math/geometry/_spec/spacegroup.spec.ts b/src/mol-math/geometry/_spec/spacegroup.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7783f936c638b226e08433d1a85a8fad57a91696
--- /dev/null
+++ b/src/mol-math/geometry/_spec/spacegroup.spec.ts
@@ -0,0 +1,36 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Spacegroup, SpacegroupCell } from '../spacegroup/construction';
+import { Vec3 } from '../../linear-algebra';
+
+function getSpacegroup(name: string) {
+ const size = Vec3.create(1, 1, 1)
+ const anglesInRadians = Vec3.create(Math.PI / 2, Math.PI / 2, Math.PI / 2)
+ const cell = SpacegroupCell.create(name, size, anglesInRadians)
+ return Spacegroup.create(cell)
+}
+
+function checkOperatorsXyz(name: string, expected: string[]) {
+ const spacegroup = getSpacegroup(name)
+ for (let i = 0, il = spacegroup.operators.length; i < il; ++i) {
+ const op = spacegroup.operators[i]
+ const actual = Spacegroup.getOperatorXyz(op)
+ expect(actual).toBe(expected[i])
+ }
+}
+
+describe('Spacegroup', () => {
+ it('operators xyz', () => {
+ checkOperatorsXyz('P 1', ['X,Y,Z'])
+ checkOperatorsXyz('P -1', ['X,Y,Z', '-X,-Y,-Z'])
+ checkOperatorsXyz('P 1 21 1', ['X,Y,Z', '-X,1/2+Y,-Z'])
+ checkOperatorsXyz('P 1 21/m 1', ['X,Y,Z', '-X,1/2+Y,-Z', '-X,-Y,-Z', 'X,1/2-Y,Z'])
+ checkOperatorsXyz('P 41', ['X,Y,Z', '-X,-Y,1/2+Z', '-Y,X,1/4+Z', 'Y,-X,3/4+Z'])
+ checkOperatorsXyz('P 41 21 2', ['X,Y,Z', '-X,-Y,1/2+Z', '1/2-Y,1/2+X,1/4+Z', '1/2+Y,1/2-X,3/4+Z', '1/2-X,1/2+Y,1/4-Z', '1/2+X,1/2-Y,3/4-Z', 'Y,X,-Z', '-Y,-X,1/2-Z'])
+ checkOperatorsXyz('P 3', ['X,Y,Z', '-Y,X-Y,Z', 'Y-X,-X,Z'])
+ });
+})
diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index 9bc4d9d6cee4cf8879c43ae978b66cbfa45a9028..944c12cf3352af1d42f0c59472d15bade372cd87 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/src/mol-math/geometry/spacegroup/construction.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>
@@ -145,6 +145,54 @@ namespace Spacegroup {
const r3 = TransformData[ids[2]];
return Mat4.ofRows([r1, r2, r3, [0, 0, 0, 1]]);
}
+
+ export function getOperatorXyz(op: Mat4) {
+ return [
+ formatElement(getRotation(op[0], op[4], op[8]), getShift(op[12])),
+ formatElement(getRotation(op[1], op[5], op[9]), getShift(op[13])),
+ formatElement(getRotation(op[2], op[6], op[10]), getShift(op[14]))
+ ].join(',')
+ }
+
+ function getRotation(x: number, y: number, z: number) {
+ let r: string[] = []
+ if (x > 0) r.push('+X')
+ else if (x < 0) r.push('-X')
+ if (y > 0) r.push('+Y')
+ else if (y < 0) r.push('-Y')
+ if (z > 0) r.push('+Z')
+ else if (z < 0) r.push('-Z')
+
+ if (r.length === 1) {
+ return r[0].charAt(0) === '+' ? r[0].substr(1) : r[0]
+ }
+ if (r.length === 2) {
+ const s0 = r[0].charAt(0)
+ const s1 = r[1].charAt(0)
+ if (s0 === '+') return `${r[0].substr(1)}${r[1]}`
+ if (s1 === '+') return `${r[1].substr(1)}${r[0]}`
+ }
+ throw new Error(`unknown rotation '${r}', ${x} ${y} ${z}`)
+ }
+
+ function getShift(s: number) {
+ switch (s) {
+ case 1/2: return '1/2'
+ case 1/4: return '1/4'
+ case 3/4: return '3/4'
+ case 1/3: return '1/3'
+ case 2/3: return '2/3'
+ case 1/6: return '1/6'
+ case 5/6: return '5/6'
+ }
+ return ''
+ }
+
+ function formatElement(rotation: string, shift: string) {
+ if (shift === '') return rotation
+ if (rotation.length > 2) return `${rotation}+${shift}`
+ return rotation.charAt(0) === '-' ? `${shift}${rotation}` : `${shift}+${rotation}`
+ }
}
export { Spacegroup, SpacegroupCell }
\ 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
index cf41cd1866c7c82aef5f6b339cdf6d5f28a8e402..554c6eea02fa352e9ec5962db71e8ab0b42b7d3c 100644
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -45,7 +45,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
}
const coarse = EmptyCoarse;
- const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy, properties.modifiedResidues.parentId)
+ const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy)
const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence)
const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
@@ -80,7 +80,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
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 sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy)
const atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence)
const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
diff --git a/src/mol-model-formats/structure/basic/properties.ts b/src/mol-model-formats/structure/basic/properties.ts
index 45ecd6e5d17ee6f0d4e13803c91981b6cf0369b0..743c57c7f71b2565896b6a587cfecc9840afcbb0 100644
--- a/src/mol-model-formats/structure/basic/properties.ts
+++ b/src/mol-model-formats/structure/basic/properties.ts
@@ -6,30 +6,13 @@
*/
import { Model } from '../../../mol-model/structure/model/model';
-import { ChemicalComponent, MissingResidue } from '../../../mol-model/structure/model/properties/common';
+import { ChemicalComponent, MissingResidue, StructAsym } 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) => {
@@ -124,11 +107,43 @@ const getUniqueComponentNames = memoize1((data: BasicData) => {
return uniqueNames
})
+
+function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap'] {
+ const map = new Map<string, StructAsym>();
+
+ const { label_asym_id, auth_asym_id, label_entity_id } = data.atom_site
+ for (let i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+ const id = label_asym_id.value(i)
+ if (!map.has(id)) {
+ map.set(id, {
+ id,
+ auth_id: auth_asym_id.value(i),
+ entity_id: label_entity_id.value(i)
+ })
+ }
+ }
+
+ if (data.struct_asym._rowCount > 0) {
+ const { id, entity_id } = data.struct_asym
+ for (let i = 0, il = id.rowCount; i < il; ++i) {
+ const _id = id.value(i)
+ if (!map.has(_id)) {
+ map.set(_id, {
+ id: _id,
+ auth_id: '',
+ entity_id: entity_id.value(i)
+ })
+ }
+ }
+ }
+ return map
+}
+
export function getProperties(data: BasicData): Model['properties'] {
return {
- modifiedResidues: getModifiedResidueNameMap(data),
missingResidues: getMissingResidues(data),
chemicalComponentMap: getChemicalComponentMap(data),
- saccharideComponentMap: getSaccharideComponentMap(data)
+ saccharideComponentMap: getSaccharideComponentMap(data),
+ structAsymMap: getStructAsymMap(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
index dea7e328e8a9db387542f49ee8c057e7fb9f73aa..670432bc674935ecfb1cb8a1acdf473f4c049417 100644
--- a/src/mol-model-formats/structure/basic/schema.ts
+++ b/src/mol-model-formats/structure/basic/schema.ts
@@ -8,7 +8,6 @@ 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']>
@@ -22,7 +21,6 @@ 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']>
@@ -41,7 +39,6 @@ export const BasicSchema = {
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,
@@ -61,7 +58,6 @@ export interface BasicData {
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
diff --git a/src/mol-model-formats/structure/basic/sequence.ts b/src/mol-model-formats/structure/basic/sequence.ts
index d73a6f84a50bf48ff02504a0002813012f49d417..8a3328d52ddfdb7e2d55876c72aa52c6fb84ffd8 100644
--- a/src/mol-model-formats/structure/basic/sequence.ts
+++ b/src/mol-model-formats/structure/basic/sequence.ts
@@ -13,9 +13,9 @@ import { Sequence } from '../../../mol-model/sequence';
import { CoarseHierarchy } from '../../../mol-model/structure/model/properties/coarse';
import { BasicData } from './schema';
-export function getSequence(data: BasicData, entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy, modResMap: ReadonlyMap<string, string>): StructureSequence {
+export function getSequence(data: BasicData, entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy): StructureSequence {
if (!data.entity_poly_seq || !data.entity_poly_seq._rowCount) {
- return StructureSequence.fromHierarchy(entities, atomicHierarchy, coarseHierarchy, modResMap);
+ return StructureSequence.fromHierarchy(entities, atomicHierarchy, coarseHierarchy);
}
const { entity_id, num, mon_id } = data.entity_poly_seq;
@@ -37,7 +37,7 @@ export function getSequence(data: BasicData, entities: Entities, atomicHierarchy
byEntityKey[entityKey] = {
entityId: id,
- sequence: Sequence.ofResidueNames(compId, seqId, modResMap)
+ sequence: Sequence.ofResidueNames(compId, seqId)
};
sequences.push(byEntityKey[entityKey]);
diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index 483ac6e95369b33506deee7132a663104a8a7b91..7dbbfa176c7bcc7eb0907b04015d539ee67c13ff 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -6,7 +6,7 @@
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 { WaterNames, PolymerNames } from '../../../mol-model/structure/model/types';
import { SetUtils } from '../../../mol-util/set';
import { BasicSchema } from '../basic/schema';
@@ -77,12 +77,14 @@ export class ComponentBuilder {
private ids: string[] = []
private names: string[] = []
private types: mmCIF_Schema['chem_comp']['type']['T'][] = []
+ private mon_nstd_flags: mmCIF_Schema['chem_comp']['mon_nstd_flag']['T'][] = []
private set(c: Component) {
this.comps.set(c.id, c)
this.ids.push(c.id)
this.names.push(c.name)
this.types.push(c.type)
+ this.mon_nstd_flags.push(PolymerNames.has(c.id) ? 'y' : 'n')
}
private getAtomIds(index: number) {
@@ -141,6 +143,7 @@ export class ComponentBuilder {
id: Column.ofStringArray(this.ids),
name: Column.ofStringArray(this.names),
type: Column.ofStringAliasArray(this.types),
+ mon_nstd_flag: Column.ofStringAliasArray(this.mon_nstd_flags),
}, this.ids.length)
}
diff --git a/src/mol-model-formats/structure/common/property.ts b/src/mol-model-formats/structure/common/property.ts
index 44bae5f2f3e0e1642a01a9fc10b3a302dde39f69..873e8bd5848a0bf1edd36a69f9001d4555c293fb 100644
--- a/src/mol-model-formats/structure/common/property.ts
+++ b/src/mol-model-formats/structure/common/property.ts
@@ -14,6 +14,10 @@ class FormatRegistry<T> {
this.map.set(kind, obtain)
}
+ remove(kind: ModelFormat['kind']) {
+ this.map.delete(kind)
+ }
+
get(kind: ModelFormat['kind']) {
return this.map.get(kind)
}
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index d52f7898ce97b0431e80ea59a6e726efa58e3660..ae7c3deb8147f42d7a2f660493581d921cc68b31 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -17,7 +17,6 @@ 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;
@@ -65,14 +64,6 @@ function structConnFromMmcif(model: Model) {
}
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 }
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index 05e0f8592689d7a48a0d44b3cac74e06f83284d5..708ff61e5a57349b16f54777780ad08075cf8f03 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.getEntityTable(),
- chem_comp: componentBuilder.getChemCompTable(),
+ entity: CifCategory.ofTable('entity', entityBuilder.getEntityTable()),
+ chem_comp: CifCategory.ofTable('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/pair-restraints/predicted-contacts.ts b/src/mol-model-formats/structure/property/pair-restraints/predicted-contacts.ts
deleted file mode 100644
index d736eabdf2c073838585736ba735813d76143d75..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/property/pair-restraints/predicted-contacts.ts
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-// TODO
-// ihm_predicted_contact_restraint: {
-// id: int,
-// entity_id_1: str,
-// entity_id_2: str,
-// asym_id_1: str,
-// asym_id_2: str,
-// comp_id_1: str,
-// comp_id_2: str,
-// seq_id_1: int,
-// seq_id_2: int,
-// atom_id_1: str,
-// atom_id_2: str,
-// distance_upper_limit: float,
-// probability: float,
-// restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
-// model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
-// dataset_list_id: int,
-// software_id: int,
-// },
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index 3dea414a939e75449f7438195624b5387c5b300f..4684a20e428f90b48a8ec7f6b404faf13f19e911 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -99,6 +99,7 @@ namespace CustomElementProperty {
return {
label: modelProperty.label,
+ category: 'Custom',
factory: Coloring,
getParams: () => ({}),
defaultValues: {},
diff --git a/src/mol-model-props/computed/accessible-surface-area.ts b/src/mol-model-props/computed/accessible-surface-area.ts
index 292ab54c6aef5fb52eed0c9259c4bec15fc9df91..b3867ca743589cb6f1fd8d90be17510dce2e1715 100644
--- a/src/mol-model-props/computed/accessible-surface-area.ts
+++ b/src/mol-model-props/computed/accessible-surface-area.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 Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -7,9 +7,12 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { ShrakeRupleyComputationParams, AccessibleSurfaceArea } from './accessible-surface-area/shrake-rupley';
-import { Structure, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Structure, CustomPropertyDescriptor, Unit } from '../../mol-model/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
+import { CustomPropSymbol } from '../../mol-script/language/symbol';
+import Type from '../../mol-script/language/type';
export const AccessibleSurfaceAreaParams = {
...ShrakeRupleyComputationParams
@@ -17,13 +20,33 @@ export const AccessibleSurfaceAreaParams = {
export type AccessibleSurfaceAreaParams = typeof AccessibleSurfaceAreaParams
export type AccessibleSurfaceAreaProps = PD.Values<AccessibleSurfaceAreaParams>
+export const AccessibleSurfaceAreaSymbols = {
+ isBuried: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'accessible-surface-area.is-buried', Type.Bool),
+ ctx => {
+ if (!Unit.isAtomic(ctx.element.unit)) return false
+ const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(ctx.element.structure).value
+ if (!accessibleSurfaceArea) return false
+ return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === AccessibleSurfaceArea.Flag.Buried
+ }
+ ),
+ isAccessible: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'accessible-surface-area.is-accessible', Type.Bool),
+ ctx => {
+ if (!Unit.isAtomic(ctx.element.unit)) return false
+ const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(ctx.element.structure).value
+ if (!accessibleSurfaceArea) return false
+ return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === AccessibleSurfaceArea.Flag.Accessible
+ }
+ ),
+}
+
export type AccessibleSurfaceAreaValue = AccessibleSurfaceArea
export const AccessibleSurfaceAreaProvider: CustomStructureProperty.Provider<AccessibleSurfaceAreaParams, AccessibleSurfaceAreaValue> = CustomStructureProperty.createProvider({
label: 'Accessible Surface Area',
descriptor: CustomPropertyDescriptor({
name: 'molstar_accessible_surface_area',
- // TODO `cifExport` and `symbol`
+ symbols: AccessibleSurfaceAreaSymbols,
+ // TODO `cifExport`
}),
type: 'root',
defaultParams: AccessibleSurfaceAreaParams,
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley.ts
index 6212d89f131d9826f87acb25af0a7b741c788223..b7b116061901f1357ffc613bcae58cb7070ac922 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley.ts
@@ -9,7 +9,7 @@ import { Task, RuntimeContext } from '../../../mol-task';
// import { BitFlags } from '../../../mol-util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition'
import { Vec3 } from '../../../mol-math/linear-algebra';
-import { Structure } from '../../../mol-model/structure';
+import { Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
import { assignRadiusForHeavyAtoms } from './shrake-rupley/radii';
import { ShrakeRupleyContext, VdWLookup, MaxAsa, DefaultMaxAsa } from './shrake-rupley/common';
import { computeArea } from './shrake-rupley/area';
@@ -86,19 +86,35 @@ namespace AccessibleSurfaceArea {
return points;
}
- // export namespace SolventAccessibility {
- // export const is: (t: number, f: Flag) => boolean = BitFlags.has
- // export const create: (f: Flag) => number = BitFlags.create
- // export const enum Flag {
- // _ = 0x0,
- // BURIED = 0x1,
- // ACCESSIBLE = 0x2
- // }
- // }
+ export const enum Flag {
+ NA = 0x0,
+ Buried = 0x1,
+ Accessible = 0x2
+ }
/** Get relative area for a given component id */
export function normalize(compId: string, asa: number) {
const maxAsa = MaxAsa[compId] || DefaultMaxAsa;
return asa / maxAsa
}
+
+ export function getValue(location: StructureElement.Location, accessibleSurfaceArea: AccessibleSurfaceArea) {
+ const { getSerialIndex } = location.structure.root.serialMapping
+ const { area, serialResidueIndex } = accessibleSurfaceArea
+ const rSI = serialResidueIndex[getSerialIndex(location.unit, location.element)]
+ if (rSI === -1) return -1
+ return area[rSI]
+ }
+
+ export function getNormalizedValue(location: StructureElement.Location, accessibleSurfaceArea: AccessibleSurfaceArea) {
+ const value = getValue(location, accessibleSurfaceArea)
+ return value === -1 ? -1 : normalize(StructureProperties.residue.label_comp_id(location), value)
+ }
+
+ export function getFlag(location: StructureElement.Location, accessibleSurfaceArea: AccessibleSurfaceArea) {
+ const value = getNormalizedValue(location, accessibleSurfaceArea)
+ return value === -1 ? Flag.NA :
+ value < 0.16 ? Flag.Buried :
+ Flag.Accessible
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-props/computed/interactions/interactions.ts b/src/mol-model-props/computed/interactions/interactions.ts
index 881163733e3549460322b933d2297b734621be20..85411d94db757a29b5eaedb7a75b81f5eccb07f3 100644
--- a/src/mol-model-props/computed/interactions/interactions.ts
+++ b/src/mol-model-props/computed/interactions/interactions.ts
@@ -38,8 +38,9 @@ interface Interactions {
}
namespace Interactions {
+ type StructureInteractions = { readonly structure: Structure, readonly interactions: Interactions }
+
export interface Element {
- structure: Structure,
unitA: Unit
/** Index into features of unitA */
indexA: Features.FeatureIndex
@@ -47,11 +48,12 @@ namespace Interactions {
/** Index into features of unitB */
indexB: Features.FeatureIndex
}
- export interface Location extends DataLocation<Interactions, Element> {}
+
+ export interface Location extends DataLocation<StructureInteractions, Element> {}
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 });
+ return DataLocation('interactions', { structure, interactions },
+ { unitA: unitA as any, indexA: indexA as any, unitB: unitB as any, indexB: indexB as any });
}
export function isLocation(x: any): x is Location {
@@ -60,7 +62,8 @@ namespace Interactions {
export function areLocationsEqual(locA: Location, locB: Location) {
return (
- locA.data === locB.data &&
+ locA.data.structure === locB.data.structure &&
+ locA.data.interactions === locB.data.interactions &&
locA.element.indexA === locB.element.indexA &&
locA.element.indexB === locB.element.indexB &&
locA.element.unitA === locB.element.unitA &&
@@ -82,10 +85,9 @@ namespace Interactions {
}
export function locationLabel(location: Location): string {
- return _label(location.data, location.element)
+ return _label(location.data.interactions, location.element)
}
- type StructureInteractions = { readonly structure: Structure, readonly interactions: Interactions }
export interface Loci extends DataLoci<StructureInteractions, Element> { }
export function Loci(structure: Structure, interactions: Interactions, elements: ReadonlyArray<Element>): Loci {
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 a13a95720688fd97ff2f042fa9ad144fb688971e..1895d5e5536bcc212138f0ec3fda1c01c2ae6d68 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
@@ -101,8 +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, [
- { 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 },
+ { unitA: c.unitA, indexA: c.indexA, unitB: c.unitB, indexB: c.indexB },
+ { unitA: c.unitB, indexA: c.indexB, unitB: c.unitA, indexB: c.indexA },
])
}
return EmptyLoci
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 66a03f6ac7ee24d281c2251051e40bbf4e9a22ba..3e0b864a7bfb1718587e070f2b68718fbda39d95 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
@@ -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, [
- { structure, unitA: unit, indexA: a[groupId], unitB: unit, indexB: b[groupId] },
- { structure, unitA: unit, indexA: b[groupId], unitB: unit, indexB: a[groupId] },
+ { unitA: unit, indexA: a[groupId], unitB: unit, indexB: b[groupId] },
+ { unitA: unit, indexA: b[groupId], unitB: unit, indexB: a[groupId] },
])
}
return EmptyLoci
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index d80c58b383b9a8725daed90eb9632203986e2f17..5a373f6d0334ee5065675fa655cb6809c7e1ecd6 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.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 { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
import { DSSPComputationParams, DSSPComputationProps, computeUnitDSSP } from './secondary-structure/dssp';
import { SecondaryStructure } from '../../mol-model/structure/model/properties/seconday-structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -13,9 +13,10 @@ 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';
+import { CustomPropertyDescriptor } from '../../mol-model/structure/common/custom-property';
function getSecondaryStructureParams(data?: Structure) {
- let defaultType = 'mmcif' as 'mmcif' | 'dssp'
+ let defaultType = 'model' as 'model' | 'dssp'
if (data) {
defaultType = 'dssp'
for (let i = 0, il = data.models.length; i < il; ++i) {
@@ -27,7 +28,7 @@ function getSecondaryStructureParams(data?: Structure) {
) {
// if there is any secondary structure definition given or if there is
// an archival model, don't calculate dssp by default
- defaultType = 'mmcif'
+ defaultType = 'model'
break
}
}
@@ -35,9 +36,9 @@ function getSecondaryStructureParams(data?: Structure) {
}
return {
type: PD.MappedStatic(defaultType, {
- 'mmcif': PD.EmptyGroup({ label: 'mmCIF' }),
+ 'model': PD.EmptyGroup({ label: 'Model' }),
'dssp': PD.Group(DSSPComputationParams, { label: 'DSSP', isFlat: true })
- }, { options: [['mmcif', 'mmCIF'], ['dssp', 'DSSP']] })
+ }, { options: [['model', 'Model'], ['dssp', 'DSSP']] })
}
}
@@ -45,6 +46,7 @@ export const SecondaryStructureParams = getSecondaryStructureParams()
export type SecondaryStructureParams = typeof SecondaryStructureParams
export type SecondaryStructureProps = PD.Values<SecondaryStructureParams>
+/** Maps `unit.id` to `SecondaryStructure` */
export type SecondaryStructureValue = Map<number, SecondaryStructure>
export const SecondaryStructureProvider: CustomStructureProperty.Provider<SecondaryStructureParams, SecondaryStructureValue> = CustomStructureProperty.createProvider({
@@ -61,7 +63,7 @@ export const SecondaryStructureProvider: CustomStructureProperty.Provider<Second
const p = { ...PD.getDefaultValues(SecondaryStructureParams), ...props }
switch (p.type.name) {
case 'dssp': return await computeDssp(data, p.type.params)
- case 'mmcif': return await computeMmcif(data)
+ case 'model': return await computeModel(data)
}
}
})
@@ -80,7 +82,7 @@ async function computeDssp(structure: Structure, props: DSSPComputationProps): P
return map
}
-async function computeMmcif(structure: Structure): Promise<SecondaryStructureValue> {
+async function computeModel(structure: Structure): Promise<SecondaryStructureValue> {
const map = new Map<number, SecondaryStructure>()
for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
const u = structure.unitSymmetryGroups[i].units[0]
diff --git a/src/mol-model-props/computed/themes/accessible-surface-area.ts b/src/mol-model-props/computed/themes/accessible-surface-area.ts
index fe2a60134c831deb06d546d4bec2c49f7ec8252c..5de7df9837f50baec785434be678d0ebf43c8cec 100644
--- a/src/mol-model-props/computed/themes/accessible-surface-area.ts
+++ b/src/mol-model-props/computed/themes/accessible-surface-area.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 Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,7 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition'
import { Color, ColorScale } from '../../../mol-util/color'
import { ThemeDataContext } from '../../../mol-theme/theme'
import { ColorTheme, LocationColor } from '../../../mol-theme/color'
-import { StructureProperties, StructureElement, Unit } from '../../../mol-model/structure'
+import { StructureElement, Unit } from '../../../mol-model/structure'
import { AccessibleSurfaceAreaProvider } from '../accessible-surface-area'
import { AccessibleSurfaceArea } from '../accessible-surface-area/shrake-rupley'
import { CustomProperty } from '../../common/custom-property'
@@ -36,18 +36,16 @@ export function AccessibleSurfaceAreaColorTheme(ctx: ThemeDataContext, props: PD
domain: [0.0, 1.0]
})
- const { label_comp_id } = StructureProperties.residue
const accessibleSurfaceArea = ctx.structure && AccessibleSurfaceAreaProvider.get(ctx.structure)
const contextHash = accessibleSurfaceArea?.version
if (accessibleSurfaceArea?.value && ctx.structure) {
- const { getSerialIndex } = ctx.structure.root.serialMapping
- const { area, serialResidueIndex } = accessibleSurfaceArea.value
+ const asa = accessibleSurfaceArea.value
color = (location: Location): Color => {
if (StructureElement.Location.is(location) && Unit.isAtomic(location.unit)) {
- const rSI = serialResidueIndex[getSerialIndex(location.unit, location.element)]
- return rSI === -1 ? DefaultColor : scale.color(AccessibleSurfaceArea.normalize(label_comp_id(location), area[rSI]))
+ const value = AccessibleSurfaceArea.getNormalizedValue(location, asa)
+ return value === -1 ? DefaultColor : scale.color(value)
}
return DefaultColor
}
@@ -68,6 +66,7 @@ export function AccessibleSurfaceAreaColorTheme(ctx: ThemeDataContext, props: PD
export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<AccessibleSurfaceAreaColorThemeParams> = {
label: 'Accessible Surface Area',
+ category: ColorTheme.Category.Residue,
factory: AccessibleSurfaceAreaColorTheme,
getParams: getAccessibleSurfaceAreaColorThemeParams,
defaultValues: PD.getDefaultValues(AccessibleSurfaceAreaColorThemeParams),
diff --git a/src/mol-model-props/computed/themes/interaction-type.ts b/src/mol-model-props/computed/themes/interaction-type.ts
index 32e0a9174c3494f48f07bf930b5cdb824d6d4329..70c88fd04979d9616f22bfd086f191b9a65c56a4 100644
--- a/src/mol-model-props/computed/themes/interaction-type.ts
+++ b/src/mol-model-props/computed/themes/interaction-type.ts
@@ -78,7 +78,7 @@ export function InteractionTypeColorTheme(ctx: ThemeDataContext, props: PD.Value
if (interactions && interactions.value) {
color = (location: Location) => {
if (Interactions.isLocation(location)) {
- const { unitsContacts, contacts } = location.data
+ const { unitsContacts, contacts } = location.data.interactions
const { unitA, unitB, indexA, indexB } = location.element
if (unitA === unitB) {
const links = unitsContacts.get(unitA.id)
@@ -108,6 +108,7 @@ export function InteractionTypeColorTheme(ctx: ThemeDataContext, props: PD.Value
export const InteractionTypeColorThemeProvider: ColorTheme.Provider<InteractionTypeColorThemeParams> = {
label: 'Interaction Type',
+ category: ColorTheme.Category.Misc,
factory: InteractionTypeColorTheme,
getParams: getInteractionTypeColorThemeParams,
defaultValues: PD.getDefaultValues(InteractionTypeColorThemeParams),
diff --git a/src/mol-theme/color/cross-link.ts b/src/mol-model-props/integrative/cross-link-restraint/color.ts
similarity index 51%
rename from src/mol-theme/color/cross-link.ts
rename to src/mol-model-props/integrative/cross-link-restraint/color.ts
index d744e44b4cc9f22126a9c018173b25d1a09f8fbd..0ff69cd16f2a016ca9907c76aa0ab662570255e3 100644
--- a/src/mol-theme/color/cross-link.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/color.ts
@@ -1,23 +1,23 @@
/**
- * 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>
*/
-import { Bond } from '../../mol-model/structure';
-import { Color, ColorScale } from '../../mol-util/color';
-import { Location } from '../../mol-model/location';
-import { ColorTheme, LocationColor } from '../color';
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { ParamDefinition as PD } from '../../mol-util/param-definition'
-import { ThemeDataContext } from '../../mol-theme/theme';
-import { ColorListName, ColorListOptionsScale } from '../../mol-util/color/lists';
+import { Color, ColorScale } from '../../../mol-util/color';
+import { Location } from '../../../mol-model/location';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition'
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ColorListName, ColorListOptionsScale } from '../../../mol-util/color/lists';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { CustomProperty } from '../../common/custom-property';
+import { CrossLinkRestraintProvider, CrossLinkRestraint } from './property';
const DefaultColor = Color(0xCCCCCC)
-const Description = 'Colors cross-links by the deviation of the observed distance versus the modeled distance (e.g. `ihm_cross_link_restraint.distance_threshold`).'
+const Description = 'Colors cross-links by the deviation of the observed distance versus the modeled distance (e.g. modeled / `ihm_cross_link_restraint.distance_threshold`).'
export const CrossLinkColorThemeParams = {
- domain: PD.Interval([-10, 10]),
+ domain: PD.Interval([0.5, 1.5], { step: 0.01 }),
list: PD.ColorList<ColorListName>('red-grey', ColorListOptionsScale),
}
export type CrossLinkColorThemeParams = typeof CrossLinkColorThemeParams
@@ -25,19 +25,13 @@ export function getCrossLinkColorThemeParams(ctx: ThemeDataContext) {
return CrossLinkColorThemeParams // TODO return copy
}
-const distVecA = Vec3.zero(), distVecB = Vec3.zero()
-function linkDistance(link: Bond.Location) {
- link.aUnit.conformation.position(link.aUnit.elements[link.aIndex], distVecA)
- link.bUnit.conformation.position(link.bUnit.elements[link.bIndex], distVecB)
- return Vec3.distance(distVecA, distVecB)
-}
-
export function CrossLinkColorTheme(ctx: ThemeDataContext, props: PD.Values<CrossLinkColorThemeParams>): ColorTheme<CrossLinkColorThemeParams> {
let color: LocationColor
let scale: ColorScale | undefined = undefined
- if (ctx.structure) {
- const crosslinks = ctx.structure.crossLinkRestraints
+ const crossLinkRestraints = ctx.structure && CrossLinkRestraintProvider.get(ctx.structure).value
+
+ if (crossLinkRestraints) {
scale = ColorScale.create({
domain: props.domain,
listOrName: props.list
@@ -45,10 +39,10 @@ export function CrossLinkColorTheme(ctx: ThemeDataContext, props: PD.Values<Cros
const scaleColor = scale.color
color = (location: Location): Color => {
- if (Bond.isLocation(location)) {
- const pairs = crosslinks.getPairs(location.aIndex, location.aUnit, location.bIndex, location.bUnit)
- if (pairs) {
- return scaleColor(linkDistance(location) - pairs[0].distanceThreshold)
+ if (CrossLinkRestraint.isLocation(location)) {
+ const pair = crossLinkRestraints.pairs[location.element]
+ if (pair) {
+ return scaleColor(CrossLinkRestraint.distance(pair) / pair.distanceThreshold)
}
}
return DefaultColor
@@ -69,8 +63,12 @@ export function CrossLinkColorTheme(ctx: ThemeDataContext, props: PD.Values<Cros
export const CrossLinkColorThemeProvider: ColorTheme.Provider<CrossLinkColorThemeParams> = {
label: 'Cross Link',
+ category: ColorTheme.Category.Misc,
factory: CrossLinkColorTheme,
getParams: getCrossLinkColorThemeParams,
defaultValues: PD.getDefaultValues(CrossLinkColorThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.crossLinkRestraints.count > 0
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && CrossLinkRestraint.isApplicable(ctx.structure),
+ ensureCustomProperties: (ctx: CustomProperty.Context, data: ThemeDataContext) => {
+ return data.structure ? CrossLinkRestraintProvider.attach(ctx, data.structure) : Promise.resolve()
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/property/pair-restraints/cross-links.ts b/src/mol-model-props/integrative/cross-link-restraint/format.ts
similarity index 89%
rename from src/mol-model-formats/structure/property/pair-restraints/cross-links.ts
rename to src/mol-model-props/integrative/cross-link-restraint/format.ts
index 484645a3a921c46bc2aa3f63aa26766043b3569d..a4e9c0c738a9aaaace9628f3fcb4497e54892b43 100644
--- a/src/mol-model-formats/structure/property/pair-restraints/cross-links.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/format.ts
@@ -4,12 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-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 { Unit, CustomPropertyDescriptor } from '../../../../mol-model/structure';
-import { ElementIndex } from '../../../../mol-model/structure/model/indexing';
-import { FormatPropertyProvider } from '../../common/property';
+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 { Unit, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { ElementIndex } from '../../../mol-model/structure/model/indexing';
+import { FormatPropertyProvider } from '../../../mol-model-formats/structure/common/property';
export { ModelCrossLinkRestraint }
diff --git a/src/mol-model-props/integrative/cross-link-restraint/property.ts b/src/mol-model-props/integrative/cross-link-restraint/property.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5deb93896a949af60ea84b5774a24e7ccb183bb4
--- /dev/null
+++ b/src/mol-model-props/integrative/cross-link-restraint/property.ts
@@ -0,0 +1,221 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ModelCrossLinkRestraint } from './format';
+import { Unit, StructureElement, Structure, CustomPropertyDescriptor, Bond} from '../../../mol-model/structure';
+import { PairRestraints, PairRestraint } from '../pair-restraints';
+import { CustomStructureProperty } from '../../common/custom-structure-property';
+import { CustomProperty } from '../../common/custom-property';
+import { DataLocation } from '../../../mol-model/location';
+import { DataLoci } from '../../../mol-model/loci';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
+import { bondLabel } from '../../../mol-theme/label';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+
+export type CrossLinkRestraintValue = PairRestraints<CrossLinkRestraint>
+
+export const CrossLinkRestraintProvider: CustomStructureProperty.Provider<{}, CrossLinkRestraintValue> = CustomStructureProperty.createProvider({
+ label: 'Cross Link Restraint',
+ descriptor: CustomPropertyDescriptor({
+ name: 'integrative-cross-link-restraint',
+ // TODO `cifExport` and `symbol`
+ }),
+ type: 'local',
+ defaultParams: {},
+ getParams: (data: Structure) => ({}),
+ isApplicable: (data: Structure) => data.models.some(m => !!ModelCrossLinkRestraint.Provider.get(m)),
+ obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<{}>) => {
+ return extractCrossLinkRestraints(data)
+ }
+})
+
+export { CrossLinkRestraint }
+
+interface CrossLinkRestraint extends PairRestraint {
+ readonly restraintType: 'harmonic' | 'upper bound' | 'lower bound'
+ readonly distanceThreshold: number
+ readonly psi: number
+ readonly sigma1: number
+ readonly sigma2: number
+}
+
+namespace CrossLinkRestraint {
+ export enum Tag {
+ CrossLinkRestraint = 'cross-link-restraint'
+ }
+
+ export function isApplicable(structure: Structure) {
+ return structure.models.some(m => !!ModelCrossLinkRestraint.Provider.get(m))
+ }
+
+ const distVecA = Vec3(), distVecB = Vec3()
+ export function distance(pair: CrossLinkRestraint) {
+ pair.unitA.conformation.position(pair.unitA.elements[pair.indexA], distVecA)
+ pair.unitB.conformation.position(pair.unitB.elements[pair.indexB], distVecB)
+ return Vec3.distance(distVecA, distVecB)
+ }
+
+ type StructureCrossLinkRestraints = { readonly structure: Structure, readonly crossLinkRestraints: CrossLinkRestraintValue }
+
+ export type Element = number
+ export interface Location extends DataLocation<StructureCrossLinkRestraints, Element> {}
+
+ export function Location(crossLinkRestraints: CrossLinkRestraintValue, structure: Structure, index?: number): Location {
+ return DataLocation('cross-link-restraints', { structure, crossLinkRestraints }, index as any);
+ }
+
+ export function isLocation(x: any): x is Location {
+ return !!x && x.kind === 'data-location' && x.tag === 'cross-link-restraints';
+ }
+
+ export function areLocationsEqual(locA: Location, locB: Location) {
+ return (
+ locA.data.structure === locB.data.structure &&
+ locA.data.crossLinkRestraints === locB.data.crossLinkRestraints &&
+ locA.element === locB.element
+ )
+ }
+
+ function _label(crossLinkRestraints: CrossLinkRestraintValue, element: Element): string {
+ const p = crossLinkRestraints.pairs[element]
+ return `Cross Link Restraint | Type: ${p.restraintType} | Threshold: ${p.distanceThreshold} \u212B | Psi: ${p.psi} | Sigma 1: ${p.sigma1} | Sigma 2: ${p.sigma2} | Distance: ${distance(p).toFixed(2)} \u212B`
+ }
+
+ export function locationLabel(location: Location): string {
+ return _label(location.data.crossLinkRestraints, location.element)
+ }
+
+ export interface Loci extends DataLoci<StructureCrossLinkRestraints, Element> { }
+
+ export function Loci(structure: Structure, crossLinkRestraints: CrossLinkRestraintValue, elements: ReadonlyArray<Element>): Loci {
+ return DataLoci('cross-link-restraints', { structure, crossLinkRestraints }, elements,
+ (boundingSphere) => getBoundingSphere(crossLinkRestraints, elements, boundingSphere),
+ () => getLabel(structure, crossLinkRestraints, elements));
+ }
+
+ export function isLoci(x: any): x is Loci {
+ return !!x && x.kind === 'data-loci' && x.tag === 'interactions';
+ }
+
+ export function getBoundingSphere(crossLinkRestraints: CrossLinkRestraintValue, elements: ReadonlyArray<Element>, boundingSphere: Sphere3D) {
+ return CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
+ const p = crossLinkRestraints.pairs[elements[i]]
+ p.unitA.conformation.position(p.unitA.elements[p.indexA], pA)
+ p.unitB.conformation.position(p.unitB.elements[p.indexB], pB)
+ }, boundingSphere)
+ }
+
+ export function getLabel(structure: Structure, crossLinkRestraints: CrossLinkRestraintValue, elements: ReadonlyArray<Element>) {
+ const element = elements[0]
+ if (element === undefined) return ''
+ const p = crossLinkRestraints.pairs[element]
+ return [
+ _label(crossLinkRestraints, element),
+ bondLabel(Bond.Location(structure, p.unitA, p.indexA, structure, p.unitB, p.indexB))
+ ].join('</br>')
+ }
+}
+
+//
+
+function _addRestraints(map: Map<number, number>, unit: Unit, restraints: ModelCrossLinkRestraint) {
+ const { elements } = unit;
+ const elementCount = elements.length;
+ const kind = unit.kind
+
+ for (let i = 0; i < elementCount; i++) {
+ const e = elements[i];
+ restraints.getIndicesByElement(e, kind).forEach(ri => map.set(ri, i))
+ }
+}
+
+function extractInter(pairs: CrossLinkRestraint[], unitA: Unit, unitB: Unit) {
+ if (unitA.model !== unitB.model) return
+ if (unitA.model.sourceData.kind !== 'mmCIF') return
+
+ const restraints = ModelCrossLinkRestraint.Provider.get(unitA.model)
+ if (!restraints) return
+
+ const rA = new Map<number, StructureElement.UnitIndex>();
+ const rB = new Map<number, StructureElement.UnitIndex>();
+ _addRestraints(rA, unitA, restraints)
+ _addRestraints(rB, unitB, restraints)
+
+ rA.forEach((indexA, ri) => {
+ const indexB = rB.get(ri)
+ if (indexB !== undefined) {
+ pairs.push(
+ createCrossLinkRestraint(unitA, indexA, unitB, indexB, restraints, ri),
+ createCrossLinkRestraint(unitB, indexB, unitA, indexA, restraints, ri)
+ )
+ }
+ })
+}
+
+function extractIntra(pairs: CrossLinkRestraint[], unit: Unit) {
+ if (unit.model.sourceData.kind !== 'mmCIF') return
+
+ const restraints = ModelCrossLinkRestraint.Provider.get(unit.model)
+ if (!restraints) return
+
+ const { elements } = unit;
+ const elementCount = elements.length;
+ const kind = unit.kind
+
+ const r = new Map<number, StructureElement.UnitIndex[]>();
+
+ for (let i = 0; i < elementCount; i++) {
+ const e = elements[i];
+ restraints.getIndicesByElement(e, kind).forEach(ri => {
+ const il = r.get(ri)
+ if (il) il.push(i as StructureElement.UnitIndex)
+ else r.set(ri, [i as StructureElement.UnitIndex])
+ })
+ }
+
+ r.forEach((il, ri) => {
+ if (il.length < 2) return
+ const [ indexA, indexB ] = il
+ pairs.push(
+ createCrossLinkRestraint(unit, indexA, unit, indexB, restraints, ri),
+ createCrossLinkRestraint(unit, indexB, unit, indexA, restraints, ri)
+ )
+ })
+}
+
+function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: ModelCrossLinkRestraint, row: number): CrossLinkRestraint {
+ return {
+ unitA, indexA, unitB, indexB,
+
+ restraintType: restraints.data.restraint_type.value(row),
+ distanceThreshold: restraints.data.distance_threshold.value(row),
+ psi: restraints.data.psi.value(row),
+ sigma1: restraints.data.sigma_1.value(row),
+ sigma2: restraints.data.sigma_2.value(row),
+ }
+}
+
+function extractCrossLinkRestraints(structure: Structure): PairRestraints<CrossLinkRestraint> {
+ const pairs: CrossLinkRestraint[] = []
+ if (!structure.models.some(m => ModelCrossLinkRestraint.Provider.get(m))) {
+ return new PairRestraints(pairs)
+ }
+
+ const n = structure.units.length
+ for (let i = 0; i < n; ++i) {
+ const unitA = structure.units[i]
+ extractIntra(pairs, unitA)
+ for (let j = i + 1; j < n; ++j) {
+ const unitB = structure.units[j]
+ if (unitA.model === unitB.model) {
+ extractInter(pairs, unitA, unitB)
+ }
+ }
+ }
+
+ return new PairRestraints(pairs)
+}
\ No newline at end of file
diff --git a/src/mol-model-props/integrative/cross-link-restraint/representation.ts b/src/mol-model-props/integrative/cross-link-restraint/representation.ts
new file mode 100644
index 0000000000000000000000000000000000000000..31718c637cfc91321088ad32d386856011d639d1
--- /dev/null
+++ b/src/mol-model-props/integrative/cross-link-restraint/representation.ts
@@ -0,0 +1,149 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
+import { ThemeRegistryContext } from '../../../mol-theme/theme';
+import { Theme } from '../../../mol-theme/theme';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { PickingId } from '../../../mol-geo/geometry/picking';
+import { EmptyLoci, Loci } from '../../../mol-model/loci';
+import { Interval } from '../../../mol-data/int';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Structure, StructureElement } from '../../../mol-model/structure';
+import { VisualContext } from '../../../mol-repr/visual';
+import { createLinkCylinderMesh, LinkCylinderParams } from '../../../mol-repr/structure/visual/util/link';
+import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual } from '../../../mol-repr/structure/complex-visual';
+import { VisualUpdateState } from '../../../mol-repr/util';
+import { ComplexRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider } from '../../../mol-repr/structure/representation';
+import { UnitKind, UnitKindOptions } from '../../../mol-repr/structure/visual/util/common';
+import { CustomProperty } from '../../common/custom-property';
+import { CrossLinkRestraintProvider, CrossLinkRestraint } from './property';
+
+function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CrossLinkRestraintCylinderParams>, mesh?: Mesh) {
+
+ const crossLinks = CrossLinkRestraintProvider.get(structure).value!
+ if (!crossLinks.count) return Mesh.createEmpty(mesh)
+ const { sizeFactor } = props
+
+ const location = StructureElement.Location.create(structure)
+
+ const builderProps = {
+ linkCount: crossLinks.count,
+ position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+ const b = crossLinks.pairs[edgeIndex]
+ const uA = b.unitA, uB = b.unitB
+ uA.conformation.position(uA.elements[b.indexA], posA)
+ uB.conformation.position(uB.elements[b.indexB], posB)
+ },
+ radius: (edgeIndex: number) => {
+ const b = crossLinks.pairs[edgeIndex]
+ location.unit = b.unitA
+ location.element = b.unitA.elements[b.indexA]
+ return theme.size.size(location) * sizeFactor
+ },
+ }
+
+ return createLinkCylinderMesh(ctx, builderProps, props, mesh)
+}
+
+export const CrossLinkRestraintCylinderParams = {
+ ...ComplexMeshParams,
+ ...LinkCylinderParams,
+ sizeFactor: PD.Numeric(0.5, { min: 0, max: 10, step: 0.1 }),
+}
+export type CrossLinkRestraintCylinderParams = typeof CrossLinkRestraintCylinderParams
+
+export function CrossLinkRestraintVisual(materialId: number): ComplexVisual<CrossLinkRestraintCylinderParams> {
+ return ComplexMeshVisual<CrossLinkRestraintCylinderParams>({
+ defaultProps: PD.getDefaultValues(CrossLinkRestraintCylinderParams),
+ createGeometry: createCrossLinkRestraintCylinderMesh,
+ createLocationIterator: createCrossLinkRestraintIterator,
+ getLoci: getLinkLoci,
+ eachLocation: eachCrossLink,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CrossLinkRestraintCylinderParams>, currentProps: PD.Values<CrossLinkRestraintCylinderParams>) => {
+ state.createGeometry = (
+ newProps.sizeFactor !== currentProps.sizeFactor ||
+ newProps.radialSegments !== currentProps.radialSegments ||
+ newProps.linkCap !== currentProps.linkCap
+ )
+ }
+ }, materialId)
+}
+
+function createCrossLinkRestraintIterator(structure: Structure): LocationIterator {
+ const crossLinkRestraints = CrossLinkRestraintProvider.get(structure).value!
+ const { pairs } = crossLinkRestraints
+ const groupCount = pairs.length
+ const instanceCount = 1
+ const location = CrossLinkRestraint.Location(crossLinkRestraints, structure)
+ const getLocation = (groupIndex: number) => {
+ location.element = groupIndex
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation, true)
+}
+
+function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
+ const { objectId, groupId } = pickingId
+ if (id === objectId) {
+ const crossLinkRestraints = CrossLinkRestraintProvider.get(structure).value!
+ const pair = crossLinkRestraints.pairs[groupId]
+ if (pair) {
+ return CrossLinkRestraint.Loci(structure, crossLinkRestraints, [groupId])
+ }
+ }
+ return EmptyLoci
+}
+
+function eachCrossLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+ let changed = false
+ if (CrossLinkRestraint.isLoci(loci)) {
+ if (!Structure.areEquivalent(loci.data.structure, structure)) return false
+ const crossLinkRestraints = CrossLinkRestraintProvider.get(structure).value!
+ if (loci.data.crossLinkRestraints !== crossLinkRestraints) return false
+
+ for (const e of loci.elements) {
+ if (apply(Interval.ofSingleton(e))) changed = true
+ }
+ }
+ return changed
+}
+
+//
+
+const CrossLinkRestraintVisuals = {
+ 'cross-link-restraint': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintCylinderParams>) => ComplexRepresentation('Cross-link restraint', ctx, getParams, CrossLinkRestraintVisual),
+}
+
+export const CrossLinkRestraintParams = {
+ ...CrossLinkRestraintCylinderParams,
+ unitKinds: PD.MultiSelect<UnitKind>(['atomic', 'spheres'], UnitKindOptions),
+}
+export type CrossLinkRestraintParams = typeof CrossLinkRestraintParams
+export function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, structure: Structure) {
+ return PD.clone(CrossLinkRestraintParams)
+}
+
+export type CrossLinkRestraintRepresentation = StructureRepresentation<CrossLinkRestraintParams>
+export function CrossLinkRestraintRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintParams>): CrossLinkRestraintRepresentation {
+ return Representation.createMulti('CrossLinkRestraint', ctx, getParams, StructureRepresentationStateBuilder, CrossLinkRestraintVisuals as unknown as Representation.Def<Structure, CrossLinkRestraintParams>)
+}
+
+export const CrossLinkRestraintRepresentationProvider: StructureRepresentationProvider<CrossLinkRestraintParams> = {
+ label: 'Cross Link Restraint',
+ description: 'Displays cross-link restraints.',
+ factory: CrossLinkRestraintRepresentation,
+ getParams: getCrossLinkRestraintParams,
+ defaultValues: PD.getDefaultValues(CrossLinkRestraintParams),
+ defaultColorTheme: { name: CrossLinkRestraint.Tag.CrossLinkRestraint },
+ defaultSizeTheme: { name: 'uniform' },
+ isApplicable: (structure: Structure) => CrossLinkRestraint.isApplicable(structure),
+ ensureCustomProperties: (ctx: CustomProperty.Context, structure: Structure) => {
+ return CrossLinkRestraintProvider.attach(ctx, structure)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-props/integrative/pair-restraints.ts b/src/mol-model-props/integrative/pair-restraints.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7a74a4412957f165d44893263ec4a01082894c01
--- /dev/null
+++ b/src/mol-model-props/integrative/pair-restraints.ts
@@ -0,0 +1,49 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StructureElement, Unit } from '../../mol-model/structure';
+
+const emptyArray: number[] = []
+
+export interface PairRestraint {
+ readonly unitA: Unit,
+ readonly unitB: Unit,
+ readonly indexA: StructureElement.UnitIndex,
+ readonly indexB: StructureElement.UnitIndex,
+}
+
+function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit) {
+ return `${indexA}|${unitA.id}|${indexB}|${unitB.id}`
+}
+
+export class PairRestraints<T extends PairRestraint> {
+ readonly count: number
+ private readonly pairKeyIndices: Map<string, number[]>
+
+ /** Indices into this.pairs */
+ getPairIndices(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): ReadonlyArray<number> {
+ const key = getPairKey(indexA, unitA, indexB, unitB)
+ return this.pairKeyIndices.get(key) || emptyArray
+ }
+
+ getPairs(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): T[] {
+ const indices = this.getPairIndices(indexA, unitA, indexB, unitB)
+ return indices.map(idx => this.pairs[idx])
+ }
+
+ constructor(public pairs: ReadonlyArray<T>) {
+ const pairKeyIndices = new Map<string, number[]>()
+ this.pairs.forEach((p, i) => {
+ const key = getPairKey(p.indexA, p.unitA, p.indexB, p.unitB)
+ const indices = pairKeyIndices.get(key)
+ if (indices) indices.push(i)
+ else pairKeyIndices.set(key, [i])
+ })
+
+ this.count = pairs.length
+ this.pairKeyIndices = pairKeyIndices
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index e153de014ba3749c37f0700edb55b9f0a01698b3..1950f925299c9d2e8f684e5831dbefe1f36e870c 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -119,7 +119,7 @@ export type StructureQualityReportParams = typeof StructureQualityReportParams
export type StructureQualityReportProps = PD.Values<StructureQualityReportParams>
export const StructureQualityReportProvider: CustomModelProperty.Provider<StructureQualityReportParams, StructureQualityReport> = CustomModelProperty.createProvider({
- label: 'PDBe Structure Quality Report',
+ label: 'Structure Quality Report',
descriptor: CustomPropertyDescriptor<ReportExportContext, any>({
name: 'pdbe_structure_quality_report',
cifExport: {
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 e3296bab946d7dc478f50b5b20c3cfe05a533ef4..5f624e0f26a1944fb890826b3b7a72a8cee56ec0 100644
--- a/src/mol-model-props/pdbe/themes/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
@@ -72,13 +72,14 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
granularity: 'group',
color: color,
props: props,
- description: 'Assigns residue colors according to the number of issues or a specific issue in the PDBe Validation Report.',
+ description: 'Assigns residue colors according to the number of quality issues or a specific quality issue. Data from wwPDB Validation Report, obtained via PDBe.',
legend: TableLegend(ValidationColorTable)
}
}
export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params> = {
- label: 'PDBe Structure Quality Report',
+ label: 'Structure Quality Report',
+ category: ColorTheme.Category.Validation,
factory: StructureQualityReportColorTheme,
getParams: ctx => {
const issueTypes = StructureQualityReport.getIssueTypes(ctx.structure);
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index 6dce3e871e3ebd414256ecc7fb2af5825fe524f6..09a370b2ecd52b8a91fafcb91b73a5e9654190bf 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -15,6 +15,7 @@ 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';
+import { ReadonlyVec3 } from '../../mol-math/linear-algebra/3d/vec3';
const BiologicalAssemblyNames = new Set([
'author_and_software_defined_assembly',
@@ -26,6 +27,11 @@ const BiologicalAssemblyNames = new Set([
])
export namespace AssemblySymmetry {
+ export enum Tag {
+ Cluster = 'rcsb-assembly-symmetry-cluster',
+ Representation = 'rcsb-assembly-symmetry-3d'
+ }
+
export const DefaultServerUrl = 'https://data-beta.rcsb.org/graphql'
export function isApplicable(structure?: Structure): boolean {
@@ -37,6 +43,7 @@ export namespace AssemblySymmetry {
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
+ if (id === '' || id === 'deposited') return true
const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id)
if (indices.length !== 1) return false
const details = mmcif.pdbx_struct_assembly.details.value(indices[0])
@@ -48,27 +55,35 @@ export namespace AssemblySymmetry {
const client = new GraphQLClient(props.serverUrl, ctx.fetch)
const variables: AssemblySymmetryQueryVariables = {
- assembly_id: structure.units[0].conformation.operator.assembly.id,
+ assembly_id: structure.units[0].conformation.operator.assembly.id || 'deposited',
entry_id: structure.units[0].model.entryId
}
const result = await client.request<AssemblySymmetryQuery>(ctx.runtime, query, variables)
if (!result.assembly?.rcsb_struct_symmetry) {
- throw new Error('missing fields')
+ console.error('expected `rcsb_struct_symmetry` field')
+ return []
}
return result.assembly.rcsb_struct_symmetry as AssemblySymmetryValue
}
+
+ export type RotationAxes = ReadonlyArray<{ order: number, start: ReadonlyVec3, end: ReadonlyVec3 }>
+ export function isRotationAxes(x: AssemblySymmetryValue[0]['rotation_axes']): x is RotationAxes {
+ return !!x && x.length > 0
+ }
}
export function getSymmetrySelectParam(structure?: Structure) {
- const param = PD.Select<number>(0, [[0, 'No Symmetries']])
+ const param = PD.Select<number>(-1, [[-1, 'No Symmetries']])
if (structure) {
const assemblySymmetry = AssemblySymmetryProvider.get(structure).value
if (assemblySymmetry) {
const options: [number, string][] = []
for (let i = 0, il = assemblySymmetry.length; i < il; ++i) {
const { symbol, kind } = assemblySymmetry[i]
- options.push([ i, `${i + 1}: ${symbol} ${kind}` ])
+ if (symbol !== 'C1') {
+ options.push([ i, `${i + 1}: ${symbol} ${kind}` ])
+ }
}
if (options.length) {
param.options = options
diff --git a/src/mol-model-props/rcsb/representations/assembly-symmetry.ts b/src/mol-model-props/rcsb/representations/assembly-symmetry.ts
index b2c2d994f281bc48e7d52175fdc73f0e2e427969..b18fc0b27b51ac96c22d0337d13bb6f3e56e7e29 100644
--- a/src/mol-model-props/rcsb/representations/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/representations/assembly-symmetry.ts
@@ -5,7 +5,7 @@
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { AssemblySymmetryValue, getSymmetrySelectParam, AssemblySymmetryProvider } from '../assembly-symmetry';
+import { AssemblySymmetryValue, getSymmetrySelectParam, AssemblySymmetryProvider, AssemblySymmetry } from '../assembly-symmetry';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
@@ -29,7 +29,6 @@ import { TetrahedronCage } from '../../../mol-geo/primitive/tetrahedron';
import { IcosahedronCage } from '../../../mol-geo/primitive/icosahedron';
import { degToRad, radToDeg } from '../../../mol-math/misc';
import { Mutable } from '../../../mol-util/type-helpers';
-import { ReadonlyVec3 } from '../../../mol-math/linear-algebra/3d/vec3';
import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
import { Structure } from '../../../mol-model/structure';
import { isInteger } from '../../../mol-util/number';
@@ -87,11 +86,6 @@ export type AssemblySymmetryProps = PD.Values<AssemblySymmetryParams>
//
-type RotationAxes = ReadonlyArray<{ order: number, start: ReadonlyVec3, end: ReadonlyVec3 }>
-function isRotationAxes(x: AssemblySymmetryValue[0]['rotation_axes']): x is RotationAxes {
- return !!x && x.length > 0
-}
-
function getAssemblyName(s: Structure) {
const { id } = s.units[0].conformation.operator.assembly
return isInteger(id) ? `Assembly ${id}` : id
@@ -122,7 +116,7 @@ function getAxesMesh(data: AssemblySymmetryValue, props: PD.Values<AxesParams>,
const { symmetryIndex, scale } = props
const { rotation_axes } = data[symmetryIndex]
- if (!isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh)
+ if (!AssemblySymmetry.isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh)
const { start, end } = rotation_axes[0]
const radius = (Vec3.distance(start, end) / 500) * scale
@@ -227,11 +221,11 @@ function getSymbolScale(symbol: string) {
return 1
}
-function setSymbolTransform(t: Mat4, symbol: string, axes: RotationAxes, size: number, structure: Structure) {
+function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.RotationAxes, size: number, structure: Structure) {
const eye = Vec3()
const target = Vec3()
const up = Vec3()
- let pair: Mutable<RotationAxes> | undefined = undefined
+ let pair: Mutable<AssemblySymmetry.RotationAxes> | undefined = undefined
if (symbol.startsWith('C')) {
pair = [axes[0]]
@@ -288,7 +282,7 @@ function getCageMesh(data: Structure, props: PD.Values<CageParams>, mesh?: Mesh)
const { symmetryIndex, scale } = props
const { rotation_axes, symbol } = assemblySymmetry[symmetryIndex]
- if (!isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh)
+ if (!AssemblySymmetry.isRotationAxes(rotation_axes)) return Mesh.createEmpty(mesh)
const cage = getSymbolCage(symbol)
if (!cage) return Mesh.createEmpty(mesh)
@@ -329,5 +323,5 @@ function getCageShape(ctx: RuntimeContext, data: Structure, props: AssemblySymme
export type AssemblySymmetryRepresentation = Representation<Structure, AssemblySymmetryParams>
export function AssemblySymmetryRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryParams>): AssemblySymmetryRepresentation {
- return Representation.createMulti('Symmetry', ctx, getParams, Representation.StateBuilder, AssemblySymmetryVisuals as unknown as Representation.Def<Structure, AssemblySymmetryParams>)
+ return Representation.createMulti('Assembly Symmetry', ctx, getParams, Representation.StateBuilder, AssemblySymmetryVisuals as unknown as Representation.Def<Structure, AssemblySymmetryParams>)
}
\ No newline at end of file
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 be69dbcda1645c51fda6b31ec0768f2cc15460c4..7f05f21e29f49b49b3192d30de8fa4003c9d6b82 100644
--- a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
+++ b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
@@ -279,8 +279,8 @@ export function ClashesRepresentation(ctx: RepresentationContext, getParams: Rep
}
export const ClashesRepresentationProvider: StructureRepresentationProvider<ClashesParams> = {
- label: 'RCSB Clashes',
- description: 'Displays clashes between atoms as disks.',
+ label: 'Validation Clashes',
+ description: 'Displays clashes between atoms as disks. Data from wwPDB Validation Report, obtained via RCSB PDB.',
factory: ClashesRepresentation,
getParams: getClashesParams,
defaultValues: PD.getDefaultValues(ClashesParams),
diff --git a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
index e32a62f46d426ad45635add7173fcc7039fd5b8e..5ef15770e2c16dd1b724849768f0cbb4e46d8494 100644
--- a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
+++ b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
@@ -59,11 +59,13 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
for (let j = 0, jl = members.length; j < jl; ++j) {
const asymId = members[j]!.asym_id
const operList = [...members[j]!.pdbx_struct_oper_list_ids || []] as string[]
- if (operList.length === 0) operList.push('1') // TODO hack assuming '1' is the id of the identity operator
clusterByMember.set(clusterMemberKey(asymId, operList), i)
+ if (operList.length === 0) {
+ operList.push('1') // TODO hack assuming '1' is the id of the identity operator
+ clusterByMember.set(clusterMemberKey(asymId, operList), i)
+ }
}
}
-
const palette = getPalette(clusters.length, props)
legend = palette.legend
@@ -84,13 +86,14 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
color,
props,
contextHash,
- description: 'Assigns chain colors according to assembly symmetry cluster membership.',
+ description: 'Assigns chain colors according to assembly symmetry cluster membership calculated with BioJava and obtained via RCSB PDB.',
legend
}
}
export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<AssemblySymmetryClusterColorThemeParams> = {
- label: 'RCSB Assembly Symmetry Cluster',
+ label: 'Assembly Symmetry Cluster',
+ category: ColorTheme.Category.Symmetry,
factory: AssemblySymmetryClusterColorTheme,
getParams: getAssemblySymmetryClusterColorThemeParams,
defaultValues: PD.getDefaultValues(AssemblySymmetryClusterColorThemeParams),
diff --git a/src/mol-model-props/rcsb/themes/density-fit.ts b/src/mol-model-props/rcsb/themes/density-fit.ts
index 9bc3d3d0fe4f8756e9483ad1b205e2966629a677..0661d73d228daf94cf144292aa26404113533b1c 100644
--- a/src/mol-model-props/rcsb/themes/density-fit.ts
+++ b/src/mol-model-props/rcsb/themes/density-fit.ts
@@ -55,13 +55,14 @@ export function DensityFitColorTheme(ctx: ThemeDataContext, props: {}): ColorThe
color,
props,
contextHash,
- description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0).',
+ description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0). Data from wwPDB Validation Report, obtained via RCSB PDB.',
legend: scaleRsrz.legend
}
}
export const DensityFitColorThemeProvider: ColorTheme.Provider<{}> = {
- label: 'RCSB Density Fit',
+ label: 'Density Fit',
+ category: ColorTheme.Category.Validation,
factory: DensityFitColorTheme,
getParams: () => ({}),
defaultValues: PD.getDefaultValues({}),
diff --git a/src/mol-model-props/rcsb/themes/geometry-quality.ts b/src/mol-model-props/rcsb/themes/geometry-quality.ts
index 1f39b8de4b19e47b1765c0c85ae93cbe7ab9c64f..834ccefab83e3a9807c063e41f1ab8749eac0fa6 100644
--- a/src/mol-model-props/rcsb/themes/geometry-quality.ts
+++ b/src/mol-model-props/rcsb/themes/geometry-quality.ts
@@ -95,13 +95,14 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Value
color,
props,
contextHash,
- description: 'Assigns residue colors according to the number of (filtered) geometry issues.',
+ description: 'Assigns residue colors according to the number of (filtered) geometry issues. Data from wwPDB Validation Report, obtained via RCSB PDB.',
legend: ColorLegend
}
}
export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQualityColorThemeParams> = {
- label: 'RCSB Geometry Quality',
+ label: 'Geometry Quality',
+ category: ColorTheme.Category.Validation,
factory: GeometryQualityColorTheme,
getParams: getGeometricQualityColorThemeParams,
defaultValues: PD.getDefaultValues(getGeometricQualityColorThemeParams({})),
diff --git a/src/mol-model-props/rcsb/themes/random-coil-index.ts b/src/mol-model-props/rcsb/themes/random-coil-index.ts
index 596aa205587e6fbbade46e08d205404414e226a5..1dedd686f457c9380f8b857046956a3200238fd1 100644
--- a/src/mol-model-props/rcsb/themes/random-coil-index.ts
+++ b/src/mol-model-props/rcsb/themes/random-coil-index.ts
@@ -46,13 +46,14 @@ export function RandomCoilIndexColorTheme(ctx: ThemeDataContext, props: {}): Col
color,
props,
contextHash,
- description: 'Assigns residue colors according to the Random Coil Index value.',
+ description: 'Assigns residue colors according to the Random Coil Index value. Data from wwPDB Validation Report, obtained via RCSB PDB.',
legend: scale.legend
}
}
export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}> = {
- label: 'RCSB Random Coil Index',
+ label: 'Random Coil Index',
+ category: ColorTheme.Category.Validation,
factory: RandomCoilIndexColorTheme,
getParams: () => ({}),
defaultValues: PD.getDefaultValues({}),
diff --git a/src/mol-model-props/rcsb/validation-report.ts b/src/mol-model-props/rcsb/validation-report.ts
index ada844656b5fd832507d19efae31e330cbe3d98c..307c05dc428375e0ecfe5da2a6a0e7ee95578170 100644
--- a/src/mol-model-props/rcsb/validation-report.ts
+++ b/src/mol-model-props/rcsb/validation-report.ts
@@ -19,6 +19,9 @@ 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';
+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
+import { CustomPropSymbol } from '../../mol-script/language/symbol';
+import Type from '../../mol-script/language/type';
export { ValidationReport }
@@ -118,6 +121,25 @@ namespace ValidationReport {
case 'server': return fetch(ctx, model, props.source.params)
}
}
+
+ export const symbols = {
+ hasClash: QuerySymbolRuntime.Dynamic(CustomPropSymbol('rcsb', 'validation-report.has-clash', Type.Bool),
+ ctx => {
+ const { unit, element } = ctx.element
+ if (!Unit.isAtomic(unit)) return 0
+ const validationReport = ValidationReportProvider.get(unit.model).value
+ return validationReport && validationReport.clashes.getVertexEdgeCount(element) > 0
+ }
+ ),
+ issueCount: QuerySymbolRuntime.Dynamic(CustomPropSymbol('rcsb', 'validation-report.issue-count', Type.Num),
+ ctx => {
+ const { unit, element } = ctx.element
+ if (!Unit.isAtomic(unit)) return 0
+ const validationReport = ValidationReportProvider.get(unit.model).value
+ return validationReport?.geometryIssues.get(unit.residueIndex[element])?.size || 0
+ }
+ ),
+ }
}
const FileSourceParams = {
@@ -140,10 +162,10 @@ export type ValidationReportParams = typeof ValidationReportParams
export type ValidationReportProps = PD.Values<ValidationReportParams>
export const ValidationReportProvider: CustomModelProperty.Provider<ValidationReportParams, ValidationReport> = CustomModelProperty.createProvider({
- label: 'RCSB Validation Report',
+ label: 'Validation Report',
descriptor: CustomPropertyDescriptor({
name: 'rcsb_validation_report',
- // TODO `cifExport` and `symbol`
+ symbols: ValidationReport.symbols
}),
type: 'dynamic',
defaultParams: ValidationReportParams,
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index f80c1468a9566c1f8dc0bad747490c5545ee30a0..d8151534a663129aa1ba109219ad7d3f35d1ebca 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -42,7 +42,8 @@ export function isDataLoci(x?: Loci): x is DataLoci {
return !!x && x.kind === 'data-loci';
}
export function areDataLociEqual(a: DataLoci, b: DataLoci) {
- if (a.data !== b.data || a.tag !== b.tag) return false
+ // use shallowEqual to allow simple data objects that are contructed on-the-fly
+ if (!shallowEqual(a.data, b.data) || a.tag !== b.tag) return false
if (a.elements.length !== b.elements.length) return false
for (let i = 0, il = a.elements.length; i < il; ++i) {
if (!shallowEqual(a.elements[i], b.elements[i])) return false
diff --git a/src/mol-model/sequence/sequence.ts b/src/mol-model/sequence/sequence.ts
index 946e953b38d0873a8687647bbf1bed559805d86c..5e381e198a1da2eefc611c1754a53514b799bcbb 100644
--- a/src/mol-model/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -80,11 +80,11 @@ namespace Sequence {
return code
}
- export function ofResidueNames(compId: Column<string>, seqId: Column<number>, modifiedMap?: ReadonlyMap<string, string>): Sequence {
+ export function ofResidueNames(compId: Column<string>, seqId: Column<number>): Sequence {
if (seqId.rowCount === 0) throw new Error('cannot be empty');
const kind = determineKind(compId);
- return new ResidueNamesImpl(kind, compId, seqId, modifiedMap) as Sequence;
+ return new ResidueNamesImpl(kind, compId, seqId) as Sequence;
}
class ResidueNamesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
@@ -154,11 +154,7 @@ namespace Sequence {
const code = this.codeFromName(name);
// in case of MICROHETEROGENEITY `sequenceArray[idx]` may already be set
if (!sequenceArray[idx] || sequenceArray[idx] === '-') {
- if (code === 'X' && this.modifiedMap && this.modifiedMap.has(name)) {
- sequenceArray[idx] = this.modifiedMap.get(name)!
- } else {
- sequenceArray[idx] = code;
- }
+ sequenceArray[idx] = code;
}
labels[idx].push(code === 'X' ? name : code);
compIds[seqId].push(name);
@@ -183,7 +179,7 @@ namespace Sequence {
this._length = count
}
- constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>, private modifiedMap?: ReadonlyMap<string, string>) {
+ constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>) {
this.codeFromName = codeProvider(kind)
}
diff --git a/src/mol-model/structure/export/categories/modified-residues.ts b/src/mol-model/structure/export/categories/modified-residues.ts
deleted file mode 100644
index 51726e8c6b2a1df02b78335e1b9087f7c01b3a33..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/export/categories/modified-residues.ts
+++ /dev/null
@@ -1,64 +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>
- */
-
-import { Segmentation } from '../../../../mol-data/int';
-import { CifWriter } from '../../../../mol-io/writer/cif';
-import { StructureElement, StructureProperties as P, Unit } from '../../../structure';
-import { CifExportContext } from '../mmcif';
-
-import CifField = CifWriter.Field
-import CifCategory = CifWriter.Category
-
-const pdbx_struct_mod_residue_fields: CifField<number, StructureElement.Location[]>[] = [
- CifField.index('id'),
- CifField.str(`label_comp_id`, (i, xs) => P.residue.label_comp_id(xs[i])),
- CifField.int(`label_seq_id`, (i, xs) => P.residue.label_seq_id(xs[i])),
- CifField.str(`pdbx_PDB_ins_code`, (i, xs) => P.residue.pdbx_PDB_ins_code(xs[i])),
- CifField.str(`label_asym_id`, (i, xs) => P.chain.label_asym_id(xs[i])),
- CifField.str(`label_entity_id`, (i, xs) => P.chain.label_entity_id(xs[i])),
- CifField.str(`auth_comp_id`, (i, xs) => P.residue.auth_comp_id(xs[i])),
- CifField.int(`auth_seq_id`, (i, xs) => P.residue.auth_seq_id(xs[i])),
- CifField.str(`auth_asym_id`, (i, xs) => P.chain.auth_asym_id(xs[i])),
- CifField.str<number, StructureElement.Location[]>('parent_comp_id', (i, xs) => xs[i].unit.model.properties.modifiedResidues.parentId.get(P.residue.label_comp_id(xs[i]))!),
- CifField.str('details', (i, xs) => xs[i].unit.model.properties.modifiedResidues.details.get(P.residue.label_comp_id(xs[i]))!)
-];
-
-function getModifiedResidues({ structures }: CifExportContext): StructureElement.Location[] {
- // TODO: can different models (in the same mmCIF file) have different modified residues?
- const structure = structures[0], model = structure.model;
- const map = model.properties.modifiedResidues.parentId;
- if (!map.size) return [];
-
- const ret = [];
- const prop = P.residue.label_comp_id;
- 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);
- loc.unit = unit;
- while (residues.hasNext) {
- const seg = residues.move();
- loc.element = unit.elements[seg.start];
- const name = prop(loc);
- if (map.has(name)) {
- ret[ret.length] = StructureElement.Location.clone(loc);
- }
- }
- }
- return ret;
-}
-
-export const _pdbx_struct_mod_residue: CifCategory<CifExportContext> = {
- name: 'pdbx_struct_mod_residue',
- instance(ctx) {
- const residues = getModifiedResidues(ctx);
- return {
- fields: pdbx_struct_mod_residue_fields,
- source: [{ data: residues, rowCount: residues.length }]
- };
- }
-}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 45071c82cddc16fb1654c76e1e69595d1bef0622..c90223bb94e5df514d24d19cb64df12c4b04cb4d 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -11,7 +11,6 @@ import { Structure } from '../structure'
import { _atom_site } from './categories/atom_site';
import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
-import { _pdbx_struct_mod_residue } from './categories/modified-residues';
import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
import { Model } from '../model';
import { getUniqueEntityIndicesFromStructures, copy_mmCif_category } from './categories/utils';
@@ -83,7 +82,6 @@ const Categories = [
copy_mmCif_category('atom_sites'),
_pdbx_nonpoly_scheme,
- _pdbx_struct_mod_residue,
// Atoms
_atom_site
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 04dd2a0dd482c28713a5bb4c68686bf244752153..220fa825faa923cf9cdcfd042940213d4248b7e6 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -9,7 +9,7 @@ import UUID from '../../../mol-util/uuid';
import StructureSequence from './properties/sequence';
import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
-import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
+import { Entities, ChemicalComponentMap, MissingResidues, StructAsymMap } from './properties/common';
import { CustomProperties } from '../common/custom-property';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from '../../../mol-model-formats/structure/format';
@@ -53,17 +53,14 @@ export interface Model extends Readonly<{
atomicRanges: AtomicRanges,
properties: {
- /** maps modified residue name to its parent */
- readonly modifiedResidues: Readonly<{
- parentId: ReadonlyMap<string, string>,
- details: ReadonlyMap<string, string>
- }>,
/** map that holds details about unobserved or zero occurrence residues */
readonly missingResidues: MissingResidues,
/** maps residue name to `ChemicalComponent` data */
readonly chemicalComponentMap: ChemicalComponentMap
/** maps residue name to `SaccharideComponent` data */
readonly saccharideComponentMap: SaccharideComponentMap
+ /** maps label_asym_id name to `StructAsym` data */
+ readonly structAsymMap: StructAsymMap
},
customProperties: CustomProperties,
diff --git a/src/mol-model/structure/model/properties/common.ts b/src/mol-model/structure/model/properties/common.ts
index 84809978a4f22079e51edfbaca0f7b1433aff234..f8ae77e6b3869499d0eae32c3db939d6c92a8111 100644
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -29,4 +29,7 @@ export interface MissingResidues {
has(model_num: number, asym_id: string, seq_id: number): boolean
get(model_num: number, asym_id: string, seq_id: number): MissingResidue | undefined
readonly size: number
-}
\ No newline at end of file
+}
+
+export type StructAsym = Table.Row<Pick<mmCIF_Schema['struct_asym'], 'id' | 'entity_id'> & { auth_id: Column.Schema.Str }>
+export type StructAsymMap = ReadonlyMap<string, StructAsym>
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/sequence.ts b/src/mol-model/structure/model/properties/sequence.ts
index 1e8b787b0bd4c7f2d50a185066df1022fcb36938..f05dd175091aad6396e32c882c774333924597e6 100644
--- a/src/mol-model/structure/model/properties/sequence.ts
+++ b/src/mol-model/structure/model/properties/sequence.ts
@@ -37,13 +37,13 @@ namespace StructureSequence {
return { sequences, byEntityKey }
}
- export function fromHierarchy(entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy, modResMap?: ReadonlyMap<string, string>): StructureSequence {
- const atomic = fromAtomicHierarchy(entities, atomicHierarchy, modResMap)
+ export function fromHierarchy(entities: Entities, atomicHierarchy: AtomicHierarchy, coarseHierarchy: CoarseHierarchy): StructureSequence {
+ const atomic = fromAtomicHierarchy(entities, atomicHierarchy)
const coarse = coarseHierarchy.isDefined ? fromCoarseHierarchy(entities, coarseHierarchy) : Empty
return merge(atomic, coarse)
}
- export function fromAtomicHierarchy(entities: Entities, hierarchy: AtomicHierarchy, modResMap?: ReadonlyMap<string, string>): StructureSequence {
+ export function fromAtomicHierarchy(entities: Entities, hierarchy: AtomicHierarchy): StructureSequence {
const { label_comp_id, label_seq_id } = hierarchy.residues
const { chainAtomSegments, residueAtomSegments } = hierarchy
const { count, offsets } = chainAtomSegments
@@ -75,7 +75,7 @@ namespace StructureSequence {
const num = Column.window(label_seq_id, rStart, rEnd);
byEntityKey[entityKey] = {
entityId: entities.data.id.value(entityKey),
- sequence: Sequence.ofResidueNames(compId, num, modResMap)
+ sequence: Sequence.ofResidueNames(compId, num)
};
sequences.push(byEntityKey[entityKey]);
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 95a1e8e41d6b9688c79b8316186748eb08501001..fd37efe1d499a5c0193eac441e13ad09cdbc80e3 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -137,7 +137,7 @@ export const PolymerTypeAtomRoleId: { [k in PolymerType]: { [k in AtomRole]: Set
export const ProteinBackboneAtoms = new Set([
'CA', 'C', 'N', 'O',
'O1', 'O2', 'OC1', 'OC2', 'OX1', 'OXT',
- 'H', 'H1', 'H2', 'H3', 'HA', 'HN',
+ 'H', 'H1', 'H2', 'H3', 'HA', 'HN', 'HXT',
'BB'
])
@@ -257,7 +257,7 @@ export const DnaBaseNames = new Set([
'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 PurineBaseNames = new Set([ 'A', 'G', 'I', 'DA', 'DG', 'DI', 'APN', 'GPN' ])
export const PyrimidineBaseNames = new Set([ 'C', 'T', 'U', 'DC', 'DT', 'DU', 'CPN', 'TPN' ])
export const BaseNames = SetUtils.unionMany(RnaBaseNames, DnaBaseNames, PeptideBaseNames)
@@ -342,7 +342,7 @@ export function getDefaultChemicalComponent(compId: string): ChemicalComponent {
formula_weight: 0,
id: compId,
name: compId,
- mon_nstd_flag: 'n',
+ mon_nstd_flag: PolymerNames.has(compId) ? 'y' : 'n',
pdbx_synonyms: [],
type: getComponentType(compId)
};
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 76746ddb8b49af4dcda61173166e9c1c6d6df908..ffe5a13d5afa36d7c701cdfa54d8915fee2b555c 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -98,6 +98,24 @@ export namespace Loci {
return Location.create(loci.structure, unit, element);
}
+ export function firstElement(loci: Loci): Loci {
+ if (isEmpty(loci)) return loci;
+ return Loci(loci.structure, [{
+ unit: loci.elements[0].unit,
+ indices: OrderedSet.ofSingleton(OrderedSet.start(loci.elements[0].indices))
+ }])
+ }
+
+ export function firstResidue(loci: Loci): Loci {
+ if (isEmpty(loci)) return loci;
+ return extendToWholeResidues(firstElement(loci))
+ }
+
+ export function firstChain(loci: Loci): Loci {
+ if (isEmpty(loci)) return loci;
+ return extendToWholeChains(firstElement(loci))
+ }
+
export function toStructure(loci: Loci): Structure {
const units: Unit[] = []
for (const e of loci.elements) {
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 48ab835a516d3c50613ad4e5004389db0f6d53a8..6890b2a742c7e14f48d490ecbaebfa0ef1e3e017 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -1,14 +1,15 @@
/**
- * 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>
*/
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';
+import { SecondaryStructureProvider } from '../../../mol-model-props/computed/secondary-structure';
function p<T>(p: StructureElement.Property<T>) { return p; }
@@ -96,28 +97,18 @@ const residue = {
pdbx_PDB_ins_code: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element])),
// Properties
- isModified: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.modifiedResidues.parentId.has(compId(l))),
- modifiedParentName: p(l => {
- if (!Unit.isAtomic(l.unit)) notAtomic()
- const id = compId(l)
- return l.unit.model.properties.modifiedResidues.parentId.get(id) || id
- }),
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),
- // 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
+ const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.id)
+ return secStruc?.type[l.unit.residueIndex[l.element]] ?? 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
+ const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.id)
+ return secStruc?.key[l.unit.residueIndex[l.element]] ?? -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 c03a2a97b212e350f5bcf609fc421b98bb2036d1..aac52cad54c5f86a8c3b55734057d100fd6178f0 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.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>
@@ -16,7 +16,6 @@ import { StructureLookup3D } from './util/lookup3d';
import { CoarseElements } from '../model/properties/coarse';
import { StructureSubsetBuilder } from './util/subset-builder';
import { InterUnitBonds, computeInterUnitBonds, Bond } from './unit/bonds';
-import { PairRestraints, CrossLinkRestraint, extractCrossLinkRestraints } from './unit/pair-restraints';
import StructureSymmetry from './symmetry';
import StructureProperties from './properties';
import { ResidueIndex, ChainIndex, EntityIndex } from '../model/indexing';
@@ -41,7 +40,6 @@ class Structure {
parent?: Structure,
lookup3d?: StructureLookup3D,
interUnitBonds?: InterUnitBonds,
- crossLinkRestraints?: PairRestraints<CrossLinkRestraint>,
unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
unitSymmetryGroupsIndexMap?: IntMap<number>,
carbohydrates?: Carbohydrates,
@@ -228,12 +226,6 @@ class Structure {
return this._props.interUnitBonds;
}
- get crossLinkRestraints() {
- if (this._props.crossLinkRestraints) return this._props.crossLinkRestraints;
- this._props.crossLinkRestraints = extractCrossLinkRestraints(this);
- return this._props.crossLinkRestraints;
- }
-
get unitSymmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
if (this._props.unitSymmetryGroups) return this._props.unitSymmetryGroups;
this._props.unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index e6c5bae4673f2379bfaeb1b2296f905b74613b70..40df81d6ed48db7c2190141b34a06a9a26476a46 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.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 { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { RuntimeContext, Task } from '../../../mol-task';
import { Symmetry, Model } from '../model';
-import { QueryContext, StructureSelection } from '../query';
+import { QueryContext, StructureSelection, Queries as Q } from '../query';
import Structure from './structure';
import Unit from './unit';
import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import StructureProperties from './properties';
namespace StructureSymmetry {
export function buildAssembly(structure: Structure, asmName: string) {
@@ -48,6 +49,40 @@ namespace StructureSymmetry {
});
}
+ export type Generators = { operators: { index: number, shift: Vec3 }[], asymIds: string[] }[]
+
+ export function buildSymmetryAssembly(structure: Structure, generators: Generators, symmetry: Symmetry) {
+ return Task.create('Build Symmetry Assembly', async ctx => {
+ const models = structure.models;
+ if (models.length !== 1) throw new Error('Can only build symmetry assemblies from structures based on 1 model.');
+
+ const modelCenter = Vec3()
+ const assembler = Structure.Builder({ label: structure.label });
+
+ const queryCtx = new QueryContext(structure);
+
+ for (const g of generators) {
+ const selector = getSelector(g.asymIds);
+ const selection = selector(queryCtx);
+ if (StructureSelection.structureCount(selection) === 0) {
+ continue;
+ }
+ const { units } = StructureSelection.unionStructure(selection);
+
+ for (const { index, shift: [i, j, k] } of g.operators) {
+ const operators = getOperatorsForIndex(symmetry, index, i, j, k, modelCenter)
+ for (const unit of units) {
+ for (const op of operators) {
+ assembler.addWithOperator(unit, op);
+ }
+ }
+ }
+ }
+
+ return assembler.getStructure();
+ });
+ }
+
export function builderSymmetryMates(structure: Structure, radius: number) {
return Task.create('Find Symmetry Mates', ctx => findMatesRadius(ctx, structure, radius));
}
@@ -96,7 +131,35 @@ namespace StructureSymmetry {
}
}
-function getOperators(symmetry: Symmetry, ijkMin: Vec3, ijkMax: Vec3, modelCenter: Vec3) {
+function getSelector(asymIds: string[]) {
+ return Q.generators.atoms({ chainTest: Q.pred.and(
+ Q.pred.eq(ctx => StructureProperties.unit.operator_name(ctx.element), SymmetryOperator.DefaultName),
+ Q.pred.inSet(ctx => StructureProperties.chain.label_asym_id(ctx.element), asymIds)
+ )});
+}
+
+function getOperatorsForIndex(symmetry: Symmetry, index: number, i: number, j: number, k: number, modelCenter: Vec3) {
+ const { spacegroup, ncsOperators } = symmetry;
+ const operators: SymmetryOperator[] = []
+
+ const { toFractional } = spacegroup.cell
+ const ref = Vec3.transformMat4(Vec3(), modelCenter, toFractional)
+
+ const symOp = Spacegroup.getSymmetryOperatorRef(spacegroup, index, i, j, k, ref)
+ if (ncsOperators && ncsOperators.length) {
+ for (let u = 0, ul = ncsOperators.length; u < ul; ++u) {
+ const ncsOp = ncsOperators![u]
+ const matrix = Mat4.mul(Mat4(), symOp.matrix, ncsOp.matrix)
+ const operator = SymmetryOperator.create(`${symOp.name} ${ncsOp.name}`, matrix, symOp.assembly, ncsOp.ncsId, symOp.hkl, symOp.spgrOp);
+ operators.push(operator)
+ }
+ } else {
+ operators.push(symOp)
+ }
+ return operators
+}
+
+function getOperatorsForRange(symmetry: Symmetry, ijkMin: Vec3, ijkMax: Vec3, modelCenter: Vec3) {
const { spacegroup, ncsOperators } = symmetry;
const ncsCount = (ncsOperators && ncsOperators.length) || 0
const operators: SymmetryOperator[] = [];
@@ -117,18 +180,7 @@ function getOperators(symmetry: Symmetry, ijkMin: Vec3, ijkMax: Vec3, modelCente
for (let k = ijkMin[2]; k <= ijkMax[2]; k++) {
// check if we have added identity as the 1st operator.
if (!ncsCount && op === 0 && i === 0 && j === 0 && k === 0) continue;
-
- const symOp = Spacegroup.getSymmetryOperatorRef(spacegroup, op, i, j, k, ref)
- if (ncsCount) {
- for (let u = 0; u < ncsCount; ++u) {
- const ncsOp = ncsOperators![u]
- const matrix = Mat4.mul(Mat4.zero(), symOp.matrix, ncsOp.matrix)
- const operator = SymmetryOperator.create(`${symOp.name} ${ncsOp.name}`, matrix, symOp.assembly, ncsOp.ncsId, symOp.hkl, symOp.spgrOp);
- operators[operators.length] = operator;
- }
- } else {
- operators[operators.length] = symOp;
- }
+ operators.push(...getOperatorsForIndex(symmetry, op, i, j, k, ref))
}
}
}
@@ -142,7 +194,7 @@ function getOperatorsCached333(symmetry: Symmetry, ref: Vec3) {
}
symmetry._operators_333 = {
ref: Vec3.clone(ref),
- operators: getOperators(symmetry, Vec3.create(-3, -3, -3), Vec3.create(3, 3, 3), ref)
+ operators: getOperatorsForRange(symmetry, Vec3.create(-3, -3, -3), Vec3.create(3, 3, 3), ref)
};
return symmetry._operators_333.operators;
}
@@ -181,7 +233,7 @@ async function findSymmetryRange(ctx: RuntimeContext, structure: Structure, ijkM
if (SpacegroupCell.isZero(spacegroup.cell)) return structure;
const modelCenter = Model.getCenter(models[0])
- const operators = getOperators(symmetry, ijkMin, ijkMax, modelCenter);
+ const operators = getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter);
return assembleOperators(structure, operators);
}
diff --git a/src/mol-model/structure/structure/unit/pair-restraints.ts b/src/mol-model/structure/structure/unit/pair-restraints.ts
deleted file mode 100644
index 890fb6b03666a40e5157d80430f0b098d2db98ad..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/pair-restraints.ts
+++ /dev/null
@@ -1,10 +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/data'
-export * from './pair-restraints/extract-cross-links'
-// export * from './pair-restraints/extract-predicted-contacts'
-// export * from './pair-restraints/extract-distance-restraints'
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/data.ts b/src/mol-model/structure/structure/unit/pair-restraints/data.ts
deleted file mode 100644
index f402aab8e991b6fbc7a03e4bdc4fb38fbb9ef622..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/pair-restraints/data.ts
+++ /dev/null
@@ -1,77 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import Unit from '../../unit';
-import { StructureElement } from '../../../structure';
-
-const emptyArray: number[] = []
-
-interface PairRestraint {
- readonly unitA: Unit,
- readonly unitB: Unit,
- readonly indexA: StructureElement.UnitIndex,
- readonly indexB: StructureElement.UnitIndex,
-}
-
-function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit) {
- return `${indexA}|${unitA.id}|${indexB}|${unitB.id}`
-}
-
-export class PairRestraints<T extends PairRestraint> {
- readonly count: number
- private readonly pairKeyIndices: Map<string, number[]>
-
- /** Indices into this.pairs */
- getPairIndices(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): ReadonlyArray<number> {
- const key = getPairKey(indexA, unitA, indexB, unitB)
- const indices = this.pairKeyIndices.get(key)
- return indices !== undefined ? indices : emptyArray
- }
-
- getPairs(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): T[] | undefined {
- const indices = this.getPairIndices(indexA, unitA, indexB, unitB)
- return indices.length ? indices.map(idx => this.pairs[idx]) : undefined
- }
-
- constructor(public pairs: ReadonlyArray<T>) {
- const pairKeyIndices = new Map<string, number[]>()
- this.pairs.forEach((p, i) => {
- const key = getPairKey(p.indexA, p.unitA, p.indexB, p.unitB)
- const indices = pairKeyIndices.get(key)
- if (indices) indices.push(i)
- else pairKeyIndices.set(key, [i])
- })
-
- this.count = pairs.length
- this.pairKeyIndices = pairKeyIndices
- }
-}
-
-export interface CrossLinkRestraint extends PairRestraint {
- readonly restraintType: 'harmonic' | 'upper bound' | 'lower bound'
- readonly distanceThreshold: number
- readonly psi: number
- readonly sigma1: number
- readonly sigma2: number
-}
-
-export interface PredictedContactRestraint extends PairRestraint {
- readonly distance_lower_limit: number
- readonly distance_upper_limit: number
- readonly probability: number
- readonly restraint_type: 'lower bound' | 'upper bound' | 'lower and upper bound'
- readonly model_granularity: 'by-residue' | 'by-feature' | 'by-atom'
-}
-
-export interface DistanceRestraint extends PairRestraint {
- readonly upper_limit: number
- readonly upper_limit_esd: number
- readonly lower_limit: number
- readonly lower_limit_esd: number
- readonly probability: number
- readonly restraint_type: 'lower bound' | 'upper bound' | 'lower and upper bound'
- readonly granularity: 'by-residue' | 'by-atom'
-}
\ No newline at end of file
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
deleted file mode 100644
index 0b98c288cd7e44f5409655d1919e232a726fdb0b..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
+++ /dev/null
@@ -1,111 +0,0 @@
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import Unit from '../../unit';
-import Structure from '../../structure';
-import { PairRestraints, CrossLinkRestraint } from './data';
-import { StructureElement } from '../../../structure';
-import { ModelCrossLinkRestraint } from '../../../../../mol-model-formats/structure/property/pair-restraints/cross-links';
-
-function _addRestraints(map: Map<number, number>, unit: Unit, restraints: ModelCrossLinkRestraint) {
- const { elements } = unit;
- const elementCount = elements.length;
- const kind = unit.kind
-
- for (let i = 0; i < elementCount; i++) {
- const e = elements[i];
- restraints.getIndicesByElement(e, kind).forEach(ri => map.set(ri, i))
- }
-}
-
-function extractInter(pairs: CrossLinkRestraint[], unitA: Unit, unitB: Unit) {
- if (unitA.model !== unitB.model) return
- if (unitA.model.sourceData.kind !== 'mmCIF') return
-
- const restraints = ModelCrossLinkRestraint.Provider.get(unitA.model)
- if (!restraints) return
-
- const rA = new Map<number, StructureElement.UnitIndex>();
- const rB = new Map<number, StructureElement.UnitIndex>();
- _addRestraints(rA, unitA, restraints)
- _addRestraints(rB, unitB, restraints)
-
- rA.forEach((indexA, ri) => {
- const indexB = rB.get(ri)
- if (indexB !== undefined) {
- pairs.push(
- createCrossLinkRestraint(unitA, indexA, unitB, indexB, restraints, ri),
- createCrossLinkRestraint(unitB, indexB, unitA, indexA, restraints, ri)
- )
- }
- })
-}
-
-function extractIntra(pairs: CrossLinkRestraint[], unit: Unit) {
- if (unit.model.sourceData.kind !== 'mmCIF') return
-
- const restraints = ModelCrossLinkRestraint.Provider.get(unit.model)
- if (!restraints) return
-
- const { elements } = unit;
- const elementCount = elements.length;
- const kind = unit.kind
-
- const r = new Map<number, StructureElement.UnitIndex[]>();
-
- for (let i = 0; i < elementCount; i++) {
- const e = elements[i];
- restraints.getIndicesByElement(e, kind).forEach(ri => {
- const il = r.get(ri)
- if (il) il.push(i as StructureElement.UnitIndex)
- else r.set(ri, [i as StructureElement.UnitIndex])
- })
- }
-
- r.forEach((il, ri) => {
- if (il.length < 2) return
- const [ indexA, indexB ] = il
- pairs.push(
- createCrossLinkRestraint(unit, indexA, unit, indexB, restraints, ri),
- createCrossLinkRestraint(unit, indexB, unit, indexA, restraints, ri)
- )
- })
-}
-
-function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: ModelCrossLinkRestraint, row: number): CrossLinkRestraint {
- return {
- unitA, indexA, unitB, indexB,
-
- restraintType: restraints.data.restraint_type.value(row),
- distanceThreshold: restraints.data.distance_threshold.value(row),
- psi: restraints.data.psi.value(row),
- sigma1: restraints.data.sigma_1.value(row),
- sigma2: restraints.data.sigma_2.value(row),
- }
-}
-
-function extractCrossLinkRestraints(structure: Structure): PairRestraints<CrossLinkRestraint> {
- const pairs: CrossLinkRestraint[] = []
- if (!structure.models.some(m => ModelCrossLinkRestraint.Provider.get(m))) {
- return new PairRestraints(pairs)
- }
-
- const n = structure.units.length
- for (let i = 0; i < n; ++i) {
- const unitA = structure.units[i]
- extractIntra(pairs, unitA)
- for (let j = i + 1; j < n; ++j) {
- const unitB = structure.units[j]
- if (unitA.model === unitB.model) {
- extractInter(pairs, unitA, unitB)
- }
- }
- }
-
- return new PairRestraints(pairs)
-}
-
-export { extractCrossLinkRestraints };
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts
deleted file mode 100644
index f19797cb6a8dc5eed5dacaaf0201d24d458fba44..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-distance-restraints.ts
+++ /dev/null
@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-// TODO extract from `_ma_distance_restraints`
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-predicted-contacts.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-predicted-contacts.ts
deleted file mode 100644
index ad6d43f51f4d524171b5d66a2c19f4d0348c45cb..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-predicted-contacts.ts
+++ /dev/null
@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-// TODO extract from `ihm_predicted_contact_restraint`
\ No newline at end of file
diff --git a/src/mol-plugin-ui/base.tsx b/src/mol-plugin-ui/base.tsx
index d377417addc71ca14c8c4eec0c0cbccd37cdcc07..38d3977f1b6eecf3d819ab8e038ef5ea36cf048c 100644
--- a/src/mol-plugin-ui/base.tsx
+++ b/src/mol-plugin-ui/base.tsx
@@ -25,6 +25,7 @@ export abstract class PluginUIComponent<P = {}, S = {}, SS = {}> extends React.C
componentWillUnmount() {
if (!this.subs) return;
for (const s of this.subs) s.unsubscribe();
+ this.subs = [];
}
protected init?(): void;
diff --git a/src/mol-plugin-ui/controls/action-menu.tsx b/src/mol-plugin-ui/controls/action-menu.tsx
new file mode 100644
index 0000000000000000000000000000000000000000..016a4db71cf127f89be927c5dd5ec53885aa457f
--- /dev/null
+++ b/src/mol-plugin-ui/controls/action-menu.tsx
@@ -0,0 +1,157 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as React from 'react'
+import { Icon } from './common';
+import { ParamDefinition } from '../../mol-util/param-definition';
+
+export class ActionMenu extends React.PureComponent<ActionMenu.Props> {
+ hide = () => this.props.onSelect(void 0)
+
+ render() {
+ const cmd = this.props;
+
+ return <div className='msp-action-menu-options' style={{ marginTop: '1px' }}>
+ {cmd.header && <div className='msp-control-group-header' style={{ position: 'relative' }}>
+ <button className='msp-btn msp-btn-block' onClick={this.hide}>
+ <Icon name='off' style={{ position: 'absolute', right: '2px', top: 0 }} />
+ <b>{cmd.header}</b>
+ </button>
+ </div>}
+ <Section items={cmd.items} onSelect={cmd.onSelect} current={cmd.current} />
+ </div>
+ }
+}
+
+export namespace ActionMenu {
+ export type Props = { items: Items, onSelect: OnSelect, header?: string, current?: Item | undefined }
+
+ export type OnSelect = (item: Item | undefined) => void
+
+ export type Items = string | Item | [Items]
+ export type Item = { label: string, icon?: string, value: unknown }
+
+ export function Item(label: string, value: unknown): Item
+ export function Item(label: string, icon: string, value: unknown): Item
+ export function Item(label: string, iconOrValue: any, value?: unknown): Item {
+ if (value) return { label, icon: iconOrValue, value };
+ return { label, value: iconOrValue };
+ }
+
+ export function createItems<T>(xs: ArrayLike<T>, options?: { label?: (t: T) => string, value?: (t: T) => any, category?: (t: T) => string | undefined }) {
+ const { label, value, category } = options || { };
+ let cats: Map<string, (ActionMenu.Item | string)[]> | undefined = void 0;
+ const items: (ActionMenu.Item | (ActionMenu.Item | string)[] | string)[] = [];
+ for (let i = 0; i < xs.length; i++) {
+ const x = xs[i];
+
+ const catName = category?.(x);
+ const l = label ? label(x) : '' + x;
+ const v = value ? value(x) : x;
+
+ if (!!catName) {
+ if (!cats) cats = new Map<string, (ActionMenu.Item | string)[]>();
+
+ let cat = cats.get(catName);
+ if (!cat) {
+ cat = [catName];
+ cats.set(catName, cat);
+ items.push(cat);
+ }
+ cat.push(ActionMenu.Item(l, v));
+ } else {
+ items.push(ActionMenu.Item(l, v));
+ }
+ }
+ return items as ActionMenu.Items;
+ }
+
+ type Opt = ParamDefinition.Select<any>['options'][0];
+ const _selectOptions = { value: (o: Opt) => o[0], label: (o: Opt) => o[1], category: (o: Opt) => o[2] };
+
+ export function createItemsFromSelectParam(param: ParamDefinition.Select<any>) {
+ return createItems(param.options, _selectOptions);
+ }
+
+ export function findItem(items: Items, value: any): Item | undefined {
+ if (typeof items === 'string') return;
+ if (isItem(items)) return items.value === value ? items : void 0;
+ for (const s of items) {
+ const found = findItem(s, value);
+ if (found) return found;
+ }
+ }
+
+ export function getFirstItem(items: Items): Item | undefined {
+ if (typeof items === 'string') return;
+ if (isItem(items)) return items;
+ for (const s of items) {
+ const found = getFirstItem(s);
+ if (found) return found;
+ }
+ }
+}
+
+type SectionProps = { header?: string, items: ActionMenu.Items, onSelect: ActionMenu.OnSelect, current: ActionMenu.Item | undefined }
+type SectionState = { items: ActionMenu.Items, current: ActionMenu.Item | undefined, isExpanded: boolean }
+
+class Section extends React.PureComponent<SectionProps, SectionState> {
+ state = {
+ items: this.props.items,
+ current: this.props.current,
+ isExpanded: !!this.props.current && !!ActionMenu.findItem(this.props.items, this.props.current.value)
+ }
+
+ toggleExpanded = (e: React.MouseEvent<HTMLButtonElement>) => {
+ this.setState({ isExpanded: !this.state.isExpanded });
+ e.currentTarget.blur();
+ }
+
+ static getDerivedStateFromProps(props: SectionProps, state: SectionState) {
+ if (props.items === state.items && props.current === state.current) return null;
+ return { items: props.items, current: props.current, isExpanded: props.current && !!ActionMenu.findItem(props.items, props.current.value) }
+ }
+
+ render() {
+ const { header, items, onSelect, current } = this.props;
+
+ if (typeof items === 'string') return null;
+ if (isItem(items)) return <Action item={items} onSelect={onSelect} current={current} />
+
+ const hasCurrent = header && current && !!ActionMenu.findItem(items, current.value)
+
+ return <div>
+ {header && <div className='msp-control-group-header' style={{ marginTop: '1px' }}>
+ <button className='msp-btn msp-btn-block' onClick={this.toggleExpanded}>
+ <span className={`msp-icon msp-icon-${this.state.isExpanded ? 'collapse' : 'expand'}`} />
+ {hasCurrent ? <b>{header}</b> : header}
+ </button>
+ </div>}
+ <div className='msp-control-offset'>
+ {(!header || this.state.isExpanded) && items.map((x, i) => {
+ if (typeof x === 'string') return null;
+ if (isItem(x)) return <Action key={i} item={x} onSelect={onSelect} current={current} />
+ return <Section key={i} header={typeof x[0] === 'string' ? x[0] : void 0} items={x} onSelect={onSelect} current={current} />
+ })}
+ </div>
+ </div>;
+ }
+}
+
+const Action: React.FC<{ item: ActionMenu.Item, onSelect: ActionMenu.OnSelect, current: ActionMenu.Item | undefined }> = ({ item, onSelect, current }) => {
+ const isCurrent = current === item;
+ return <div className='msp-control-row'>
+ <button onClick={() => onSelect(item)}>
+ {item.icon && <Icon name={item.icon} />}
+ {isCurrent ? <b>{item.label}</b> : item.label}
+ </button>
+ </div>;
+}
+
+function isItem(x: any): x is ActionMenu.Item {
+ const v = x as ActionMenu.Item;
+ return v && !!v.label && typeof v.value !== 'undefined';
+}
\ No newline at end of file
diff --git a/src/mol-plugin-ui/controls/common.tsx b/src/mol-plugin-ui/controls/common.tsx
index c345eb5d86c0a1c0e90f8e6c7f8590700a6d5576..8faadb834ce81d0f303727627e77c69cf6a68513 100644
--- a/src/mol-plugin-ui/controls/common.tsx
+++ b/src/mol-plugin-ui/controls/common.tsx
@@ -308,16 +308,28 @@ export function SectionHeader(props: { icon?: string, title: string | JSX.Elemen
</div>
}
-// export const ToggleButton = (props: {
-// onChange: (v: boolean) => void,
-// value: boolean,
-// label: string,
-// title?: string
-// }) => <div className='lm-control-row lm-toggle-button' title={props.title}>
-// <span>{props.label}</span>
-// <div>
-// <button onClick={e => { props.onChange.call(null, !props.value); (e.target as HTMLElement).blur(); }}>
-// <span className={ `lm-icon lm-icon-${props.value ? 'ok' : 'off'}` }></span> {props.value ? 'On' : 'Off'}
-// </button>
-// </div>
-// </div>
\ No newline at end of file
+export type ToggleButtonProps = {
+ style?: React.CSSProperties,
+ className?: string,
+ disabled?: boolean,
+ label: string | JSX.Element,
+ title?: string,
+ isSelected?: boolean,
+ toggle: () => void
+}
+
+export class ToggleButton extends React.PureComponent<ToggleButtonProps> {
+ onClick = (e: React.MouseEvent<HTMLButtonElement>) => {
+ e.currentTarget.blur();
+ this.props.toggle();
+ }
+
+ render() {
+ const props = this.props;
+ const label = props.label;
+ return <button onClick={this.onClick} title={this.props.title}
+ disabled={props.disabled} style={props.style} className={props.className}>
+ {this.props.isSelected ? <b>{label}</b> : label}
+ </button>;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-plugin-ui/controls/parameters.tsx b/src/mol-plugin-ui/controls/parameters.tsx
index 49363d5cd68a1fa21a03855f4ffe426dd887a1a4..ddb081b50dd7dc3449f0fc282d76f4cd980aafed 100644
--- a/src/mol-plugin-ui/controls/parameters.tsx
+++ b/src/mol-plugin-ui/controls/parameters.tsx
@@ -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>
@@ -8,27 +8,33 @@
import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
import { Color } from '../../mol-util/color';
import { ColorListName, getColorListFromName } from '../../mol-util/color/lists';
-import { memoize1 } from '../../mol-util/memoize';
+import { memoize1, memoizeLatest } from '../../mol-util/memoize';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { camelCaseToWords } from '../../mol-util/string';
import * as React from 'react';
import LineGraphComponent from './line-graph/line-graph-component';
import { Slider, Slider2 } from './slider';
-import { NumericInput, IconButton, ControlGroup } from './common';
-import { _Props, _State } from '../base';
+import { NumericInput, IconButton, ControlGroup, ToggleButton } from './common';
+import { _Props, _State, PluginUIComponent } from '../base';
import { legendFor } from './legend';
import { Legend as LegendData } from '../../mol-util/legend';
import { CombinedColorControl, ColorValueOption, ColorOptions } from './color';
+import { getPrecision } from '../../mol-util/number';
+import { ParamMapping } from '../../mol-util/param-mapping';
+import { PluginContext } from '../../mol-plugin/context';
+import { ActionMenu } from './action-menu';
export interface ParameterControlsProps<P extends PD.Params = PD.Params> {
params: P,
values: any,
- onChange: ParamOnChange,
+ onChange: ParamsOnChange<PD.Values<P>>,
isDisabled?: boolean,
onEnter?: () => void
}
export class ParameterControls<P extends PD.Params> extends React.PureComponent<ParameterControlsProps<P>, {}> {
+ onChange: ParamOnChange = (params) => this.props.onChange(params, this.props.values);
+
render() {
const params = this.props.params;
const values = this.props.values;
@@ -40,12 +46,31 @@ export class ParameterControls<P extends PD.Params> extends React.PureComponent<
if (param.isHidden) return null;
const Control = controlFor(param);
if (!Control) return null;
- return <Control param={param} key={key} onChange={this.props.onChange} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} name={key} value={values[key]} />
+ return <Control param={param} key={key} onChange={this.onChange} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} name={key} value={values[key]} />
})}
</>;
}
}
+export class ParameterMappingControl<S, T> extends PluginUIComponent<{ mapping: ParamMapping<S, T, PluginContext> }> {
+ setSettings = (p: { param: PD.Base<any>, name: string, value: any }, old: any) => {
+ const values = { ...old, [p.name]: p.value };
+ const t = this.props.mapping.update(values, this.plugin);
+ this.props.mapping.apply(t, this.plugin);
+ }
+
+ componentDidMount() {
+ this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+ }
+
+ render() {
+ const t = this.props.mapping.getTarget(this.plugin);
+ const values = this.props.mapping.getValues(t, this.plugin);
+ const params = this.props.mapping.params(this.plugin) as any as PD.Params;
+ return <ParameterControls params={params} values={values} onChange={this.setSettings} />
+ }
+}
+
function controlFor(param: PD.Any): ParamControl | undefined {
switch (param.type) {
case 'value': return void 0;
@@ -90,6 +115,7 @@ export class ParamHelp<L extends LegendData> extends React.PureComponent<{ legen
}
}
+export type ParamsOnChange<P> = (params: { param: PD.Base<any>, name: string, value: any }, values: Readonly<P>) => void
export type ParamOnChange = (params: { param: PD.Base<any>, name: string, value: any }) => void
export interface ParamProps<P extends PD.Base<any> = PD.Base<any>> {
name: string,
@@ -101,51 +127,63 @@ export interface ParamProps<P extends PD.Base<any> = PD.Base<any>> {
}
export type ParamControl = React.ComponentClass<ParamProps<any>>
-export abstract class SimpleParam<P extends PD.Any> extends React.PureComponent<ParamProps<P>, { isExpanded: boolean }> {
- state = { isExpanded: false };
+function renderSimple(options: { props: ParamProps<any>, state: { showHelp: boolean }, control: JSX.Element, addOn: JSX.Element | null, toggleHelp: () => void }) {
+ const { props, state, control, toggleHelp, addOn } = options;
+
+ const _className = ['msp-control-row'];
+ if (props.param.shortLabel) _className.push('msp-control-label-short')
+ if (props.param.twoColumns) _className.push('msp-control-col-2')
+ const className = _className.join(' ');
+
+ const label = props.param.label || camelCaseToWords(props.name);
+ const help = props.param.help
+ ? props.param.help(props.value)
+ : { description: props.param.description, legend: props.param.legend }
+ const desc = props.param.description;
+ const hasHelp = help.description || help.legend
+ return <>
+ <div className={className}>
+ <span title={desc}>
+ {label}
+ {hasHelp &&
+ <button className='msp-help msp-btn-link msp-btn-icon msp-control-group-expander' onClick={toggleHelp}
+ title={desc || `${state.showHelp ? 'Hide' : 'Show'} help`}
+ style={{ background: 'transparent', textAlign: 'left', padding: '0' }}>
+ <span className={`msp-icon msp-icon-help-circle-${state.showHelp ? 'collapse' : 'expand'}`} />
+ </button>
+ }
+ </span>
+ <div>
+ {control}
+ </div>
+ </div>
+ {hasHelp && state.showHelp && <div className='msp-control-offset'>
+ <ParamHelp legend={help.legend} description={help.description} />
+ </div>}
+ {addOn}
+ </>;
+}
+
+export abstract class SimpleParam<P extends PD.Any> extends React.PureComponent<ParamProps<P>, { showHelp: boolean }> {
+ state = { showHelp: false };
protected update(value: P['defaultValue']) {
this.props.onChange({ param: this.props.param, name: this.props.name, value });
}
abstract renderControl(): JSX.Element;
+ renderAddOn(): JSX.Element | null { return null; }
- private get className() {
- const className = ['msp-control-row'];
- if (this.props.param.shortLabel) className.push('msp-control-label-short')
- if (this.props.param.twoColumns) className.push('msp-control-col-2')
- return className.join(' ')
- }
-
- toggleExpanded = () => this.setState({ isExpanded: !this.state.isExpanded });
+ toggleHelp = () => this.setState({ showHelp: !this.state.showHelp });
render() {
- const label = this.props.param.label || camelCaseToWords(this.props.name);
- const help = this.props.param.help
- ? this.props.param.help(this.props.value)
- : { description: this.props.param.description, legend: this.props.param.legend }
- const desc = this.props.param.description;
- const hasHelp = help.description || help.legend
- return <>
- <div className={this.className}>
- <span title={desc}>
- {label}
- {hasHelp &&
- <button className='msp-help msp-btn-link msp-btn-icon msp-control-group-expander' onClick={this.toggleExpanded}
- title={desc || `${this.state.isExpanded ? 'Hide' : 'Show'} help`}
- style={{ background: 'transparent', textAlign: 'left', padding: '0' }}>
- <span className={`msp-icon msp-icon-help-circle-${this.state.isExpanded ? 'collapse' : 'expand'}`} />
- </button>
- }
- </span>
- <div>
- {this.renderControl()}
- </div>
- </div>
- {hasHelp && this.state.isExpanded && <div className='msp-control-offset'>
- <ParamHelp legend={help.legend} description={help.description} />
- </div>}
- </>;
+ return renderSimple({
+ props: this.props,
+ state: this.state,
+ control: this.renderControl(),
+ toggleHelp: this.toggleHelp,
+ addOn: this.renderAddOn()
+ });
}
}
@@ -214,17 +252,20 @@ export class NumberInputControl extends React.PureComponent<ParamProps<PD.Numeri
state = { value: '0' };
update = (value: number) => {
+ const p = getPrecision(this.props.param.step || 0.01)
+ value = parseFloat(value.toFixed(p))
this.props.onChange({ param: this.props.param, name: this.props.name, value });
}
render() {
const placeholder = this.props.param.label || camelCaseToWords(this.props.name);
const label = this.props.param.label || camelCaseToWords(this.props.name);
+ const p = getPrecision(this.props.param.step || 0.01)
return <div className='msp-control-row'>
<span title={this.props.param.description}>{label}</span>
<div>
<NumericInput
- value={this.props.value} onEnter={this.props.onEnter} placeholder={placeholder}
+ value={parseFloat(this.props.value.toFixed(p))} onEnter={this.props.onEnter} placeholder={placeholder}
isDisabled={this.props.isDisabled} onChange={this.update} />
</div>
</div>;
@@ -289,27 +330,97 @@ export class PureSelectControl extends React.PureComponent<ParamProps<PD.Select
}
}
-export class SelectControl extends SimpleParam<PD.Select<string | number>> {
- onChange = (e: React.ChangeEvent<HTMLSelectElement>) => {
- if (typeof this.props.param.defaultValue === 'number') {
- this.update(parseInt(e.target.value, 10));
+export class SelectControl extends React.PureComponent<ParamProps<PD.Select<string | number>>, { showHelp: boolean, showOptions: boolean }> {
+ state = { showHelp: false, showOptions: false };
+
+ onSelect: ActionMenu.OnSelect = item => {
+ if (!item || item.value === this.props.value) {
+ this.setState({ showOptions: false });
} else {
- this.update(e.target.value);
+ this.setState({ showOptions: false }, () => {
+ this.props.onChange({ param: this.props.param, name: this.props.name, value: item.value });
+ });
}
}
+
+ toggle = () => this.setState({ showOptions: !this.state.showOptions });
+
+ items = memoizeLatest((param: PD.Select<any>) => ActionMenu.createItemsFromSelectParam(param));
+
renderControl() {
- const isInvalid = this.props.value !== void 0 && !this.props.param.options.some(e => e[0] === this.props.value);
- return <select value={this.props.value !== void 0 ? this.props.value : this.props.param.defaultValue} onChange={this.onChange} disabled={this.props.isDisabled}>
- {isInvalid && <option key={this.props.value} value={this.props.value}>{`[Invalid] ${this.props.value}`}</option>}
- {this.props.param.options.map(([value, label]) => <option key={value} value={value}>{label}</option>)}
- </select>;
+ const items = this.items(this.props.param);
+ const current = this.props.value !== undefined ? ActionMenu.findItem(items, this.props.value) : void 0;
+ const label = current
+ ? current.label
+ : typeof this.props.value === 'undefined'
+ ? `${ActionMenu.getFirstItem(items)?.label || ''} [Default]`
+ : `[Invalid] ${this.props.value}`;
+
+ return <ToggleButton disabled={this.props.isDisabled} style={{ textAlign: 'left', overflow: 'hidden', textOverflow: 'ellipsis' }}
+ label={label} title={label as string} toggle={this.toggle} isSelected={this.state.showOptions} />;
+ }
+
+ renderAddOn() {
+ if (!this.state.showOptions) return null;
+
+ const items = this.items(this.props.param);
+ const current = ActionMenu.findItem(items, this.props.value);
+
+ return <ActionMenu items={items} current={current} onSelect={this.onSelect} />;
+ }
+
+ toggleHelp = () => this.setState({ showHelp: !this.state.showHelp });
+
+ render() {
+ return renderSimple({
+ props: this.props,
+ state: this.state,
+ control: this.renderControl(),
+ toggleHelp: this.toggleHelp,
+ addOn: this.renderAddOn()
+ });
}
}
-export class IntervalControl extends SimpleParam<PD.Interval> {
- onChange = (v: [number, number]) => { this.update(v); }
- renderControl() {
- return <span>interval TODO</span>;
+export class IntervalControl extends React.PureComponent<ParamProps<PD.Interval>, { isExpanded: boolean }> {
+ state = { isExpanded: false }
+
+ components = {
+ 0: PD.Numeric(0, { step: this.props.param.step }, { label: 'Min' }),
+ 1: PD.Numeric(0, { step: this.props.param.step }, { label: 'Max' })
+ }
+
+ change(value: PD.MultiSelect<any>['defaultValue']) {
+ this.props.onChange({ name: this.props.name, param: this.props.param, value });
+ }
+
+ componentChange: ParamOnChange = ({ name, value }) => {
+ const v = [...this.props.value];
+ v[+name] = value;
+ this.change(v);
+ }
+
+ toggleExpanded = (e: React.MouseEvent<HTMLButtonElement>) => {
+ this.setState({ isExpanded: !this.state.isExpanded });
+ e.currentTarget.blur();
+ }
+
+ render() {
+ const v = this.props.value;
+ const label = this.props.param.label || camelCaseToWords(this.props.name);
+ const p = getPrecision(this.props.param.step || 0.01)
+ const value = `[${v[0].toFixed(p)}, ${v[1].toFixed(p)}]`;
+ return <>
+ <div className='msp-control-row'>
+ <span>{label}</span>
+ <div>
+ <button onClick={this.toggleExpanded}>{value}</button>
+ </div>
+ </div>
+ <div className='msp-control-offset' style={{ display: this.state.isExpanded ? 'block' : 'none' }}>
+ <ParameterControls params={this.components} values={v} onChange={this.componentChange} onEnter={this.props.onEnter} />
+ </div>
+ </>;
}
}
@@ -399,9 +510,9 @@ export class Vec3Control extends React.PureComponent<ParamProps<PD.Vec3>, { isEx
state = { isExpanded: false }
components = {
- 0: PD.Numeric(0, void 0, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.x) || 'X' }),
- 1: PD.Numeric(0, void 0, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.y) || 'Y' }),
- 2: PD.Numeric(0, void 0, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.z) || 'Z' })
+ 0: PD.Numeric(0, { step: this.props.param.step }, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.x) || 'X' }),
+ 1: PD.Numeric(0, { step: this.props.param.step }, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.y) || 'Y' }),
+ 2: PD.Numeric(0, { step: this.props.param.step }, { label: (this.props.param.fieldLabels && this.props.param.fieldLabels.z) || 'Z' })
}
change(value: PD.MultiSelect<any>['defaultValue']) {
@@ -422,7 +533,8 @@ export class Vec3Control extends React.PureComponent<ParamProps<PD.Vec3>, { isEx
render() {
const v = this.props.value;
const label = this.props.param.label || camelCaseToWords(this.props.name);
- const value = `[${v[0].toFixed(2)}, ${v[1].toFixed(2)}, ${v[2].toFixed(2)}]`;
+ const p = getPrecision(this.props.param.step || 0.01)
+ const value = `[${v[0].toFixed(p)}, ${v[1].toFixed(p)}, ${v[2].toFixed(p)}]`;
return <>
<div className='msp-control-row'>
<span>{label}</span>
@@ -529,7 +641,7 @@ export class MultiSelectControl extends React.PureComponent<ParamProps<PD.MultiS
}
}
-export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>, { isExpanded: boolean }> {
+export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>> & { inMapped?: boolean }, { isExpanded: boolean }> {
state = { isExpanded: !!this.props.param.isExpanded }
change(value: any) {
@@ -552,6 +664,10 @@ export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>,
const controls = <ParameterControls params={params} onChange={this.onChangeParam} values={this.props.value} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />;
+ if (this.props.inMapped) {
+ return <div className='msp-control-offset'>{controls}</div>;
+ }
+
if (this.props.param.isFlat) {
return controls;
}
@@ -570,7 +686,9 @@ export class GroupControl extends React.PureComponent<ParamProps<PD.Group<any>>,
}
}
-export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>>> {
+export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>>, { isExpanded: boolean }> {
+ state = { isExpanded: false }
+
private valuesCache: { [name: string]: PD.Values<any> } = {}
private setValues(name: string, values: PD.Values<any>) {
this.valuesCache[name] = values
@@ -596,6 +714,8 @@ export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>
this.change({ name: this.props.value.name, params: e.value });
}
+ toggleExpanded = () => this.setState({ isExpanded: !this.state.isExpanded });
+
render() {
const value: PD.Mapped<any>['defaultValue'] = this.props.value;
const param = this.props.param.map(value.name);
@@ -618,6 +738,14 @@ export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>
return Select;
}
+ if (param.type === 'group' && !param.isFlat && Object.keys(param.params).length > 0) {
+ return <div className='msp-mapped-parameter-group'>
+ {Select}
+ <IconButton icon='log' onClick={this.toggleExpanded} toggleState={this.state.isExpanded} title={`${label} Properties`} />
+ {this.state.isExpanded && <GroupControl inMapped param={param} value={value.params} name={`${label} Properties`} onChange={this.onChangeParam} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />}
+ </div>
+ }
+
return <>
{Select}
<Mapped param={param} value={value.params} name={`${label} Properties`} onChange={this.onChangeParam} onEnter={this.props.onEnter} isDisabled={this.props.isDisabled} />
diff --git a/src/mol-plugin-ui/skin/base/components/controls.scss b/src/mol-plugin-ui/skin/base/components/controls.scss
index 8a0f44a4cd5bf72828f1d4e5ce42f92b582f6c6f..725039cf8f025c6aae4781b2134ec1b1a5a9686c 100644
--- a/src/mol-plugin-ui/skin/base/components/controls.scss
+++ b/src/mol-plugin-ui/skin/base/components/controls.scss
@@ -31,6 +31,7 @@
overflow: hidden;
text-overflow: ellipsis;
white-space: nowrap;
+ position: relative;
@include non-selectable;
}
diff --git a/src/mol-plugin-ui/skin/base/components/misc.scss b/src/mol-plugin-ui/skin/base/components/misc.scss
index 5208ebcec37b932de09e6fc9d5dc5103b51b38cd..a37bb0d4367c29a9d3a6fe8a3ed2fc31b6ff0709 100644
--- a/src/mol-plugin-ui/skin/base/components/misc.scss
+++ b/src/mol-plugin-ui/skin/base/components/misc.scss
@@ -166,4 +166,21 @@
.msp-scrollable-container {
left: $row-height + 1px;
}
+}
+
+.msp-mapped-parameter-group {
+ position: relative;
+
+ > .msp-control-row:first-child {
+ > div:nth-child(2) {
+ right: 33px;
+ }
+ }
+
+ > .msp-btn-icon {
+ position: absolute;
+ right: 0;
+ width: 32px;
+ top: 0;
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin-ui/skin/base/components/temp.scss b/src/mol-plugin-ui/skin/base/components/temp.scss
index 004a90f172d7f88a990b195e914aeb6ba1fda3e5..b614362ecbc4390fb85adbda052cbabca7ee8fc4 100644
--- a/src/mol-plugin-ui/skin/base/components/temp.scss
+++ b/src/mol-plugin-ui/skin/base/components/temp.scss
@@ -66,6 +66,7 @@
text-align-last: center;
background: none;
padding: 0 $control-spacing;
+ overflow: hidden;
> option[value = _] {
display: none;
@@ -274,4 +275,34 @@
.msp-transform-wrapper:last-child {
margin-bottom: 10px;
}
+}
+
+.msp-button-row {
+ display:flex;
+ flex-direction:row;
+ height: $row-height;
+ width: inherit;
+
+ > button {
+ margin: 0;
+ flex: 1 1 auto;
+ margin-right: 1px;
+ height: $row-height;
+
+ text-align-last: center;
+ background: none;
+ padding: 0 $control-spacing;
+ overflow: hidden;
+ }
+}
+
+.msp-action-menu-options {
+ .msp-control-row, button, .msp-icon {
+ height: 24px;
+ line-height: 24px;
+ }
+
+ button {
+ text-align: left;
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin-ui/structure/representation.tsx b/src/mol-plugin-ui/structure/representation.tsx
index 2dcc444e1c6fb6f544967c3355526cb32ba2e121..bef7495baf6691e21d9856a7994657fd18883185 100644
--- a/src/mol-plugin-ui/structure/representation.tsx
+++ b/src/mol-plugin-ui/structure/representation.tsx
@@ -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>
*/
@@ -13,8 +13,6 @@ import { Color } from '../../mol-util/color';
import { ButtonSelect, Options } from '../controls/common'
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { VisualQuality, VisualQualityOptions } from '../../mol-geo/geometry/base';
-import { StructureRepresentationPresets as P } from '../../mol-plugin/util/structure-representation-helper';
-import { camelCaseToWords } from '../../mol-util/string';
import { CollapsableControls } from '../base';
import { StateSelection, StateObject } from '../../mol-state';
import { PluginStateObject } from '../../mol-plugin/state/objects';
@@ -133,13 +131,6 @@ export class StructureRepresentationControls extends CollapsableControls<Collaps
this.subscribe(this.plugin.state.dataState.events.isUpdating, v => this.setState({ isDisabled: v }))
}
- preset = async (value: string) => {
- const presetFn = P[value as keyof typeof P]
- if (presetFn) {
- await presetFn(this.plugin.helpers.structureRepresentation)
- }
- }
-
onChange = async (p: { param: PD.Base<any>, name: string, value: any }) => {
if (p.name === 'options') {
await this.plugin.helpers.structureRepresentation.setIgnoreHydrogens(!p.value.showHydrogens)
@@ -178,15 +169,7 @@ export class StructureRepresentationControls extends CollapsableControls<Collaps
}
renderControls() {
- const presets = PD.objectToOptions(P, camelCaseToWords);
return <div>
- <div className='msp-control-row'>
- <div className='msp-select-row'>
- <ButtonSelect label='Preset' onChange={this.preset}>
- <optgroup label='Preset'>{Options(presets)}</optgroup>
- </ButtonSelect>
- </div>
- </div>
<EverythingStructureRepresentationControls />
<SelectionStructureRepresentationControls />
diff --git a/src/mol-plugin-ui/structure/selection.tsx b/src/mol-plugin-ui/structure/selection.tsx
index 8847ccc0b9e8154c62ce29936bed0e2e6c4bcae3..f7e380a84963e0cfea31e5e74c3aed2c9bc0bedd 100644
--- a/src/mol-plugin-ui/structure/selection.tsx
+++ b/src/mol-plugin-ui/structure/selection.tsx
@@ -1,28 +1,26 @@
/**
- * 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>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
import * as React from 'react';
import { CollapsableControls, CollapsableState } from '../base';
-import { StructureSelectionQueries, SelectionModifier } from '../../mol-plugin/util/structure-selection-helper';
-import { ButtonSelect, Options } from '../controls/common';
+import { StructureSelectionQuery, SelectionModifier, StructureSelectionQueryList } from '../../mol-plugin/util/structure-selection-helper';
import { PluginCommands } from '../../mol-plugin/command';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Interactivity } from '../../mol-plugin/util/interactivity';
import { ParameterControls } from '../controls/parameters';
import { stripTags } from '../../mol-util/string';
import { StructureElement } from '../../mol-model/structure';
+import { ActionMenu } from '../controls/action-menu';
+import { ToggleButton } from '../controls/common';
-const SSQ = StructureSelectionQueries
-const DefaultQueries: (keyof typeof SSQ)[] = [
- 'all', 'polymer', 'trace', 'backbone', 'protein', 'nucleic',
- 'helix', 'beta',
- 'water', 'branched', 'ligand', 'nonStandardPolymer',
- 'ring', 'aromaticRing',
- 'surroundings', 'complement', 'bonded'
-]
+export const DefaultQueries = ActionMenu.createItems(StructureSelectionQueryList, {
+ label: q => q.label,
+ category: q => q.category
+});
const StructureSelectionParams = {
granularity: Interactivity.Params.granularity,
@@ -33,7 +31,9 @@ interface StructureSelectionControlsState extends CollapsableState {
extraRadius: number,
durationMs: number,
- isDisabled: boolean
+ isDisabled: boolean,
+
+ queryAction?: SelectionModifier
}
export class StructureSelectionControls<P, S extends StructureSelectionControlsState> extends CollapsableControls<P, S> {
@@ -46,7 +46,9 @@ export class StructureSelectionControls<P, S extends StructureSelectionControlsS
this.forceUpdate()
});
- this.subscribe(this.plugin.state.dataState.events.isUpdating, v => this.setState({ isDisabled: v }))
+ this.subscribe(this.plugin.state.dataState.events.isUpdating, v => {
+ this.setState({ isDisabled: v, queryAction: void 0 })
+ })
}
get stats() {
@@ -115,38 +117,41 @@ export class StructureSelectionControls<P, S extends StructureSelectionControlsS
}
}
- set = (modifier: SelectionModifier, value: string) => {
- const query = SSQ[value as keyof typeof SSQ]
- this.plugin.helpers.structureSelection.set(modifier, query.query, false)
- }
-
- add = (value: string) => this.set('add', value)
- remove = (value: string) => this.set('remove', value)
- only = (value: string) => this.set('only', value)
-
- queries = Options(Object.keys(StructureSelectionQueries)
- .map(name => [name, SSQ[name as keyof typeof SSQ].label] as [string, string])
- .filter(pair => DefaultQueries.includes(pair[0] as keyof typeof SSQ)));
-
- controls = <div className='msp-control-row'>
- <div className='msp-select-row'>
- <ButtonSelect label='Select' onChange={this.add} disabled={this.state.isDisabled}>
- <optgroup label='Select'>
- {this.queries}
- </optgroup>
- </ButtonSelect>
- <ButtonSelect label='Deselect' onChange={this.remove} disabled={this.state.isDisabled}>
- <optgroup label='Deselect'>
- {this.queries}
- </optgroup>
- </ButtonSelect>
- <ButtonSelect label='Only' onChange={this.only} disabled={this.state.isDisabled}>
- <optgroup label='Only'>
- {this.queries}
- </optgroup>
- </ButtonSelect>
+ set = (modifier: SelectionModifier, selectionQuery: StructureSelectionQuery) => {
+ this.plugin.helpers.structureSelection.set(modifier, selectionQuery, false)
+ }
+
+ selectQuery: ActionMenu.OnSelect = item => {
+ if (!item || !this.state.queryAction) {
+ this.setState({ queryAction: void 0 });
+ return;
+ }
+ const q = this.state.queryAction!;
+ this.setState({ queryAction: void 0 }, () => {
+ this.set(q, item.value as StructureSelectionQuery);
+ })
+ }
+
+ queries = DefaultQueries
+
+ private showQueries(q: SelectionModifier) {
+ return () => this.setState({ queryAction: this.state.queryAction === q ? void 0 : q });
+ }
+
+ toggleAdd = this.showQueries('add')
+ toggleRemove = this.showQueries('remove')
+ toggleOnly = this.showQueries('only')
+
+ get controls() {
+ return <div>
+ <div className='msp-control-row msp-button-row'>
+ <ToggleButton label='Select' toggle={this.toggleAdd} isSelected={this.state.queryAction === 'add'} disabled={this.state.isDisabled} />
+ <ToggleButton label='Deselect' toggle={this.toggleRemove} isSelected={this.state.queryAction === 'remove'} disabled={this.state.isDisabled} />
+ <ToggleButton label='Only' toggle={this.toggleOnly} isSelected={this.state.queryAction === 'only'} disabled={this.state.isDisabled} />
+ </div>
+ {this.state.queryAction && <ActionMenu items={this.queries} onSelect={this.selectQuery} />}
</div>
- </div>
+ }
defaultState() {
return {
@@ -157,6 +162,8 @@ export class StructureSelectionControls<P, S extends StructureSelectionControlsS
extraRadius: 4,
durationMs: 250,
+ queryAction: void 0,
+
isDisabled: false
} as S
}
diff --git a/src/mol-plugin-ui/viewport/simple-settings.tsx b/src/mol-plugin-ui/viewport/simple-settings.tsx
index 387e0154319e1b650725ccdc27eeaecbc10c2596..11c6b703f18c3bf991e0acbf09e81bd15f0c34b0 100644
--- a/src/mol-plugin-ui/viewport/simple-settings.tsx
+++ b/src/mol-plugin-ui/viewport/simple-settings.tsx
@@ -9,10 +9,23 @@ import * as React from 'react';
import { Canvas3DParams } from '../../mol-canvas3d/canvas3d';
import { PluginCommands } from '../../mol-plugin/command';
import { ColorNames } from '../../mol-util/color/names';
-import { ParameterControls } from '../controls/parameters';
+import { ParameterMappingControl } from '../controls/parameters';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PluginUIComponent } from '../base';
import { Color } from '../../mol-util/color';
+import { ParamMapping } from '../../mol-util/param-mapping';
+import { PluginContext } from '../../mol-plugin/context';
+
+export class SimpleSettingsControl extends PluginUIComponent {
+ componentDidMount() {
+ this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+ }
+
+ render() {
+ if (!this.plugin.canvas3d) return null;
+ return <ParameterMappingControl mapping={SimpleSettingsMapping} />
+ }
+}
const SimpleSettingsParams = {
spin: Canvas3DParams.trackball.params.spin,
@@ -21,80 +34,21 @@ 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', [['flat', 'Flat'], ['matte', 'Matte'], ['glossy', 'Glossy'], ['metallic', 'Metallic']], { description: 'Style in which the 3D scene is rendered' }),
+ renderStyle: PD.Select('glossy', PD.arrayToOptions(['flat', 'matte', 'glossy', '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' }),
clipFar: PD.Boolean(true, { description: 'Clip scene in the distance' }),
};
-export class SimpleSettingsControl extends PluginUIComponent {
- setSettings = (p: { param: PD.Base<any>, name: keyof typeof SimpleSettingsParams | string, value: any }) => {
- if (p.name === 'spin') {
- if (!this.plugin.canvas3d) return;
- const trackball = this.plugin.canvas3d.props.trackball;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: p.value } } });
- } else if (p.name === 'camera') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { cameraMode: p.value }});
- } else if (p.name === 'background') {
- if (!this.plugin.canvas3d) return;
- const renderer = this.plugin.canvas3d.props.renderer;
- const color: typeof SimpleSettingsParams['background']['defaultValue'] = p.value;
- if (color.name === 'transparent') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white }, transparentBackground: true } });
- } else {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: color.params.color }, transparentBackground: false } });
- }
- } else if (p.name === 'renderStyle') {
- if (!this.plugin.canvas3d) return;
-
- const renderer = this.plugin.canvas3d.props.renderer;
- if (p.value === 'flat') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- renderer: { ...renderer, lightIntensity: 0, ambientIntensity: 1, roughness: 0.4, metalness: 0 }
- } });
- } else if (p.value === 'matte') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 1, metalness: 0 }
- } });
- } else if (p.value === 'glossy') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.4, metalness: 0 }
- } });
- } else if (p.value === 'metallic') {
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.6, metalness: 0.4 }
- } });
- }
- } else if (p.name === 'occlusion') {
- if (!this.plugin.canvas3d) return;
- const postprocessing = this.plugin.canvas3d.props.postprocessing;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- postprocessing: { ...postprocessing, occlusionEnable: p.value, occlusionBias: 0.5, occlusionRadius: 64 },
- } });
- } else if (p.name === 'outline') {
- if (!this.plugin.canvas3d) return;
- const postprocessing = this.plugin.canvas3d.props.postprocessing;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- postprocessing: { ...postprocessing, outlineEnable: p.value },
- } });
- } else if (p.name === 'fog') {;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- cameraFog: p.value ? 50 : 0,
- } });
- } else if (p.name === 'clipFar') {;
- PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
- cameraClipFar: p.value,
- } });
- }
- }
-
- get values () {
- const renderer = this.plugin.canvas3d?.props.renderer;
-
- let renderStyle = 'custom'
- let background: typeof SimpleSettingsParams['background']['defaultValue'] = { name: 'transparent', params: { } }
+type SimpleSettingsParams = typeof SimpleSettingsParams
+const SimpleSettingsMapping = ParamMapping({
+ params: SimpleSettingsParams,
+ target(ctx: PluginContext) { return ctx.canvas3d?.props!; } })({
+ values(t, ctx) {
+ const renderer = t.renderer;
+ let renderStyle: SimpleSettingsParams['renderStyle']['defaultValue'] = 'custom' as any;
if (renderer) {
if (renderer.lightIntensity === 0 && renderer.ambientIntensity === 1 && renderer.roughness === 0.4 && renderer.metalness === 0) {
renderStyle = 'flat'
@@ -107,31 +61,42 @@ export class SimpleSettingsControl extends PluginUIComponent {
renderStyle = 'metallic'
}
}
-
- if (renderer.backgroundColor === ColorNames.white && this.plugin.canvas3d?.props.transparentBackground) {
- background = { name: 'transparent', params: { } }
- } else {
- background = { name: 'opaque', params: { color: renderer.backgroundColor } }
- }
}
return {
- spin: !!this.plugin.canvas3d?.props.trackball.spin,
- camera: this.plugin.canvas3d?.props.cameraMode,
- background,
+ spin: !!t.trackball.spin,
+ camera: t.cameraMode,
+ background: (renderer.backgroundColor === ColorNames.white && t.transparentBackground)
+ ? { name: 'transparent', params: { } }
+ : { name: 'opaque', params: { color: renderer.backgroundColor } },
renderStyle,
- occlusion: this.plugin.canvas3d?.props.postprocessing.occlusionEnable,
- outline: this.plugin.canvas3d?.props.postprocessing.outlineEnable,
- fog: this.plugin.canvas3d ? this.plugin.canvas3d.props.cameraFog > 1 : false,
- clipFar: this.plugin.canvas3d?.props.cameraClipFar
+ occlusion: t.postprocessing.occlusionEnable,
+ outline: t.postprocessing.outlineEnable,
+ fog: ctx.canvas3d ? t.cameraFog > 1 : false,
+ clipFar: t.cameraClipFar
+ };
+ },
+ update(s, t) {
+ t.trackball.spin = s.spin;
+ t.cameraMode = s.camera;
+ t.transparentBackground = s.background.name === 'transparent';
+ t.renderer.backgroundColor = s.background.name === 'transparent' ? ColorNames.white : s.background.params.color;
+ switch (s.renderStyle) {
+ case 'flat': Object.assign(t.renderer, { lightIntensity: 0, ambientIntensity: 1, roughness: 0.4, metalness: 0 }); break;
+ case 'matte': Object.assign(t.renderer, { lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 1, metalness: 0 }); break;
+ case 'glossy': Object.assign(t.renderer, { lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.4, metalness: 0 }); break;
+ case 'metallic': Object.assign(t.renderer, { lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.6, metalness: 0.4 }); break;
}
+ t.postprocessing.occlusionEnable = s.occlusion;
+ if (s.occlusion) {
+ t.postprocessing.occlusionBias = 0.5;
+ t.postprocessing.occlusionRadius = 64;
+ }
+ t.postprocessing.outlineEnable = s.outline;
+ t.cameraFog = s.fog ? 50 : 0;
+ t.cameraClipFar = s.clipFar;
+ },
+ apply(settings, ctx) {
+ return PluginCommands.Canvas3D.SetSettings.dispatch(ctx, { settings });
}
-
- componentDidMount() {
- this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
- }
-
- render() {
- return <ParameterControls params={SimpleSettingsParams} values={this.values} onChange={this.setSettings} />
- }
-}
\ No newline at end of file
+})
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/custom-props.ts b/src/mol-plugin/behavior/dynamic/custom-props.ts
index 6b5428cacbec1b4744308c6d5f88bdef7fb5b426..91586c5cfe9ac4294e0b5896f769604f5cee8e2e 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props.ts
@@ -10,6 +10,8 @@ export { Interactions } from './custom-props/computed/interactions'
export { SecondaryStructure } from './custom-props/computed/secondary-structure'
export { ValenceModel } from './custom-props/computed/valence-model'
+export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint'
+
export { PDBeStructureQualityReport } from './custom-props/pdbe/structure-quality-report'
export { RCSBAssemblySymmetry } from './custom-props/rcsb/assembly-symmetry'
export { RCSBValidationReport } from './custom-props/rcsb/validation-report'
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts b/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
index aa95e36eb6e73a018fe22ebfbf13857eb78b0669..b5013fced3479ffdcc2b73838a4755ad3d472a5e 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
@@ -11,6 +11,7 @@ import { Loci } from '../../../../../mol-model/loci';
import { AccessibleSurfaceAreaColorThemeProvider } from '../../../../../mol-model-props/computed/themes/accessible-surface-area';
import { OrderedSet } from '../../../../../mol-data/int';
import { arraySum } from '../../../../../mol-util/array';
+import { DefaultQueryRuntimeTable } from '../../../../../mol-script/runtime/query/compiler';
export const AccessibleSurfaceArea = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'computed-accessible-surface-area-prop',
@@ -36,12 +37,17 @@ export const AccessibleSurfaceArea = PluginBehavior.create<{ autoAttach: boolean
}
register(): void {
+ DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+
this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('accessible-surface-area', AccessibleSurfaceAreaColorThemeProvider)
this.ctx.lociLabels.addProvider(this.label);
}
unregister() {
+ // TODO
+ // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+
this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('accessible-surface-area')
this.ctx.lociLabels.removeProvider(this.label);
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.ts b/src/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a1a105666a5813a1cf7583e3f6247a886b7f5ec4
--- /dev/null
+++ b/src/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.ts
@@ -0,0 +1,45 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginBehavior } from '../../../behavior';
+import { ModelCrossLinkRestraint } from '../../../../../mol-model-props/integrative/cross-link-restraint/format';
+import { Model } from '../../../../../mol-model/structure';
+import { MmcifFormat } from '../../../../../mol-model-formats/structure/mmcif';
+import { CrossLinkRestraintRepresentationProvider } from '../../../../../mol-model-props/integrative/cross-link-restraint/representation';
+import { CrossLinkColorThemeProvider } from '../../../../../mol-model-props/integrative/cross-link-restraint/color';
+import { CrossLinkRestraint as _CrossLinkRestraint } from '../../../../../mol-model-props/integrative/cross-link-restraint/property';
+
+const Tag = _CrossLinkRestraint.Tag
+
+export const CrossLinkRestraint = PluginBehavior.create<{ }>({
+ name: 'integrative-cross-link-restraint',
+ category: 'custom-props',
+ display: { name: 'Cross Link Restraint' },
+ ctor: class extends PluginBehavior.Handler<{ }> {
+ private provider = ModelCrossLinkRestraint.Provider
+
+ register(): void {
+ this.provider.formatRegistry.add('mmCIF', crossLinkRestraintFromMmcif)
+
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add(Tag.CrossLinkRestraint, CrossLinkColorThemeProvider)
+ this.ctx.structureRepresentation.registry.add(Tag.CrossLinkRestraint, CrossLinkRestraintRepresentationProvider)
+ }
+
+ unregister() {
+ this.provider.formatRegistry.remove('mmCIF')
+
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove(Tag.CrossLinkRestraint)
+ this.ctx.structureRepresentation.registry.remove(Tag.CrossLinkRestraint)
+ }
+ }
+});
+
+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)
+}
\ No newline at end of file
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 69742b2992896625fd383526de1a7e8183c90520..ce22b7c29bed4f7e5215c66bec5bbfdbdc47476e 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
@@ -15,7 +15,10 @@ import { PluginBehavior } from '../../../behavior';
export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'pdbe-structure-quality-report-prop',
category: 'custom-props',
- display: { name: 'PDBe Structure Quality Report' },
+ display: {
+ name: 'Structure Quality Report',
+ description: 'Data from wwPDB Validation Report, obtained via PDBe.'
+ },
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
private provider = StructureQualityReportProvider
@@ -32,8 +35,8 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
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(', ')}`;
+ if (issues.length === 0) return 'Validation: No Issues';
+ return `Validation: ${issues.join(', ')}`;
default: return void 0;
}
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
index 803f2b45daeed063f6e8d43ead4fde991f1f5df0..32aeba1bd6b85eec5bbd8d2580a64fc0686b1900 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
@@ -14,17 +14,22 @@ import { Task } from '../../../../../mol-task';
import { PluginContext } from '../../../../context';
import { StateTransformer, StateAction, StateObject } from '../../../../../mol-state';
+const Tag = AssemblySymmetry.Tag
+
export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean }>({
name: 'rcsb-assembly-symmetry-prop',
category: 'custom-props',
- display: { name: 'RCSB Assembly Symmetry' },
+ display: {
+ name: 'Assembly Symmetry',
+ description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.'
+ },
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
private provider = AssemblySymmetryProvider
register(): void {
this.ctx.state.dataState.actions.add(InitAssemblySymmetry3D)
this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
- this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('rcsb-assembly-symmetry-cluster', AssemblySymmetryClusterColorThemeProvider)
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add(Tag.Cluster, AssemblySymmetryClusterColorThemeProvider)
}
update(p: { autoAttach: boolean }) {
@@ -37,7 +42,7 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
unregister() {
this.ctx.state.dataState.actions.remove(InitAssemblySymmetry3D)
this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
- this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('rcsb-assembly-symmetry-cluster')
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove(Tag.Cluster)
}
},
params: () => ({
@@ -47,24 +52,32 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
});
const InitAssemblySymmetry3D = StateAction.build({
- display: { name: 'RCSB Assembly Symmetry' },
+ display: {
+ name: 'Assembly Symmetry',
+ description: 'Initialize Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+ },
from: PluginStateObject.Molecule.Structure,
isApplicable: (a) => AssemblySymmetry.isApplicable(a.data)
-})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init RCSB Assembly Symmetry', async ctx => {
+})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => {
try {
await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
} catch(e) {
- plugin.log.error(`RCSB Assembly Symmetry: ${e}`)
+ plugin.log.error(`Assembly Symmetry: ${e}`)
return
}
const tree = state.build().to(ref).apply(AssemblySymmetry3D);
await state.updateTree(tree).runInContext(ctx);
}));
+export { AssemblySymmetry3D }
+
type AssemblySymmetry3D = typeof AssemblySymmetry3D
const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
- name: 'rcsb-assembly-symmetry-3d',
- display: 'RCSB Assembly Symmetry',
+ name: Tag.Representation,
+ display: {
+ name: 'Assembly Symmetry',
+ description: 'Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+ },
from: PluginStateObject.Molecule.Structure,
to: PluginStateObject.Shape.Representation3D,
params: (a) => {
@@ -78,7 +91,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
return true;
},
apply({ a, params }, plugin: PluginContext) {
- return Task.create('RCSB Assembly Symmetry', async ctx => {
+ return Task.create('Assembly Symmetry', async ctx => {
await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value
if (!assemblySymmetry || assemblySymmetry.length === 0) {
@@ -91,7 +104,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
});
},
update({ a, b, newParams }, plugin: PluginContext) {
- return Task.create('RCSB Assembly Symmetry', async ctx => {
+ return Task.create('Assembly Symmetry', async ctx => {
await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value
if (!assemblySymmetry || assemblySymmetry.length === 0) {
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
index e8ec2fad939d038830e26bdad8da2d1c762361f7..94b90517cc7f6da20f045dcce6f745acb00e1afd 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
@@ -14,13 +14,17 @@ import { OrderedSet } from '../../../../../mol-data/int';
import { ClashesRepresentationProvider } from '../../../../../mol-model-props/rcsb/representations/validation-report-clashes';
import { DensityFitColorThemeProvider } from '../../../../../mol-model-props/rcsb/themes/density-fit';
import { cantorPairing } from '../../../../../mol-data/util';
+import { DefaultQueryRuntimeTable } from '../../../../../mol-script/runtime/query/compiler';
const Tag = ValidationReport.Tag
export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'rcsb-validation-report-prop',
category: 'custom-props',
- display: { name: 'RCSB Validation Report' },
+ display: {
+ name: 'Validation Report',
+ description: 'Data from wwPDB Validation Report, obtained via RCSB PDB.'
+ },
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
private provider = ValidationReportProvider
@@ -34,6 +38,8 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
}
register(): void {
+ DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+
this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
this.ctx.lociLabels.addProvider(this.label);
@@ -54,6 +60,9 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
}
unregister() {
+ // TODO
+ // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+
this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
this.ctx.lociLabels.removeProvider(this.label);
@@ -93,7 +102,7 @@ function geometryQualityLabel(loci: Loci): string | undefined {
if (angles) angles.forEach(a => issues.add(angleOutliers.data[a].tag))
if (issues.size === 0) {
- return `RCSB Geometry Quality <small>(1 Atom)</small>: no issues`;
+ return `Geometry Quality <small>(1 Atom)</small>: no issues`;
}
const summary: string[] = []
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index ed27bf3cadff50819fe399260972f5498a4b0b9d..85e873d15309e9d490c547ee8fbbff889497431e 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -93,8 +93,8 @@ export namespace VolumeStreaming {
}, { description: 'Static box defined by cartesian coords.', isFlat: true }),
'selection-box': PD.Group({
radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }, { description: 'Radius in \u212B within which the volume is shown.' }),
- bottomLeft: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
- topRight: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
+ bottomLeft: PD.Vec3(Vec3.create(0, 0, 0), {}, { isHidden: true }),
+ topRight: PD.Vec3(Vec3.create(0, 0, 0), {}, { isHidden: true }),
}, { description: 'Box around last-interacted element.', isFlat: true }),
'cell': PD.Group({}),
// 'auto': PD.Group({ }), // TODO based on camera distance/active selection/whatever, show whole structure or slice.
diff --git a/src/mol-plugin/behavior/static/camera.ts b/src/mol-plugin/behavior/static/camera.ts
index 32971d8edc6ae922e406d40e21293f20c74290a0..dbe81f4af08aa43ab72f2f00ed78f390744aa2c7 100644
--- a/src/mol-plugin/behavior/static/camera.ts
+++ b/src/mol-plugin/behavior/static/camera.ts
@@ -15,8 +15,8 @@ export function registerDefault(ctx: PluginContext) {
}
export function Reset(ctx: PluginContext) {
- PluginCommands.Camera.Reset.subscribe(ctx, () => {
- ctx.canvas3d?.requestCameraReset();
+ PluginCommands.Camera.Reset.subscribe(ctx, options => {
+ ctx.canvas3d?.requestCameraReset(options);
})
}
diff --git a/src/mol-plugin/command.ts b/src/mol-plugin/command.ts
index a861e3ba3f4b70527e3c06f5a7bda3268467bf2b..e4e8e8532dccb0eeb8e2085f230563d3830072df 100644
--- a/src/mol-plugin/command.ts
+++ b/src/mol-plugin/command.ts
@@ -59,7 +59,7 @@ export const PluginCommands = {
Hide: PluginCommand<{ key: string }>()
},
Camera: {
- Reset: PluginCommand<{}>(),
+ Reset: PluginCommand<{ durationMs?: number, snapshot?: Partial<Camera.Snapshot> }>(),
SetSnapshot: PluginCommand<{ snapshot: Partial<Camera.Snapshot>, durationMs?: number }>(),
Snapshots: {
Add: PluginCommand<{ name?: string, description?: string }>(),
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 9c43953cd18827be185aeac38a5988635e214bc9..16fcadc04e4c3a240ebadd97ee9f6c7e2377d3ab 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -70,14 +70,17 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
+ PluginSpec.Behavior(StructureRepresentationInteraction),
+
PluginSpec.Behavior(PluginBehaviors.CustomProps.AccessibleSurfaceArea),
PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
+ PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
+
PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport, { autoAttach: true, showTooltip: true }),
PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBAssemblySymmetry),
PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBValidationReport),
- PluginSpec.Behavior(StructureRepresentationInteraction)
],
customParamEditors: [
[CreateVolumeStreamingBehavior, VolumeStreamingCustomControls]
diff --git a/src/mol-plugin/state/representation/model.ts b/src/mol-plugin/state/representation/model.ts
index 47abb3649f33ac19334f3edca6fddc52675692c9..fee6cbda0b3429fbb55548eb5b03127da3f9b3e0 100644
--- a/src/mol-plugin/state/representation/model.ts
+++ b/src/mol-plugin/state/representation/model.ts
@@ -1,12 +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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Model, Structure, StructureSymmetry } from '../../../mol-model/structure';
import { stringToWords } from '../../../mol-util/string';
-import { SpacegroupCell } from '../../../mol-math/geometry';
+import { SpacegroupCell, Spacegroup } from '../../../mol-math/geometry';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { RuntimeContext } from '../../../mol-task';
@@ -16,12 +17,28 @@ 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') {
+ export function getParams(model?: Model, defaultValue?: 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {
const symmetry = model && ModelSymmetry.Provider.get(model)
const assemblyIds = symmetry ? symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : [];
const showSymm = !symmetry ? true : !SpacegroupCell.isZero(symmetry.spacegroup.cell);
+ const operatorOptions: [number, string][] = []
+ if (symmetry) {
+ const { operators } = symmetry.spacegroup
+ for (let i = 0, il = operators.length; i < il; i++) {
+ operatorOptions.push([i, `${i + 1}: ${Spacegroup.getOperatorXyz(operators[i])}`])
+ }
+ }
+
+ const asymIdsOptions: [string, string][] = []
+ if (model) {
+ model.properties.structAsymMap.forEach(v => {
+ const label = v.id === v.auth_id ? v.id : `${v.id} [auth ${v.auth_id}]`
+ asymIdsOptions.push([v.id, label])
+ })
+ }
+
const modes = {
deposited: PD.EmptyGroup(),
assembly: PD.Group({
@@ -33,8 +50,21 @@ export namespace ModelStructureRepresentation {
radius: PD.Numeric(5)
}, { isFlat: true }),
'symmetry': PD.Group({
- ijkMin: PD.Vec3(Vec3.create(-1, -1, -1), { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }),
- ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
+ ijkMin: PD.Vec3(Vec3.create(-1, -1, -1), { step: 1 }, { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }),
+ ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
+ }, { isFlat: true }),
+ 'symmetry-assembly': PD.Group({
+ generators: PD.ObjectList({
+ operators: PD.ObjectList({
+ index: PD.Select(0, operatorOptions),
+ shift: PD.Vec3(Vec3(), { step: 1 }, { label: 'IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
+ }, e => `${e.index + 1}_${e.shift.map(a => a + 5).join('')}`, {
+ defaultValue: [] as { index: number, shift: Vec3 }[]
+ }),
+ asymIds: PD.MultiSelect([] as string[], asymIdsOptions)
+ }, e => `${e.asymIds.length} asym ids, ${e.operators.length} operators`, {
+ defaultValue: [] as { operators: { index: number, shift: Vec3 }[], asymIds: string[] }[]
+ })
}, { isFlat: true })
};
@@ -49,6 +79,7 @@ export namespace ModelStructureRepresentation {
if (showSymm) {
options.push(['symmetry-mates', 'Symmetry Mates']);
options.push(['symmetry', 'Symmetry (indices)']);
+ options.push(['symmetry-assembly', 'Symmetry (assembly)']);
}
return {
@@ -105,8 +136,16 @@ export namespace ModelStructureRepresentation {
return new SO.Molecule.Structure(s, props);
}
+ async function buildSymmetryAssembly(ctx: RuntimeContext, model: Model, generators: StructureSymmetry.Generators, symmetry: Symmetry) {
+ const base = Structure.ofModel(model);
+ const s = await StructureSymmetry.buildSymmetryAssembly(base, generators, symmetry).runInContext(ctx);
+ const props = { label: `Symmetry Assembly`, description: Structure.elementDescription(s) };
+ return new SO.Molecule.Structure(s, props);
+ }
+
export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise<SO.Molecule.Structure> {
- if (!params || params.name === 'deposited') {
+ const symmetry = ModelSymmetry.Provider.get(model)
+ if (!symmetry || !params || params.name === 'deposited') {
const s = Structure.ofModel(model);
return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
}
@@ -119,6 +158,9 @@ export namespace ModelStructureRepresentation {
if (params.name === 'symmetry-mates') {
return buildSymmetryMates(ctx, model, params.params.radius)
}
+ if (params.name === 'symmetry-assembly') {
+ return buildSymmetryAssembly(ctx, model, params.params.generators, symmetry)
+ }
throw new Error(`Unknown represetation type: ${(params as any).name}`);
}
diff --git a/src/mol-plugin/state/representation/structure/preset.ts b/src/mol-plugin/state/representation/structure/preset.ts
index 418cbb6405616bf58e8c5bb0770f51922380e938..f9bebdd26fc8923bed8ce14d8a929d7f9ee4240b 100644
--- a/src/mol-plugin/state/representation/structure/preset.ts
+++ b/src/mol-plugin/state/representation/structure/preset.ts
@@ -52,7 +52,7 @@ const defaultPreset = StructureRepresentationProvider({
const ligandRepr = ligand.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure));
- applyComplex(root, 'modified')
+ applyComplex(root, 'non-standard')
.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.getDefaultParamsWithTheme(plugin, 'ball-and-stick', 'polymer-id', structure, void 0));
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index d593a97b01f8ae8f2aa79c5d5577ee468e0eee94..bb25ec0f9a602b8581483ce21003e4c117dbe993 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -16,7 +16,6 @@ import Expression from '../../../mol-script/language/expression';
import { StateObject, StateTransformer } from '../../../mol-state';
import { RuntimeContext, Task } from '../../../mol-task';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { stringToWords } from '../../../mol-util/string';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { trajectoryFromGRO } from '../../../mol-model-formats/structure/gro';
import { parseGRO } from '../../../mol-io/reader/gro/parser';
@@ -32,7 +31,6 @@ 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 };
@@ -45,7 +43,6 @@ export { TrajectoryFrom3DG };
export { ModelFromTrajectory };
export { StructureFromTrajectory };
export { StructureFromModel };
-export { StructureAssemblyFromModel };
export { TransformStructureConformation };
export { TransformStructureConformationByMatrix };
export { StructureSelectionFromExpression };
@@ -290,32 +287,6 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
}
});
-// TODO: deprecate this in favor of StructureFromModel
-type StructureAssemblyFromModel = typeof StructureAssemblyFromModel
-const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
- name: 'structure-assembly-from-model',
- display: { name: 'Structure Assembly', description: 'Create a molecular structure assembly.' },
- from: SO.Molecule.Model,
- to: SO.Molecule.Structure,
- params(a) {
- 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 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' }))
- };
- }
-})({
- apply({ a, params }, plugin: PluginContext) {
- return Task.create('Build Assembly', async ctx => {
- return ModelStructureRepresentation.create(plugin, ctx, a.data, { name: 'assembly', params });
- })
- }
-});
-
const _translation = Vec3(), _m = Mat4(), _n = Mat4();
type TransformStructureConformation = typeof TransformStructureConformation
const TransformStructureConformation = PluginStateTransform.BuiltIn({
@@ -643,7 +614,7 @@ export const StructureComplexElementTypes = {
'branched': 'branched', // = carbs
'ligand': 'ligand',
- 'modified': 'modified',
+ 'non-standard': 'non-standard',
'coarse': 'coarse',
@@ -678,7 +649,7 @@ const StructureComplexElement = PluginStateTransform.BuiltIn({
case 'branched': query = StructureSelectionQueries.branchedPlusConnected.query; label = 'Branched'; break;
case 'ligand': query = StructureSelectionQueries.ligandPlusConnected.query; label = 'Ligand'; break;
- case 'modified': query = StructureSelectionQueries.modified.query; label = 'Modified'; break;
+ case 'non-standard': query = StructureSelectionQueries.nonStandardPolymer.query; label = 'Non-standard'; break;
case 'coarse': query = StructureSelectionQueries.coarse.query; label = 'Coarse'; break;
@@ -719,7 +690,7 @@ async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: Runti
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]
+ const props = properties[name]
if (autoAttach.includes(name)) {
try {
await property.attach(propertyCtx, model, props)
@@ -754,7 +725,7 @@ async function attachStructureProps(structure: Structure, ctx: PluginContext, ta
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]
+ const props = properties[name]
if (autoAttach.includes(name)) {
try {
await property.attach(propertyCtx, structure, props)
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 611d19c55790844b5bd6f68bb60c8121f857f134..263060eaa25003721fdcc19f05d5eb62270cc4a2 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -63,37 +63,40 @@ namespace StructureRepresentation3DHelpers {
})
}
+ export type Props<R extends RepresentationProvider<Structure, any, any> = any, C extends ColorTheme.Provider<any> = any, S extends SizeTheme.Provider<any> = any> = {
+ repr?: R | [R, (r: R, ctx: ThemeRegistryContext, s: Structure) => Partial<RepresentationProvider.ParamValues<R>>],
+ color?: C | [C, (c: C, ctx: ThemeRegistryContext) => Partial<ColorTheme.ParamValues<C>>],
+ size?: S | [S, (c: S, ctx: ThemeRegistryContext) => Partial<SizeTheme.ParamValues<S>>]
+ }
+
export function createParams<R extends RepresentationProvider<Structure, any, any>, C extends ColorTheme.Provider<any>, S extends SizeTheme.Provider<any>>(
- ctx: PluginContext, structure: Structure, params: {
- repr?: R | [R, (r: R, ctx: ThemeRegistryContext, s: Structure) => Partial<RepresentationProvider.ParamValues<R>>],
- color?: C | [C, (c: C, ctx: ThemeRegistryContext) => Partial<ColorTheme.ParamValues<C>>],
- size?: S | [S, (c: S, ctx: ThemeRegistryContext) => Partial<SizeTheme.ParamValues<S>>]
- }): StateTransformer.Params<StructureRepresentation3D> {
+ ctx: PluginContext, structure: Structure, props: Props<R, C, S> = {}): StateTransformer.Params<StructureRepresentation3D> {
- const themeCtx = ctx.structureRepresentation.themeCtx
+ const { themeCtx } = ctx.structureRepresentation
+ const themeDataCtx = { structure }
- const repr = params.repr
- ? params.repr instanceof Array ? params.repr[0] : params.repr
+ const repr = props.repr
+ ? props.repr instanceof Array ? props.repr[0] : props.repr
: ctx.structureRepresentation.registry.default.provider;
const reprDefaultParams = PD.getDefaultValues(repr.getParams(themeCtx, structure));
- const reprParams = params.repr instanceof Array
- ? { ...reprDefaultParams, ...params.repr[1](repr as R, themeCtx, structure) }
+ const reprParams = props.repr instanceof Array
+ ? { ...reprDefaultParams, ...props.repr[1](repr as R, themeCtx, structure) }
: reprDefaultParams;
- const color = params.color
- ? params.color instanceof Array ? params.color[0] : params.color
+ const color = props.color
+ ? props.color instanceof Array ? props.color[0] : props.color
: themeCtx.colorThemeRegistry.get(repr.defaultColorTheme.name);
- const colorDefaultParams = { ...PD.getDefaultValues(color.getParams(themeCtx)), ...repr.defaultColorTheme.props }
- const colorParams = params.color instanceof Array
- ? { ...colorDefaultParams, ...params.color[1](color as C, themeCtx) }
+ const colorDefaultParams = { ...PD.getDefaultValues(color.getParams(themeDataCtx)), ...repr.defaultColorTheme.props }
+ const colorParams = props.color instanceof Array
+ ? { ...colorDefaultParams, ...props.color[1](color as C, themeCtx) }
: colorDefaultParams;
- const size = params.size
- ? params.size instanceof Array ? params.size[0] : params.size
+ const size = props.size
+ ? props.size instanceof Array ? props.size[0] : props.size
: themeCtx.sizeThemeRegistry.get(repr.defaultSizeTheme.name);
- const sizeDefaultParams = { ...PD.getDefaultValues(size.getParams(themeCtx)), ...repr.defaultSizeTheme.props }
- const sizeParams = params.size instanceof Array
- ? { ...sizeDefaultParams, ...params.size[1](size as S, themeCtx) }
+ const sizeDefaultParams = { ...PD.getDefaultValues(size.getParams(themeDataCtx)), ...repr.defaultSizeTheme.props }
+ const sizeParams = props.size instanceof Array
+ ? { ...sizeDefaultParams, ...props.size[1](size as S, themeCtx) }
: sizeDefaultParams;
return ({
diff --git a/src/mol-plugin/util/structure-complex-helper.ts b/src/mol-plugin/util/structure-complex-helper.ts
index 59a428cc8f037ba995e6dfad62ef1d1384c9558e..af783510d5b2d0fe6786adf52226b8e17497b97e 100644
--- a/src/mol-plugin/util/structure-complex-helper.ts
+++ b/src/mol-plugin/util/structure-complex-helper.ts
@@ -22,7 +22,7 @@ export function createDefaultStructureComplex(
.apply(StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick'));
- root.apply(StateTransforms.Model.StructureComplexElement, { type: 'modified' }, { tags: StructureComplexElementTypes.modified })
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'non-standard' }, { tags: StructureComplexElementTypes['non-standard'] })
.apply(StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', void 0, 'polymer-id'));
diff --git a/src/mol-plugin/util/structure-overpaint-helper.ts b/src/mol-plugin/util/structure-overpaint-helper.ts
index 05d7ea690925ad9ce6b893b9be46daafeb38c0a7..5a2b2da67e59e51c4b2e3c93618aa93c0cbda5ad 100644
--- a/src/mol-plugin/util/structure-overpaint-helper.ts
+++ b/src/mol-plugin/util/structure-overpaint-helper.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>
*/
@@ -7,10 +7,12 @@
import { PluginStateObject } from '../../mol-plugin/state/objects';
import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
-import { Structure, StructureElement } from '../../mol-model/structure';
+import { Structure, StructureElement, StructureSelection, QueryContext } from '../../mol-model/structure';
import { PluginContext } from '../context';
import { Color } from '../../mol-util/color';
import { Overpaint } from '../../mol-theme/overpaint';
+import Expression from '../../mol-script/language/expression';
+import { compile } from '../../mol-script/runtime/query/compiler';
type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle>>) => void
const OverpaintManagerTag = 'overpaint-controls'
@@ -29,7 +31,7 @@ export class StructureOverpaintHelper {
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
}
- async set(color: Color | -1, lociGetter: (structure: Structure) => StructureElement.Loci, types?: string[]) {
+ async set(color: Color | -1, lociGetter: (structure: Structure) => StructureElement.Loci, types?: string[], alpha = 1) {
await this.eachRepr((update, repr, overpaintCell) => {
if (types && !types.includes(repr.params!.values.type.name)) return
@@ -48,15 +50,23 @@ export class StructureOverpaintHelper {
if (overpaintCell) {
const bundleLayers = [ ...overpaintCell.params!.values.layers, layer ]
const filtered = getFilteredBundle(bundleLayers, structure)
- update.to(overpaintCell).update(Overpaint.toBundle(filtered, 1))
+ update.to(overpaintCell).update(Overpaint.toBundle(filtered, alpha))
} else {
const filtered = getFilteredBundle([ layer ], structure)
update.to(repr.transform.ref)
- .apply(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, Overpaint.toBundle(filtered, 1), { tags: OverpaintManagerTag });
+ .apply(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, Overpaint.toBundle(filtered, alpha), { tags: OverpaintManagerTag });
}
})
}
+ async setFromExpression(color: Color | -1, expression: Expression, types?: string[], alpha = 1) {
+ return this.set(color, (structure) => {
+ const compiled = compile<StructureSelection>(expression)
+ const result = compiled(new QueryContext(structure))
+ return StructureSelection.toLociWithSourceUnits(result)
+ }, types, alpha)
+ }
+
constructor(private plugin: PluginContext) {
}
diff --git a/src/mol-plugin/util/structure-representation-helper.ts b/src/mol-plugin/util/structure-representation-helper.ts
index 6e58d3cae071cc81f2b5f1670cbd63048d9a2380..241d632bd9c4b8437f77e894de6b57c6f3c7770e 100644
--- a/src/mol-plugin/util/structure-representation-helper.ts
+++ b/src/mol-plugin/util/structure-representation-helper.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>
*/
@@ -12,8 +12,6 @@ import { PluginContext } from '../context';
import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
import Expression from '../../mol-script/language/expression';
import { compile } from '../../mol-script/runtime/query/compiler';
-import { StructureSelectionQueries as Q } from '../util/structure-selection-helper';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { VisualQuality } from '../../mol-geo/geometry/base';
type StructureTransform = StateObjectCell<PSO.Molecule.Structure, StateTransform<StateTransformer<any, PSO.Molecule.Structure, any>>>
@@ -34,6 +32,12 @@ function getCombinedLoci(mode: SelectionModifier, loci: StructureElement.Loci, c
type SelectionModifier = 'add' | 'remove' | 'only'
+type ReprProps = {
+ repr?: {},
+ color?: string | [string, {}],
+ size?: string | [string, {}],
+}
+
export class StructureRepresentationHelper {
getRepresentationStructure(rootRef: string, type: string) {
const state = this.plugin.state.dataState
@@ -49,12 +53,52 @@ export class StructureRepresentationHelper {
return selections.length > 0 ? selections[0] : undefined
}
- private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform, props = {}) {
+ private getRepresentationParams(structure: Structure, type: string, repr: RepresentationTransform | undefined, props: ReprProps = {}) {
+ const reprProps = {
+ ...(repr?.params && repr.params.values.type.params),
+ ignoreHydrogens: this._ignoreHydrogens,
+ quality: this._quality,
+ ...props.repr
+ }
+ const { themeCtx } = this.plugin.structureRepresentation
+
+ const p: StructureRepresentation3DHelpers.Props = {
+ repr: [
+ this.plugin.structureRepresentation.registry.get(type),
+ () => reprProps
+ ]
+ }
+ if (props.color) {
+ const colorType = props.color instanceof Array ? props.color[0] : props.color
+ const colorTheme = themeCtx.colorThemeRegistry.get(colorType)
+ const colorProps = {
+ ...(repr?.params && repr.params.values.colorTheme.name === colorType && repr.params.values.colorTheme.params),
+ ...(props.color instanceof Array ? props.color[1] : {})
+ }
+ p.color = [colorTheme, () => colorProps]
+ }
+ if (props.size) {
+ const sizeType = props.size instanceof Array ? props.size[0] : props.size
+ const sizeTheme = themeCtx.sizeThemeRegistry.get(sizeType)
+ const sizeProps = {
+ ...(repr?.params && repr.params.values.sizeTheme.name === sizeType && repr.params.values.sizeTheme.params),
+ ...(props.size instanceof Array ? props.size[1] : {})
+ }
+ p.size = [sizeTheme, () => sizeProps]
+ }
+ if (props.size) p.size = props.size
+
+ return StructureRepresentation3DHelpers.createParams(this.plugin, structure, p)
+ }
+
+ private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform, props: ReprProps = {}) {
const state = this.plugin.state.dataState
const update = state.build()
const s = structure.obj!.data
+ const repr = this.getRepresentation(structure.transform.ref, type)
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
+ const reprParams = this.getRepresentationParams(s.root, type, repr, props)
if (reprStructure) {
const currentLoci = StructureElement.Bundle.toLoci(reprStructure.params!.values.bundle, s)
@@ -64,14 +108,9 @@ export class StructureRepresentationHelper {
...reprStructure.params!.values,
bundle: StructureElement.Bundle.fromLoci(combinedLoci)
})
+ if (repr) update.to(repr).update(reprParams)
} else {
const combinedLoci = getCombinedLoci(modifier, loci, StructureElement.Loci.none(s))
- const params = StructureRepresentation3DHelpers.getDefaultParams(this.plugin, type as any, s)
-
- const p = params.type.params
- Object.assign(p, props)
- if (p.ignoreHydrogens !== undefined) p.ignoreHydrogens = this._ignoreHydrogens
- if (p.quality !== undefined) p.quality = this._quality
update.to(structure.transform.ref)
.apply(
@@ -79,13 +118,13 @@ export class StructureRepresentationHelper {
{ bundle: StructureElement.Bundle.fromLoci(combinedLoci), label: type },
{ tags: [ RepresentationManagerTag, getRepresentationManagerTag(type) ] }
)
- .apply( StateTransforms.Representation.StructureRepresentation3D, params)
+ .apply(StateTransforms.Representation.StructureRepresentation3D, reprParams)
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
- async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci, props = {}) {
+ async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci, props: ReprProps = {}) {
const state = this.plugin.state.dataState;
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
@@ -96,7 +135,7 @@ export class StructureRepresentationHelper {
}
}
- async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression, props = {}) {
+ async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression, props: ReprProps = {}) {
return this.set(modifier, type, (structure) => {
const compiled = compile<StructureSelection>(expression)
const result = compiled(new QueryContext(structure))
@@ -104,44 +143,76 @@ export class StructureRepresentationHelper {
}, props)
}
- async clear() {
+ async eachStructure(callback: (structure: StructureTransform, type: string, update: StateBuilder.Root) => void) {
const { registry } = this.plugin.structureRepresentation
const state = this.plugin.state.dataState;
const update = state.build()
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
- const bundle = StructureElement.Bundle.Empty
for (const structure of structures) {
for (let i = 0, il = registry.types.length; i < il; ++i) {
const type = registry.types[i][0]
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
- if (reprStructure) {
- update.to(reprStructure).update({ ...reprStructure.params!.values, bundle })
- }
+ if (reprStructure) callback(reprStructure, type, update)
}
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
- async eachRepresentation(callback: (repr: RepresentationTransform, update: StateBuilder.Root) => void) {
+ async clear() {
+ const bundle = StructureElement.Bundle.Empty
+ await this.eachStructure((structure, type, update) => {
+ update.to(structure).update({ ...structure.params!.values, bundle })
+ })
+ }
+
+ async clearExcept(exceptTypes: string[]) {
+ const bundle = StructureElement.Bundle.Empty
+ await this.eachStructure((structure, type, update) => {
+ if (!exceptTypes.includes(type)) {
+ update.to(structure).update({ ...structure.params!.values, bundle })
+ }
+ })
+ }
+
+ async eachRepresentation(callback: (repr: RepresentationTransform, type: string, update: StateBuilder.Root) => void) {
const { registry } = this.plugin.structureRepresentation
const state = this.plugin.state.dataState;
const update = state.build()
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
for (const structure of structures) {
for (let i = 0, il = registry.types.length; i < il; ++i) {
- const repr = this.getRepresentation(structure.transform.ref, registry.types[i][0])
- if (repr) callback(repr, update)
+ const type = registry.types[i][0]
+ const repr = this.getRepresentation(structure.transform.ref, type)
+ if (repr) callback(repr, type, update)
}
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
+ setRepresentationParams(repr: RepresentationTransform, type: string, update: StateBuilder.Root, props: ReprProps) {
+ const state = this.plugin.state.dataState;
+ const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
+
+ for (const structure of structures) {
+ const s = structure.obj!.data
+ const reprParams = this.getRepresentationParams(s.root, type, repr, props)
+ update.to(repr).update(reprParams)
+ }
+ }
+
+ async updateRepresentation(repr: RepresentationTransform, type: string, props: ReprProps) {
+ const state = this.plugin.state.dataState;
+ const update = state.build()
+ this.setRepresentationParams(repr, type, update, props)
+ await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
+ }
+
private _ignoreHydrogens = false
get ignoreHydrogens () { return this._ignoreHydrogens }
async setIgnoreHydrogens(ignoreHydrogens: boolean) {
if (ignoreHydrogens === this._ignoreHydrogens) return
- await this.eachRepresentation((repr, update) => {
+ await this.eachRepresentation((repr, type, update) => {
if (repr.params && repr.params.values.type.params.ignoreHydrogens !== undefined) {
const { name, params } = repr.params.values.type
update.to(repr.transform.ref).update(
@@ -157,7 +228,7 @@ export class StructureRepresentationHelper {
get quality () { return this._quality }
async setQuality(quality: VisualQuality) {
if (quality === this._quality) return
- await this.eachRepresentation((repr, update) => {
+ await this.eachRepresentation((repr, type, update) => {
if (repr.params && repr.params.values.type.params.quality !== undefined) {
const { name, params } = repr.params.values.type
update.to(repr.transform.ref).update(
@@ -169,74 +240,7 @@ export class StructureRepresentationHelper {
this._quality = quality
}
- async preset() {
- // TODO option to limit to specific structure
- const state = this.plugin.state.dataState;
- const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
-
- if (structures.length === 0) return
- const s = structures[0].obj!.data
-
- if (s.elementCount < 50000) {
- await polymerAndLigand(this)
- } else if (s.elementCount < 200000) {
- await proteinAndNucleic(this)
- } else {
- if (s.unitSymmetryGroups[0].units.length > 10) {
- await capsid(this)
- } else {
- await coarseCapsid(this)
- }
- }
- }
-
constructor(private plugin: PluginContext) {
}
-}
-
-//
-
-async function polymerAndLigand(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'cartoon', Q.polymer.expression)
- await r.setFromExpression('add', 'carbohydrate', Q.branchedPlusConnected.expression)
- await r.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
- MS.struct.combinator.merge([
- Q.ligandPlusConnected.expression,
- Q.branchedConnectedOnly.expression,
- Q.disulfideBridges.expression,
- Q.nonStandardPolymer.expression,
- Q.water.expression
- ])
- ]))
-}
-
-async function proteinAndNucleic(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'cartoon', Q.protein.expression)
- await r.setFromExpression('add', 'gaussian-surface', Q.nucleic.expression)
-}
-
-async function capsid(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'gaussian-surface', Q.polymer.expression, {
- smoothness: 0.5,
- })
-}
-
-async function coarseCapsid(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'gaussian-surface', Q.trace.expression, {
- radiusOffset: 1,
- smoothness: 0.5,
- visuals: ['structure-gaussian-surface-mesh']
- })
-}
-
-export const StructureRepresentationPresets = {
- polymerAndLigand,
- proteinAndNucleic,
- capsid,
- coarseCapsid
}
\ No newline at end of file
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
index e8b3c455305d0d85a04cb3d7f407d91abae352f2..377c6507a249752adc9d183299bcbc951afff6e9 100644
--- a/src/mol-plugin/util/structure-selection-helper.ts
+++ b/src/mol-plugin/util/structure-selection-helper.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>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -8,32 +8,76 @@
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { StateSelection, StateBuilder } from '../../mol-state';
import { PluginStateObject } from '../state/objects';
-import { QueryContext, StructureSelection, StructureQuery, StructureElement } from '../../mol-model/structure';
+import { QueryContext, StructureSelection, StructureQuery, StructureElement, Structure } from '../../mol-model/structure';
import { compile } from '../../mol-script/runtime/query/compiler';
import { Loci } from '../../mol-model/loci';
import { PluginContext } from '../context';
import Expression from '../../mol-script/language/expression';
import { BondType, ProteinBackboneAtoms, NucleicBackboneAtoms, SecondaryStructureType } from '../../mol-model/structure/model/types';
import { StateTransforms } from '../state/transforms';
+import { SetUtils } from '../../mol-util/set';
+import { ValidationReport, ValidationReportProvider } from '../../mol-model-props/rcsb/validation-report';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { Task } from '../../mol-task';
+import { AccessibleSurfaceAreaSymbols, AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
+import { stringToWords } from '../../mol-util/string';
+
+export enum StructureSelectionCategory {
+ Type = 'Type',
+ Structure = 'Structure Property',
+ Atom = 'Atom Property',
+ Bond = 'Bond Property',
+ Residue = 'Residue Property',
+ AminoAcid = 'Amino Acid',
+ NucleicBase = 'Nucleic Base',
+ Manipulate = 'Manipulate Selection',
+ Validation = 'Validation',
+ Misc = 'Miscellaneous',
+ Internal = 'Internal',
+}
+
+export { StructureSelectionQuery }
+
+interface StructureSelectionQuery {
+ readonly label: string
+ readonly expression: Expression
+ readonly description: string
+ readonly category: string
+ readonly isHidden: boolean
+ readonly query: StructureQuery
+ readonly ensureCustomProperties?: (ctx: CustomProperty.Context, structure: Structure) => Promise<void>
+}
-export interface StructureSelectionQuery {
- label: string
- query: StructureQuery
- expression: Expression
- description: string
+interface StructureSelectionQueryProps {
+ description?: string,
+ category?: string
+ isHidden?: boolean
+ ensureCustomProperties?: (ctx: CustomProperty.Context, structure: Structure) => Promise<void>
}
-export function StructureSelectionQuery(label: string, expression: Expression, description = ''): StructureSelectionQuery {
- return { label, expression, query: compile<StructureSelection>(expression), description }
+function StructureSelectionQuery(label: string, expression: Expression, props: StructureSelectionQueryProps = {}): StructureSelectionQuery {
+ let _query: StructureQuery
+ return {
+ label,
+ expression,
+ description: props.description || '',
+ category: props.category ?? StructureSelectionCategory.Misc,
+ isHidden: !!props.isHidden,
+ get query() {
+ if (!_query) _query = compile<StructureSelection>(expression)
+ return _query
+ },
+ ensureCustomProperties: props.ensureCustomProperties
+ }
}
-const all = StructureSelectionQuery('All', MS.struct.generator.all())
+const all = StructureSelectionQuery('All', MS.struct.generator.all(), { category: '' })
const polymer = StructureSelectionQuery('Polymer', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const trace = StructureSelectionQuery('Trace', MS.struct.modifier.union([
MS.struct.combinator.merge([
@@ -53,7 +97,7 @@ const trace = StructureSelectionQuery('Trace', MS.struct.modifier.union([
})
])
])
-]))
+]), { category: StructureSelectionCategory.Structure })
// TODO maybe pre-calculate atom properties like backbone/sidechain
const backbone = StructureSelectionQuery('Backbone', MS.struct.modifier.union([
@@ -68,7 +112,7 @@ const backbone = StructureSelectionQuery('Backbone', MS.struct.modifier.union([
])
]),
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
- 'atom-test': MS.core.set.has([MS.set(...Array.from(ProteinBackboneAtoms.values())), MS.ammp('label_atom_id')])
+ 'atom-test': MS.core.set.has([MS.set(...SetUtils.toArray(ProteinBackboneAtoms)), MS.ammp('label_atom_id')])
})
]),
MS.struct.modifier.union([
@@ -81,11 +125,11 @@ const backbone = StructureSelectionQuery('Backbone', MS.struct.modifier.union([
])
]),
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
- 'atom-test': MS.core.set.has([MS.set(...Array.from(NucleicBackboneAtoms.values())), MS.ammp('label_atom_id')])
+ 'atom-test': MS.core.set.has([MS.set(...SetUtils.toArray(NucleicBackboneAtoms)), MS.ammp('label_atom_id')])
})
])
])
-]))
+]), { category: StructureSelectionCategory.Structure })
const protein = StructureSelectionQuery('Protein', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -97,7 +141,7 @@ const protein = StructureSelectionQuery('Protein', MS.struct.modifier.union([
])
])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const nucleic = StructureSelectionQuery('Nucleic', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -109,7 +153,7 @@ const nucleic = StructureSelectionQuery('Nucleic', MS.struct.modifier.union([
])
])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const proteinOrNucleic = StructureSelectionQuery('Protein or Nucleic', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -121,7 +165,7 @@ const proteinOrNucleic = StructureSelectionQuery('Protein or Nucleic', MS.struct
])
])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -137,7 +181,7 @@ const helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
MS.core.type.bitflags([SecondaryStructureType.Flag.Helix])
])
})
-]))
+]), { category: StructureSelectionCategory.Residue })
const beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -153,13 +197,13 @@ const beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.uni
MS.core.type.bitflags([SecondaryStructureType.Flag.Beta])
])
})
-]))
+]), { category: StructureSelectionCategory.Residue })
const water = StructureSelectionQuery('Water', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'water'])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const branched = StructureSelectionQuery('Carbohydrate', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -174,20 +218,20 @@ const branched = StructureSelectionQuery('Carbohydrate', MS.struct.modifier.unio
])
])
})
-]))
+]), { category: StructureSelectionCategory.Type })
const branchedPlusConnected = StructureSelectionQuery('Carbohydrate with Connected', MS.struct.modifier.union([
MS.struct.modifier.includeConnected({
0: branched.expression, 'layer-count': 1, 'as-whole-residues': true
})
-]))
+]), { category: StructureSelectionCategory.Internal })
const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate', MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
0: branchedPlusConnected.expression,
by: branched.expression
})
-]))
+]), { category: StructureSelectionCategory.Internal })
const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
MS.struct.combinator.merge([
@@ -221,7 +265,7 @@ const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
})
])
]),
-]))
+]), { category: StructureSelectionCategory.Residue })
// don't include branched entities as they have their own link representation
const ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.struct.modifier.union([
@@ -241,14 +285,14 @@ const ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.
]),
by: branched.expression
})
-]))
+]), { category: StructureSelectionCategory.Internal })
const ligandConnectedOnly = StructureSelectionQuery('Connected to Ligand', MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
0: ligandPlusConnected.expression,
by: ligand.expression
})
-]))
+]), { category: StructureSelectionCategory.Internal })
// residues connected to ligands or branched entities
const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydrate', MS.struct.modifier.union([
@@ -256,7 +300,7 @@ const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydra
branchedConnectedOnly.expression,
ligandConnectedOnly.expression
]),
-]))
+]), { category: StructureSelectionCategory.Internal })
const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.modifier.union([
MS.struct.modifier.wholeResidues([
@@ -269,14 +313,7 @@ const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.
})
])
])
-]))
-
-const modified = StructureSelectionQuery('Modified Residues', MS.struct.modifier.union([
- MS.struct.generator.atomGroups({
- 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
- 'residue-test': MS.ammp('isModified')
- })
-]))
+]), { category: StructureSelectionCategory.Bond })
const nonStandardPolymer = StructureSelectionQuery('Non-standard Residues in Polymers', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -284,7 +321,7 @@ const nonStandardPolymer = StructureSelectionQuery('Non-standard Residues in Pol
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
'residue-test': MS.ammp('isNonStandard')
})
-]))
+]), { category: StructureSelectionCategory.Residue })
const coarse = StructureSelectionQuery('Coarse Elements', MS.struct.modifier.union([
MS.struct.generator.atomGroups({
@@ -292,15 +329,15 @@ const coarse = StructureSelectionQuery('Coarse Elements', MS.struct.modifier.uni
MS.set('sphere', 'gaussian'), MS.ammp('objectPrimitive')
])
})
-]))
+]), { category: StructureSelectionCategory.Residue })
const ring = StructureSelectionQuery('Rings in Residues', MS.struct.modifier.union([
MS.struct.generator.rings()
-]))
+]), { category: StructureSelectionCategory.Residue })
const aromaticRing = StructureSelectionQuery('Aromatic Rings in Residues', MS.struct.modifier.union([
MS.struct.generator.rings({ 'only-aromatic': true })
-]))
+]), { category: StructureSelectionCategory.Residue })
const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Selection', MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
@@ -311,20 +348,121 @@ const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of
}),
by: MS.internal.generator.current()
})
-]), 'Select residues within 5 \u212B of the current selection.')
+]), {
+ description: 'Select residues within 5 \u212B of the current selection.',
+ category: StructureSelectionCategory.Manipulate
+})
const complement = StructureSelectionQuery('Inverse / Complement of Selection', MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
0: MS.struct.generator.all(),
by: MS.internal.generator.current()
})
-]), 'Select everything not in the current selection.')
+]), {
+ description: 'Select everything not in the current selection.',
+ category: StructureSelectionCategory.Manipulate
+})
const bonded = StructureSelectionQuery('Residues Bonded to Selection', MS.struct.modifier.union([
MS.struct.modifier.includeConnected({
0: MS.internal.generator.current(), 'layer-count': 1, 'as-whole-residues': true
})
-]), 'Select residues covalently bonded to current selection.')
+]), {
+ description: 'Select residues covalently bonded to current selection.',
+ category: StructureSelectionCategory.Manipulate
+})
+
+const hasClash = StructureSelectionQuery('Residues with Clashes', MS.struct.modifier.union([
+ MS.struct.modifier.wholeResidues([
+ MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+ 'atom-test': ValidationReport.symbols.hasClash.symbol(),
+ })
+ ])
+ ])
+]), {
+ description: 'Select residues with clashes in the wwPDB validation report.',
+ category: StructureSelectionCategory.Residue,
+ ensureCustomProperties: (ctx, structure) => {
+ return ValidationReportProvider.attach(ctx, structure.models[0])
+ }
+})
+
+const isBuried = StructureSelectionQuery('Buried Protein Residues', MS.struct.modifier.union([
+ MS.struct.modifier.wholeResidues([
+ MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+ 'residue-test': AccessibleSurfaceAreaSymbols.isBuried.symbol(),
+ })
+ ])
+ ])
+]), {
+ description: 'Select buried protein residues.',
+ category: StructureSelectionCategory.Residue,
+ ensureCustomProperties: (ctx, structure) => {
+ return AccessibleSurfaceAreaProvider.attach(ctx, structure)
+ }
+})
+
+const isAccessible = StructureSelectionQuery('Accessible Protein Residues', MS.struct.modifier.union([
+ MS.struct.modifier.wholeResidues([
+ MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+ 'residue-test': AccessibleSurfaceAreaSymbols.isAccessible.symbol(),
+ })
+ ])
+ ])
+]), {
+ description: 'Select accessible protein residues.',
+ category: StructureSelectionCategory.Residue,
+ ensureCustomProperties: (ctx, structure) => {
+ return AccessibleSurfaceAreaProvider.attach(ctx, structure)
+ }
+})
+
+const StandardAminoAcids = [
+ [['HIS'], 'HISTIDINE'],
+ [['ARG'], 'ARGININE'],
+ [['LYS'], 'LYSINE'],
+ [['ILE'], 'ISOLEUCINE'],
+ [['PHE'], 'PHENYLALANINE'],
+ [['LEU'], 'LEUCINE'],
+ [['TRP'], 'TRYPTOPHAN'],
+ [['ALA'], 'ALANINE'],
+ [['MET'], 'METHIONINE'],
+ [['CYS'], 'CYSTEINE'],
+ [['ASN'], 'ASPARAGINE'],
+ [['VAL'], 'VALINE'],
+ [['GLY'], 'GLYCINE'],
+ [['SER'], 'SERINE'],
+ [['GLN'], 'GLUTAMINE'],
+ [['TYR'], 'TYROSINE'],
+ [['ASP'], 'ASPARTIC ACID'],
+ [['GLU'], 'GLUTAMIC ACID'],
+ [['THR'], 'THREONINE'],
+ [['SEC'], 'SELENOCYSTEINE'],
+ [['PYL'], 'PYRROLYSINE'],
+].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][]
+
+const StandardNucleicBases = [
+ [['A', 'DA'], 'ADENOSINE'],
+ [['C', 'DC'], 'CYTIDINE'],
+ [['T', 'DT'], 'THYMIDINE'],
+ [['G', 'DG'], 'GUANOSINE'],
+ [['I', 'DI'], 'INOSINE'],
+ [['U', 'DU'], 'URIDINE'],
+].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][]
+
+function ResidueQuery([names, label]: [string[], string], category: string) {
+ return StructureSelectionQuery(`${stringToWords(label)} (${names.join(', ')})`, MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.set.has([MS.set(...names), MS.ammp('auth_comp_id')])
+ })
+ ]), { category })
+}
export const StructureSelectionQueries = {
all,
@@ -345,7 +483,6 @@ export const StructureSelectionQueries = {
ligandConnectedOnly,
connectedOnly,
disulfideBridges,
- modified,
nonStandardPolymer,
coarse,
ring,
@@ -353,8 +490,18 @@ export const StructureSelectionQueries = {
surroundings,
complement,
bonded,
+
+ hasClash,
+ isBuried,
+ isAccessible
}
+export const StructureSelectionQueryList = [
+ ...Object.values(StructureSelectionQueries),
+ ...StandardAminoAcids.map(v => ResidueQuery(v, StructureSelectionCategory.AminoAcid)),
+ ...StandardNucleicBases.map(v => ResidueQuery(v, StructureSelectionCategory.NucleicBase)),
+]
+
export function applyBuiltInSelection(to: StateBuilder.To<PluginStateObject.Molecule.Structure>, query: keyof typeof StructureSelectionQueries, customTag?: string) {
return to.apply(StateTransforms.Model.StructureSelectionFromExpression,
{ expression: StructureSelectionQueries[query].expression, label: StructureSelectionQueries[query].label },
@@ -384,17 +531,24 @@ export class StructureSelectionHelper {
}
}
- set(modifier: SelectionModifier, query: StructureQuery, applyGranularity = true) {
- for (const s of this.structures) {
- const current = this.plugin.helpers.structureSelectionManager.get(s)
- const currentSelection = Loci.isEmpty(current)
- ? StructureSelection.Empty(s)
- : StructureSelection.Singletons(s, StructureElement.Loci.toStructure(current))
-
- const result = query(new QueryContext(s, { currentSelection }))
- const loci = StructureSelection.toLociWithSourceUnits(result)
- this._set(modifier, loci, applyGranularity)
- }
+ async set(modifier: SelectionModifier, selectionQuery: StructureSelectionQuery, applyGranularity = true) {
+ this.plugin.runTask(Task.create('Structure Selection', async runtime => {
+ const ctx = { fetch: this.plugin.fetch, runtime }
+ for (const s of this.structures) {
+ const current = this.plugin.helpers.structureSelectionManager.get(s)
+ const currentSelection = Loci.isEmpty(current)
+ ? StructureSelection.Empty(s)
+ : StructureSelection.Singletons(s, StructureElement.Loci.toStructure(current))
+
+ if (selectionQuery.ensureCustomProperties) {
+ await selectionQuery.ensureCustomProperties(ctx, s)
+ }
+
+ const result = selectionQuery.query(new QueryContext(s, { currentSelection }))
+ const loci = StructureSelection.toLociWithSourceUnits(result)
+ this._set(modifier, loci, applyGranularity)
+ }
+ }))
}
constructor(private plugin: PluginContext) {
diff --git a/src/mol-repr/structure/registry.ts b/src/mol-repr/structure/registry.ts
index 970c5e12bc299113d8865aac03aa6dbb16fc3835..9ec7a53d1263c59f042a1a0ee4686e106ffebb70 100644
--- a/src/mol-repr/structure/registry.ts
+++ b/src/mol-repr/structure/registry.ts
@@ -11,7 +11,6 @@ import { BallAndStickRepresentationProvider } from './representation/ball-and-st
import { GaussianSurfaceRepresentationProvider } from './representation/gaussian-surface';
import { CarbohydrateRepresentationProvider } from './representation/carbohydrate';
import { SpacefillRepresentationProvider } from './representation/spacefill';
-import { DistanceRestraintRepresentationProvider } from './representation/distance-restraint';
import { PointRepresentationProvider } from './representation/point';
import { StructureRepresentationState } from './representation';
import { PuttyRepresentationProvider } from './representation/putty';
@@ -34,7 +33,6 @@ export const BuiltInStructureRepresentations = {
'cartoon': CartoonRepresentationProvider,
'ball-and-stick': BallAndStickRepresentationProvider,
'carbohydrate': CarbohydrateRepresentationProvider,
- 'distance-restraint': DistanceRestraintRepresentationProvider,
'ellipsoid': EllipsoidRepresentationProvider,
'gaussian-surface': GaussianSurfaceRepresentationProvider,
// 'gaussian-volume': GaussianVolumeRepresentationProvider, // TODO disabled for now, needs more work
diff --git a/src/mol-repr/structure/representation/distance-restraint.ts b/src/mol-repr/structure/representation/distance-restraint.ts
deleted file mode 100644
index 752a9b46d0f1d0ffb50bcf4bc81b199fbe88dd20..0000000000000000000000000000000000000000
--- a/src/mol-repr/structure/representation/distance-restraint.ts
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { CrossLinkRestraintVisual, CrossLinkRestraintParams } from '../visual/cross-link-restraint-cylinder';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { ComplexRepresentation } from '../complex-representation';
-import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
-import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
-import { ThemeRegistryContext } from '../../../mol-theme/theme';
-import { Structure } from '../../../mol-model/structure';
-import { UnitKind, UnitKindOptions } from '../visual/util/common';
-
-const DistanceRestraintVisuals = {
- 'distance-restraint': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintParams>) => ComplexRepresentation('Cross-link restraint', ctx, getParams, CrossLinkRestraintVisual),
-}
-
-export const DistanceRestraintParams = {
- ...CrossLinkRestraintParams,
- unitKinds: PD.MultiSelect<UnitKind>(['atomic', 'spheres'], UnitKindOptions),
-}
-export type DistanceRestraintParams = typeof DistanceRestraintParams
-export function getDistanceRestraintParams(ctx: ThemeRegistryContext, structure: Structure) {
- return PD.clone(DistanceRestraintParams)
-}
-
-export type DistanceRestraintRepresentation = StructureRepresentation<DistanceRestraintParams>
-export function DistanceRestraintRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, DistanceRestraintParams>): DistanceRestraintRepresentation {
- return Representation.createMulti('DistanceRestraint', ctx, getParams, StructureRepresentationStateBuilder, DistanceRestraintVisuals as unknown as Representation.Def<Structure, DistanceRestraintParams>)
-}
-
-export const DistanceRestraintRepresentationProvider: StructureRepresentationProvider<DistanceRestraintParams> = {
- label: 'Distance Restraint',
- description: 'Displays cross-link distance restraints.',
- factory: DistanceRestraintRepresentation,
- getParams: getDistanceRestraintParams,
- defaultValues: PD.getDefaultValues(DistanceRestraintParams),
- defaultColorTheme: { name: 'cross-link' },
- defaultSizeTheme: { name: 'uniform' },
- isApplicable: (structure: Structure) => structure.crossLinkRestraints.count > 0
-}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
deleted file mode 100644
index db047214479a432ea8d0e84dc57c3f5d9b3fd0d1..0000000000000000000000000000000000000000
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ /dev/null
@@ -1,119 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { VisualContext } from '../../visual';
-import { Structure, StructureElement, Bond } from '../../../mol-model/structure';
-import { Theme } from '../../../mol-theme/theme';
-import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
-import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual } from '../complex-visual';
-import { VisualUpdateState } from '../../util';
-import { LocationIterator } from '../../../mol-geo/util/location-iterator';
-import { PickingId } from '../../../mol-geo/geometry/picking';
-import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Interval } from '../../../mol-data/int';
-
-function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CrossLinkRestraintParams>, mesh?: Mesh) {
-
- const crossLinks = structure.crossLinkRestraints
- if (!crossLinks.count) return Mesh.createEmpty(mesh)
- const { sizeFactor } = props
-
- const location = StructureElement.Location.create(structure)
-
- const builderProps = {
- linkCount: crossLinks.count,
- position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
- const b = crossLinks.pairs[edgeIndex]
- const uA = b.unitA, uB = b.unitB
- uA.conformation.position(uA.elements[b.indexA], posA)
- uB.conformation.position(uB.elements[b.indexB], posB)
- },
- radius: (edgeIndex: number) => {
- const b = crossLinks.pairs[edgeIndex]
- location.unit = b.unitA
- location.element = b.unitA.elements[b.indexA]
- return theme.size.size(location) * sizeFactor
- },
- }
-
- return createLinkCylinderMesh(ctx, builderProps, props, mesh)
-}
-
-export const CrossLinkRestraintParams = {
- ...ComplexMeshParams,
- ...LinkCylinderParams,
- sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
-}
-export type CrossLinkRestraintParams = typeof CrossLinkRestraintParams
-
-export function CrossLinkRestraintVisual(materialId: number): ComplexVisual<CrossLinkRestraintParams> {
- return ComplexMeshVisual<CrossLinkRestraintParams>({
- defaultProps: PD.getDefaultValues(CrossLinkRestraintParams),
- createGeometry: createCrossLinkRestraintCylinderMesh,
- createLocationIterator: CrossLinkRestraintIterator,
- getLoci: getLinkLoci,
- eachLocation: eachCrossLink,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CrossLinkRestraintParams>, currentProps: PD.Values<CrossLinkRestraintParams>) => {
- state.createGeometry = (
- newProps.sizeFactor !== currentProps.sizeFactor ||
- newProps.radialSegments !== currentProps.radialSegments ||
- newProps.linkCap !== currentProps.linkCap
- )
- }
- }, materialId)
-}
-
-function CrossLinkRestraintIterator(structure: Structure): LocationIterator {
- const { pairs } = structure.crossLinkRestraints
- const groupCount = pairs.length
- const instanceCount = 1
- 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
- }
- return LocationIterator(groupCount, instanceCount, getLocation, true)
-}
-
-function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, groupId } = pickingId
- if (id === objectId) {
- const pair = structure.crossLinkRestraints.pairs[groupId]
- if (pair) {
- return Bond.Loci(structure, [
- Bond.Location(structure, pair.unitA, pair.indexA, structure, pair.unitB, pair.indexB),
- Bond.Location(structure, pair.unitB, pair.indexB, structure, pair.unitA, pair.indexA)
- ])
- }
- }
- return EmptyLoci
-}
-
-function eachCrossLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
- const crossLinks = structure.crossLinkRestraints
- let changed = false
- if (Bond.isLoci(loci)) {
- if (!Structure.areEquivalent(loci.structure, structure)) return false
- for (const b of loci.bonds) {
- const indices = crossLinks.getPairIndices(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
- if (indices) {
- for (let i = 0, il = indices.length; i < il; ++i) {
- if (apply(Interval.ofSingleton(indices[i]))) changed = true
- }
- }
- }
- }
- return changed
-}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index 255001edbe5f4f32d766b2506c72e33d317e7fa5..95b701f2c222eef56b850df1ea6d09f48d8ebdf6 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
@@ -53,7 +53,6 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, mesh)
const { elements, model } = unit
- const { modifiedResidues } = model.properties
const { chainAtomSegments, residueAtomSegments, residues, index: atomicIndex } = model.atomicHierarchy
const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
const { label_comp_id } = residues
@@ -72,9 +71,7 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
- let compId = label_comp_id.value(residueIndex)
- const parentId = modifiedResidues.parentId.get(compId)
- if (parentId !== undefined) compId = parentId
+ const compId = label_comp_id.value(residueIndex)
let idx1: ElementIndex | -1 = -1, idx2: ElementIndex | -1 = -1, idx3: ElementIndex | -1 = -1, idx4: ElementIndex | -1 = -1, idx5: ElementIndex | -1 = -1, idx6: ElementIndex | -1 = -1
let width = 4.5, height = 4.5, depth = 2.5 * sizeFactor
diff --git a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
index c205c3f5af71e495c8a23a30ac560dbd134b5d73..2dd871368e68d2040ba15f7ce17d8215cd7f8e9d 100644
--- a/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-ring-mesh.ts
@@ -72,7 +72,6 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, mesh)
const { elements, model } = unit
- const { modifiedResidues } = model.properties
const { chainAtomSegments, residueAtomSegments, residues, index: atomicIndex } = model.atomicHierarchy
const { moleculeType, traceElementIndex } = model.atomicHierarchy.derived.residue
const { label_comp_id } = residues
@@ -93,9 +92,7 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
- let compId = label_comp_id.value(residueIndex)
- const parentId = modifiedResidues.parentId.get(compId)
- if (parentId !== undefined) compId = parentId
+ const compId = label_comp_id.value(residueIndex)
let idxTrace: ElementIndex | -1 = -1, idxN1: ElementIndex | -1 = -1, idxC2: ElementIndex | -1 = -1, idxN3: ElementIndex | -1 = -1, idxC4: ElementIndex | -1 = -1, idxC5: ElementIndex | -1 = -1, idxC6: ElementIndex | -1 = -1, idxN7: ElementIndex | -1 = -1, idxC8: ElementIndex | -1 = -1, idxN9: ElementIndex | -1 = -1
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 390e0c57a1051c2eff7c4a63268803e1a39b2df0..2046a6bb472b1066350284515affb13749057b21 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -325,8 +325,6 @@ const symbols = [
D(MolScript.structureQuery.atomProperty.macromolecular.entitySubtype, atomProp(StructureProperties.entity.subtype)),
D(MolScript.structureQuery.atomProperty.macromolecular.objectPrimitive, atomProp(StructureProperties.unit.object_primitive)),
- D(MolScript.structureQuery.atomProperty.macromolecular.isModified, atomProp(StructureProperties.residue.isModified)),
- D(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, atomProp(StructureProperties.residue.modifiedParentName)),
D(MolScript.structureQuery.atomProperty.macromolecular.isNonStandard, atomProp(StructureProperties.residue.isNonStandard)),
D(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, atomProp(StructureProperties.residue.secondary_structure_key)),
D(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureFlags, atomProp(StructureProperties.residue.secondary_structure_type)),
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 9288607d6d919b675f76a7ddd2b686f63c5bbb55..6829233f6e18fe8642b1216451c6ad8bd7f8c84f 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -13,7 +13,6 @@ import { deepEqual } from '../mol-util';
import { ParamDefinition as PD } from '../mol-util/param-definition';
import { ThemeDataContext, ThemeRegistry, ThemeProvider } from './theme';
import { ChainIdColorThemeProvider } from './color/chain-id';
-import { CrossLinkColorThemeProvider } from './color/cross-link';
import { ElementIndexColorThemeProvider } from './color/element-index';
import { ElementSymbolColorThemeProvider } from './color/element-symbol';
import { MoleculeTypeColorThemeProvider } from './color/molecule-type';
@@ -47,6 +46,15 @@ interface ColorTheme<P extends PD.Params> {
readonly legend?: Readonly<ScaleLegend | TableLegend>
}
namespace ColorTheme {
+ export const enum Category {
+ Atom = 'Atom Property',
+ Chain = 'Chain Property',
+ Residue = 'Residue Property',
+ Symmetry = 'Symmetry',
+ Validation = 'Validation',
+ Misc = 'Miscellaneous',
+ }
+
export type Props = { [k: string]: any }
export type Factory<P extends PD.Params> = (ctx: ThemeDataContext, props: PD.Values<P>) => ColorTheme<P>
export const EmptyFactory = () => Empty
@@ -63,7 +71,7 @@ namespace ColorTheme {
}
export interface Provider<P extends PD.Params> extends ThemeProvider<ColorTheme<P>, P> { }
- export const EmptyProvider: Provider<{}> = { label: '', factory: EmptyFactory, getParams: () => ({}), defaultValues: {}, isApplicable: () => true }
+ export const EmptyProvider: Provider<{}> = { label: '', category: '', factory: EmptyFactory, getParams: () => ({}), defaultValues: {}, isApplicable: () => true }
export type Registry = ThemeRegistry<ColorTheme<any>>
export function createRegistry() {
@@ -76,7 +84,6 @@ namespace ColorTheme {
export const BuiltInColorThemes = {
'carbohydrate-symbol': CarbohydrateSymbolColorThemeProvider,
'chain-id': ChainIdColorThemeProvider,
- 'cross-link': CrossLinkColorThemeProvider,
'element-index': ElementIndexColorThemeProvider,
'element-symbol': ElementSymbolColorThemeProvider,
'entity-source': EntitySourceColorThemeProvider,
diff --git a/src/mol-theme/color/carbohydrate-symbol.ts b/src/mol-theme/color/carbohydrate-symbol.ts
index f29d10170f11dffba9626bc8ac4a212e68db3d94..39d41725491f48c9bf5ee3fcccdcc363d401d4c5 100644
--- a/src/mol-theme/color/carbohydrate-symbol.ts
+++ b/src/mol-theme/color/carbohydrate-symbol.ts
@@ -62,6 +62,7 @@ export function CarbohydrateSymbolColorTheme(ctx: ThemeDataContext, props: PD.Va
export const CarbohydrateSymbolColorThemeProvider: ColorTheme.Provider<CarbohydrateSymbolColorThemeParams> = {
label: 'Carbohydrate Symbol',
+ category: ColorTheme.Category.Residue,
factory: CarbohydrateSymbolColorTheme,
getParams: getCarbohydrateSymbolColorThemeParams,
defaultValues: PD.getDefaultValues(CarbohydrateSymbolColorThemeParams),
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index 16c072ff40491cae1f2c181df6d4eef3194fe1fa..46b587c708517f24ee6c052fe6f7c47376c21a87 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -119,6 +119,7 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
export const ChainIdColorThemeProvider: ColorTheme.Provider<ChainIdColorThemeParams> = {
label: 'Chain Id',
+ category: ColorTheme.Category.Chain,
factory: ChainIdColorTheme,
getParams: getChainIdColorThemeParams,
defaultValues: PD.getDefaultValues(ChainIdColorThemeParams),
diff --git a/src/mol-theme/color/element-index.ts b/src/mol-theme/color/element-index.ts
index be94f3376dd57a6609497ea829522055eff3e7d2..0e796512a00b6af51a604b3a92276aa49f1bf17f 100644
--- a/src/mol-theme/color/element-index.ts
+++ b/src/mol-theme/color/element-index.ts
@@ -73,6 +73,7 @@ export function ElementIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<E
export const ElementIndexColorThemeProvider: ColorTheme.Provider<ElementIndexColorThemeParams> = {
label: 'Element Index',
+ category: ColorTheme.Category.Atom,
factory: ElementIndexColorTheme,
getParams: getElementIndexColorThemeParams,
defaultValues: PD.getDefaultValues(ElementIndexColorThemeParams),
diff --git a/src/mol-theme/color/element-symbol.ts b/src/mol-theme/color/element-symbol.ts
index 6f2f8881f7d016719366e50f9c3730ad96ed996d..3582d1414f04afaac51849cf3cd262c4b8c6af71 100644
--- a/src/mol-theme/color/element-symbol.ts
+++ b/src/mol-theme/color/element-symbol.ts
@@ -69,6 +69,7 @@ export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<
export const ElementSymbolColorThemeProvider: ColorTheme.Provider<ElementSymbolColorThemeParams> = {
label: 'Element Symbol',
+ category: ColorTheme.Category.Atom,
factory: ElementSymbolColorTheme,
getParams: getElementSymbolColorThemeParams,
defaultValues: PD.getDefaultValues(ElementSymbolColorThemeParams),
diff --git a/src/mol-theme/color/entity-source.ts b/src/mol-theme/color/entity-source.ts
index a8ac312bfe1693d8be1637d780f1709702303b5d..641839576b59aba23a4e8ac23672aa9150928f64 100644
--- a/src/mol-theme/color/entity-source.ts
+++ b/src/mol-theme/color/entity-source.ts
@@ -175,6 +175,7 @@ export function EntitySourceColorTheme(ctx: ThemeDataContext, props: PD.Values<E
export const EntitySourceColorThemeProvider: ColorTheme.Provider<EntitySourceColorThemeParams> = {
label: 'Entity Source',
+ category: ColorTheme.Category.Chain,
factory: EntitySourceColorTheme,
getParams: getEntitySourceColorThemeParams,
defaultValues: PD.getDefaultValues(EntitySourceColorThemeParams),
diff --git a/src/mol-theme/color/hydrophobicity.ts b/src/mol-theme/color/hydrophobicity.ts
index b281987b2d1d828456a8c39f075f74d68f69c6ca..6ddea14a6e505d8270eca238da5ec61450a8fc6e 100644
--- a/src/mol-theme/color/hydrophobicity.ts
+++ b/src/mol-theme/color/hydrophobicity.ts
@@ -32,22 +32,16 @@ export function hydrophobicity(compId: string, scaleIndex: number): number {
}
function getAtomicCompId(unit: Unit.Atomic, element: ElementIndex) {
- const { modifiedResidues } = unit.model.properties
- const compId = unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
- const parentId = modifiedResidues.parentId.get(compId)
- return parentId === undefined ? compId : parentId
+ return unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
}
function getCoarseCompId(unit: Unit.Spheres | Unit.Gaussians, element: ElementIndex) {
const seqIdBegin = unit.coarseElements.seq_id_begin.value(element)
const seqIdEnd = unit.coarseElements.seq_id_end.value(element)
if (seqIdBegin === seqIdEnd) {
- const { modifiedResidues } = unit.model.properties
const entityKey = unit.coarseElements.entityKey[element]
const seq = unit.model.sequence.byEntityKey[entityKey].sequence
- let compId = seq.compId.value(seqIdBegin - 1) // 1-indexed
- const parentId = modifiedResidues.parentId.get(compId)
- return parentId === undefined ? compId : parentId
+ return seq.compId.value(seqIdBegin - 1) // 1-indexed
}
}
@@ -100,6 +94,7 @@ export function HydrophobicityColorTheme(ctx: ThemeDataContext, props: PD.Values
export const HydrophobicityColorThemeProvider: ColorTheme.Provider<HydrophobicityColorThemeParams> = {
label: 'Hydrophobicity',
+ category: ColorTheme.Category.Residue,
factory: HydrophobicityColorTheme,
getParams: getHydrophobicityColorThemeParams,
defaultValues: PD.getDefaultValues(HydrophobicityColorThemeParams),
diff --git a/src/mol-theme/color/illustrative.ts b/src/mol-theme/color/illustrative.ts
index 6025f1eed563a09a307540d332fc67f3f4583bd7..9b86d8b97a76e5ac85504745ffb30c46fa28b17a 100644
--- a/src/mol-theme/color/illustrative.ts
+++ b/src/mol-theme/color/illustrative.ts
@@ -76,6 +76,7 @@ export function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<I
export const IllustrativeColorThemeProvider: ColorTheme.Provider<IllustrativeColorThemeParams> = {
label: 'Illustrative',
+ category: ColorTheme.Category.Misc,
factory: IllustrativeColorTheme,
getParams: getIllustrativeColorThemeParams,
defaultValues: PD.getDefaultValues(IllustrativeColorThemeParams),
diff --git a/src/mol-theme/color/model-index.ts b/src/mol-theme/color/model-index.ts
index fd98c44f77c4797a3710b20f0313f8969e25b899..20df7e57212ef604707c73e3fd707f4f8f82109b 100644
--- a/src/mol-theme/color/model-index.ts
+++ b/src/mol-theme/color/model-index.ts
@@ -61,6 +61,7 @@ export function ModelIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<Mod
export const ModelIndexColorThemeProvider: ColorTheme.Provider<ModelIndexColorThemeParams> = {
label: 'Model Index',
+ category: ColorTheme.Category.Chain,
factory: ModelIndexColorTheme,
getParams: getModelIndexColorThemeParams,
defaultValues: PD.getDefaultValues(ModelIndexColorThemeParams),
diff --git a/src/mol-theme/color/molecule-type.ts b/src/mol-theme/color/molecule-type.ts
index 49f891381cf11888e0264233757fc4051bdc2707..1692e649728c5564deef6859b770c0bd6677e060 100644
--- a/src/mol-theme/color/molecule-type.ts
+++ b/src/mol-theme/color/molecule-type.ts
@@ -78,6 +78,7 @@ export function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<M
export const MoleculeTypeColorThemeProvider: ColorTheme.Provider<MoleculeTypeColorThemeParams> = {
label: 'Molecule Type',
+ category: ColorTheme.Category.Residue,
factory: MoleculeTypeColorTheme,
getParams: getMoleculeTypeColorThemeParams,
defaultValues: PD.getDefaultValues(MoleculeTypeColorThemeParams),
diff --git a/src/mol-theme/color/occupancy.ts b/src/mol-theme/color/occupancy.ts
index cf609f010a192f7adad85f8c1846d376b30e2627..47686503c292c9da785e2fd077b2617de628be14 100644
--- a/src/mol-theme/color/occupancy.ts
+++ b/src/mol-theme/color/occupancy.ts
@@ -60,6 +60,7 @@ export function OccupancyColorTheme(ctx: ThemeDataContext, props: PD.Values<Occu
export const OccupancyColorThemeProvider: ColorTheme.Provider<OccupancyColorThemeParams> = {
label: 'Occupancy',
+ category: ColorTheme.Category.Atom,
factory: OccupancyColorTheme,
getParams: getOccupancyColorThemeParams,
defaultValues: PD.getDefaultValues(OccupancyColorThemeParams),
diff --git a/src/mol-theme/color/operator-hkl.ts b/src/mol-theme/color/operator-hkl.ts
index 2469356eaa12799c0496bf2f27cad96a04184311..b6adab5f2161bd87dd6eb2c6a8fe864295714184 100644
--- a/src/mol-theme/color/operator-hkl.ts
+++ b/src/mol-theme/color/operator-hkl.ts
@@ -119,6 +119,7 @@ export function OperatorHklColorTheme(ctx: ThemeDataContext, props: PD.Values<Op
export const OperatorHklColorThemeProvider: ColorTheme.Provider<OperatorHklColorThemeParams> = {
label: 'Operator HKL',
+ category: ColorTheme.Category.Symmetry,
factory: OperatorHklColorTheme,
getParams: getOperatorHklColorThemeParams,
defaultValues: PD.getDefaultValues(OperatorHklColorThemeParams),
diff --git a/src/mol-theme/color/operator-name.ts b/src/mol-theme/color/operator-name.ts
index 16d48b147f4833878b6bd90452f70ac5dbb5a06d..3c4b60895f0dabda9af8c4bf6a817ed6f11d5830 100644
--- a/src/mol-theme/color/operator-name.ts
+++ b/src/mol-theme/color/operator-name.ts
@@ -85,6 +85,7 @@ export function OperatorNameColorTheme(ctx: ThemeDataContext, props: PD.Values<O
export const OperatorNameColorThemeProvider: ColorTheme.Provider<OperatorNameColorThemeParams> = {
label: 'Operator Name',
+ category: ColorTheme.Category.Symmetry,
factory: OperatorNameColorTheme,
getParams: getOperatorNameColorThemeParams,
defaultValues: PD.getDefaultValues(OperatorNameColorThemeParams),
diff --git a/src/mol-theme/color/polymer-id.ts b/src/mol-theme/color/polymer-id.ts
index 46955e905c48bad6d951683869e8c9f3fb5f94ee..68649703483620535f88e05a03f19076ad7831d2 100644
--- a/src/mol-theme/color/polymer-id.ts
+++ b/src/mol-theme/color/polymer-id.ts
@@ -127,7 +127,8 @@ export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Poly
}
export const PolymerIdColorThemeProvider: ColorTheme.Provider<PolymerIdColorThemeParams> = {
- label: 'Polymer Id',
+ label: 'Polymer Chain Id',
+ category: ColorTheme.Category.Chain,
factory: PolymerIdColorTheme,
getParams: getPolymerIdColorThemeParams,
defaultValues: PD.getDefaultValues(PolymerIdColorThemeParams),
diff --git a/src/mol-theme/color/polymer-index.ts b/src/mol-theme/color/polymer-index.ts
index 02bfa5b44266b20e431980f35b4d78545a5b5dbd..6d6c86dc9ae258c16509e6478d0b1a63ce6d974f 100644
--- a/src/mol-theme/color/polymer-index.ts
+++ b/src/mol-theme/color/polymer-index.ts
@@ -16,7 +16,7 @@ import { ColorLists } from '../../mol-util/color/lists';
const DefaultList = 'dark-2'
const DefaultColor = Color(0xCCCCCC)
-const Description = 'Gives every polymer a unique color based on the position (index) of the polymer in the list of polymers in the structure.'
+const Description = 'Gives every polymer chain instance a unique color based on the position (index) of the polymer in the list of polymers in the structure.'
export const PolymerIndexColorThemeParams = {
...getPaletteParams({ type: 'set', setList: DefaultList }),
@@ -87,7 +87,8 @@ export function PolymerIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<P
}
export const PolymerIndexColorThemeProvider: ColorTheme.Provider<PolymerIndexColorThemeParams> = {
- label: 'Polymer Index',
+ label: 'Polymer Chain Instance',
+ category: ColorTheme.Category.Chain,
factory: PolymerIndexColorTheme,
getParams: getPolymerIndexColorThemeParams,
defaultValues: PD.getDefaultValues(PolymerIndexColorThemeParams),
diff --git a/src/mol-theme/color/residue-name.ts b/src/mol-theme/color/residue-name.ts
index 1703761c3b9252c2535b70a3e0f6d8ee50454916..741601e1cd2e6f37dd068d3d59857ac24b4e45de 100644
--- a/src/mol-theme/color/residue-name.ts
+++ b/src/mol-theme/color/residue-name.ts
@@ -74,22 +74,16 @@ export function getResidueNameColorThemeParams(ctx: ThemeDataContext) {
}
function getAtomicCompId(unit: Unit.Atomic, element: ElementIndex) {
- const { modifiedResidues } = unit.model.properties
- const compId = unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
- const parentId = modifiedResidues.parentId.get(compId)
- return parentId === undefined ? compId : parentId
+ return unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
}
function getCoarseCompId(unit: Unit.Spheres | Unit.Gaussians, element: ElementIndex) {
const seqIdBegin = unit.coarseElements.seq_id_begin.value(element)
const seqIdEnd = unit.coarseElements.seq_id_end.value(element)
if (seqIdBegin === seqIdEnd) {
- const { modifiedResidues } = unit.model.properties
const entityKey = unit.coarseElements.entityKey[element]
const seq = unit.model.sequence.byEntityKey[entityKey].sequence
- let compId = seq.compId.value(seqIdBegin - 1) // 1-indexed
- const parentId = modifiedResidues.parentId.get(compId)
- return parentId === undefined ? compId : parentId
+ return seq.compId.value(seqIdBegin - 1) // 1-indexed
}
}
@@ -136,6 +130,7 @@ export function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<Re
export const ResidueNameColorThemeProvider: ColorTheme.Provider<ResidueNameColorThemeParams> = {
label: 'Residue Name',
+ category: ColorTheme.Category.Residue,
factory: ResidueNameColorTheme,
getParams: getResidueNameColorThemeParams,
defaultValues: PD.getDefaultValues(ResidueNameColorThemeParams),
diff --git a/src/mol-theme/color/secondary-structure.ts b/src/mol-theme/color/secondary-structure.ts
index 9eef3bb1c704290a78bd9cb9112104af87a1125a..12eaf2eb8df454b20d2b7b1d9cf1d7d2c6521da4 100644
--- a/src/mol-theme/color/secondary-structure.ts
+++ b/src/mol-theme/color/secondary-structure.ts
@@ -113,6 +113,7 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
export const SecondaryStructureColorThemeProvider: ColorTheme.Provider<SecondaryStructureColorThemeParams> = {
label: 'Secondary Structure',
+ category: ColorTheme.Category.Residue,
factory: SecondaryStructureColorTheme,
getParams: getSecondaryStructureColorThemeParams,
defaultValues: PD.getDefaultValues(SecondaryStructureColorThemeParams),
diff --git a/src/mol-theme/color/sequence-id.ts b/src/mol-theme/color/sequence-id.ts
index 66457c0b576b579c692cae88ab9ccdc728aec05b..26881241a45d546ec50da3cba5c17b4cf6314487 100644
--- a/src/mol-theme/color/sequence-id.ts
+++ b/src/mol-theme/color/sequence-id.ts
@@ -101,6 +101,7 @@ export function SequenceIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Seq
export const SequenceIdColorThemeProvider: ColorTheme.Provider<SequenceIdColorThemeParams> = {
label: 'Sequence Id',
+ category: ColorTheme.Category.Residue,
factory: SequenceIdColorTheme,
getParams: getSequenceIdColorThemeParams,
defaultValues: PD.getDefaultValues(SequenceIdColorThemeParams),
diff --git a/src/mol-theme/color/shape-group.ts b/src/mol-theme/color/shape-group.ts
index 1c3166fafdadbefae4f83b7b9cd12d708a46ddf3..8a8232657dec24eac00254c08ba2bf2a458b4dc7 100644
--- a/src/mol-theme/color/shape-group.ts
+++ b/src/mol-theme/color/shape-group.ts
@@ -37,6 +37,7 @@ export function ShapeGroupColorTheme(ctx: ThemeDataContext, props: PD.Values<Sha
export const ShapeGroupColorThemeProvider: ColorTheme.Provider<ShapeGroupColorThemeParams> = {
label: 'Shape Group',
+ category: ColorTheme.Category.Misc,
factory: ShapeGroupColorTheme,
getParams: getShapeGroupColorThemeParams,
defaultValues: PD.getDefaultValues(ShapeGroupColorThemeParams),
diff --git a/src/mol-theme/color/uncertainty.ts b/src/mol-theme/color/uncertainty.ts
index d7511cb0533f6554bf50d9d92797ef1b0df223f5..512dbea67781636037f14c4bbf34b9cf7202acf4 100644
--- a/src/mol-theme/color/uncertainty.ts
+++ b/src/mol-theme/color/uncertainty.ts
@@ -64,6 +64,7 @@ export function UncertaintyColorTheme(ctx: ThemeDataContext, props: PD.Values<Un
export const UncertaintyColorThemeProvider: ColorTheme.Provider<UncertaintyColorThemeParams> = {
label: 'Uncertainty/Disorder',
+ category: ColorTheme.Category.Atom,
factory: UncertaintyColorTheme,
getParams: getUncertaintyColorThemeParams,
defaultValues: PD.getDefaultValues(UncertaintyColorThemeParams),
diff --git a/src/mol-theme/color/uniform.ts b/src/mol-theme/color/uniform.ts
index 6bc0e8bdc70be6be9be3c061eb5c7936ab8d270d..2fd01719375da61b3e1693a7ba213095e8895981 100644
--- a/src/mol-theme/color/uniform.ts
+++ b/src/mol-theme/color/uniform.ts
@@ -37,6 +37,7 @@ export function UniformColorTheme(ctx: ThemeDataContext, props: PD.Values<Unifor
export const UniformColorThemeProvider: ColorTheme.Provider<UniformColorThemeParams> = {
label: 'Uniform',
+ category: ColorTheme.Category.Misc,
factory: UniformColorTheme,
getParams: getUniformColorThemeParams,
defaultValues: PD.getDefaultValues(UniformColorThemeParams),
diff --git a/src/mol-theme/color/unit-index.ts b/src/mol-theme/color/unit-index.ts
index bb6bb9c5bbc40dead1edf85da2ec110fb3011d13..3cc6cdcf26bbd93a71bda07611a6e1201cd149c7 100644
--- a/src/mol-theme/color/unit-index.ts
+++ b/src/mol-theme/color/unit-index.ts
@@ -16,7 +16,7 @@ import { ColorLists } from '../../mol-util/color/lists';
const DefaultList = 'dark-2'
const DefaultColor = Color(0xCCCCCC)
-const Description = 'Gives every unit (single chain or collection of single elements) a unique color based on the position (index) of the unit in the list of units in the structure.'
+const Description = 'Gives every chain instance (single chain or collection of single elements) a unique color based on the position (index) of the chain in the list of chains in the structure.'
export const UnitIndexColorThemeParams = {
...getPaletteParams({ type: 'set', setList: DefaultList }),
@@ -72,7 +72,8 @@ export function UnitIndexColorTheme(ctx: ThemeDataContext, props: PD.Values<Unit
}
export const UnitIndexColorThemeProvider: ColorTheme.Provider<UnitIndexColorThemeParams> = {
- label: 'Unit Index',
+ label: 'Chain Instance',
+ category: ColorTheme.Category.Chain,
factory: UnitIndexColorTheme,
getParams: getUnitIndexColorThemeParams,
defaultValues: PD.getDefaultValues(UnitIndexColorThemeParams),
diff --git a/src/mol-theme/size.ts b/src/mol-theme/size.ts
index 71c79b8d22d463ca3b3efa0779c41e5b9d77f227..2283474f79175887aa15b56780d5c71b6c01fffa 100644
--- a/src/mol-theme/size.ts
+++ b/src/mol-theme/size.ts
@@ -32,7 +32,7 @@ namespace SizeTheme {
}
export interface Provider<P extends PD.Params> extends ThemeProvider<SizeTheme<P>, P> { }
- export const EmptyProvider: Provider<{}> = { label: '', factory: EmptyFactory, getParams: () => ({}), defaultValues: {}, isApplicable: () => true }
+ export const EmptyProvider: Provider<{}> = { label: '', category: '', factory: EmptyFactory, getParams: () => ({}), defaultValues: {}, isApplicable: () => true }
export type Registry = ThemeRegistry<SizeTheme<any>>
export function createRegistry() {
diff --git a/src/mol-theme/size/physical.ts b/src/mol-theme/size/physical.ts
index 4456ad2091c98280488f9c1dd34f1e42784efc6a..8622967d19f8e774b71b9446d580530e5f9ce01d 100644
--- a/src/mol-theme/size/physical.ts
+++ b/src/mol-theme/size/physical.ts
@@ -58,6 +58,7 @@ export function PhysicalSizeTheme(ctx: ThemeDataContext, props: PD.Values<Physic
export const PhysicalSizeThemeProvider: SizeTheme.Provider<PhysicalSizeThemeParams> = {
label: 'Physical',
+ category: '',
factory: PhysicalSizeTheme,
getParams: getPhysicalSizeThemeParams,
defaultValues: PD.getDefaultValues(PhysicalSizeThemeParams),
diff --git a/src/mol-theme/size/shape-group.ts b/src/mol-theme/size/shape-group.ts
index 2e2f867d55c5910a8ca844a4cb42215c77607412..b7eaa993fe5d1afcf5af100b6c4fb2ce215f2c26 100644
--- a/src/mol-theme/size/shape-group.ts
+++ b/src/mol-theme/size/shape-group.ts
@@ -36,6 +36,7 @@ export function ShapeGroupSizeTheme(ctx: ThemeDataContext, props: PD.Values<Shap
export const ShapeGroupSizeThemeProvider: SizeTheme.Provider<ShapeGroupSizeThemeParams> = {
label: 'Shape Group',
+ category: '',
factory: ShapeGroupSizeTheme,
getParams: getShapeGroupSizeThemeParams,
defaultValues: PD.getDefaultValues(ShapeGroupSizeThemeParams),
diff --git a/src/mol-theme/size/uncertainty.ts b/src/mol-theme/size/uncertainty.ts
index 5f9da065b4b8331ac620db16e6e4b806446ac176..bbeec077745086a04cdb72d76cd9ef911cd0595f 100644
--- a/src/mol-theme/size/uncertainty.ts
+++ b/src/mol-theme/size/uncertainty.ts
@@ -54,6 +54,7 @@ export function UncertaintySizeTheme(ctx: ThemeDataContext, props: PD.Values<Unc
export const UncertaintySizeThemeProvider: SizeTheme.Provider<UncertaintySizeThemeParams> = {
label: 'Uncertainty/Disorder',
+ category: '',
factory: UncertaintySizeTheme,
getParams: getUncertaintySizeThemeParams,
defaultValues: PD.getDefaultValues(UncertaintySizeThemeParams),
diff --git a/src/mol-theme/size/uniform.ts b/src/mol-theme/size/uniform.ts
index 4d82bef1048e7b01b74c711df38221f3fd3aafdd..32b2718744f145c5ec3540eefb8a7326f46f7d0a 100644
--- a/src/mol-theme/size/uniform.ts
+++ b/src/mol-theme/size/uniform.ts
@@ -32,6 +32,7 @@ export function UniformSizeTheme(ctx: ThemeDataContext, props: PD.Values<Uniform
export const UniformSizeThemeProvider: SizeTheme.Provider<UniformSizeThemeParams> = {
label: 'Uniform',
+ category: '',
factory: UniformSizeTheme,
getParams: getUniformSizeThemeParams,
defaultValues: PD.getDefaultValues(UniformSizeThemeParams),
diff --git a/src/mol-theme/theme.ts b/src/mol-theme/theme.ts
index ce5350a5a696a2b2315415576755f1556667dea2..e4d038f175147906882d58b5df7e6c6f2e15f9da 100644
--- a/src/mol-theme/theme.ts
+++ b/src/mol-theme/theme.ts
@@ -61,6 +61,7 @@ namespace Theme {
export interface ThemeProvider<T extends ColorTheme<P> | SizeTheme<P>, P extends PD.Params> {
readonly label: string
+ readonly category: string
readonly factory: (ctx: ThemeDataContext, props: PD.Values<P>) => T
readonly getParams: (ctx: ThemeDataContext) => P
readonly defaultValues: PD.Values<P>
@@ -69,7 +70,7 @@ export interface ThemeProvider<T extends ColorTheme<P> | SizeTheme<P>, P extends
}
function getTypes(list: { name: string, provider: ThemeProvider<any, any> }[]) {
- return list.map(e => [e.name, e.provider.label] as [string, string]);
+ return list.map(e => [e.name, e.provider.label, e.provider.category] as [string, string, string]);
}
export class ThemeRegistry<T extends ColorTheme<any> | SizeTheme<any>> {
@@ -79,16 +80,26 @@ export class ThemeRegistry<T extends ColorTheme<any> | SizeTheme<any>> {
get default() { return this._list[0] }
get list() { return this._list }
- get types(): [string, string][] { return getTypes(this._list) }
+ get types(): [string, string, string][] { return getTypes(this._list) }
constructor(builtInThemes: { [k: string]: ThemeProvider<T, any> }, private emptyProvider: ThemeProvider<T, any>) {
Object.keys(builtInThemes).forEach(name => this.add(name, builtInThemes[name]))
}
+ private sort() {
+ this._list.sort((a, b) => {
+ if (a.provider.category === b.provider.category) {
+ return a.provider.label < b.provider.label ? -1 : a.provider.label > b.provider.label ? 1 : 0;
+ }
+ return a.provider.category < b.provider.category ? -1 : 1;
+ });
+ }
+
add<P extends PD.Params>(name: string, provider: ThemeProvider<T, P>) {
this._list.push({ name, provider })
this._map.set(name, provider)
this._name.set(provider, name)
+ this.sort();
}
remove(name: string) {
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index edcf9300c4635fb1ac00869978d8f9457f58906c..c835570ab397c7db04c08804bed2277b79b6d756 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -65,9 +65,9 @@ export namespace ParamDefinition {
export interface Select<T extends string | number> extends Base<T> {
type: 'select'
/** array of (value, label) tuples */
- options: readonly (readonly [T, string])[]
+ options: readonly (readonly [T, string] | readonly [T, string, string])[]
}
- export function Select<T extends string | number>(defaultValue: T, options: readonly (readonly [T, string])[], info?: Info): Select<T> {
+ export function Select<T extends string | number>(defaultValue: T, options: readonly (readonly [T, string] | readonly [T, string, string])[], info?: Info): Select<T> {
return setInfo<Select<T>>({ type: 'select', defaultValue: checkDefaultKey(defaultValue, options), options }, info)
}
@@ -111,11 +111,11 @@ export namespace ParamDefinition {
return setInfo<Color>({ type: 'color', defaultValue }, info)
}
- export interface Vec3 extends Base<Vec3Data> {
+ export interface Vec3 extends Base<Vec3Data>, Range {
type: 'vec3'
}
- export function Vec3(defaultValue: Vec3Data, info?: Info): Vec3 {
- return setInfo<Vec3>({ type: 'vec3', defaultValue }, info)
+ export function Vec3(defaultValue: Vec3Data, range?: { min?: number, max?: number, step?: number }, info?: Info): Vec3 {
+ return setInfo<Vec3>(setRange({ type: 'vec3', defaultValue }, range), info)
}
export interface FileParam extends Base<File> {
@@ -149,7 +149,7 @@ export namespace ParamDefinition {
*/
step?: number
}
- function setRange<T extends Numeric | Interval>(p: T, range?: { min?: number, max?: number, step?: number }) {
+ function setRange<T extends Numeric | Interval | Vec3>(p: T, range?: { min?: number, max?: number, step?: number }) {
if (!range) return p;
if (typeof range.min !== 'undefined') p.min = range.min;
if (typeof range.max !== 'undefined') p.max = range.max;
@@ -201,7 +201,7 @@ export namespace ParamDefinition {
select: Select<string>,
map(name: string): Any
}
- export function Mapped<T>(defaultKey: string, names: [string, string][], map: (name: string) => Any, info?: Info): Mapped<NamedParams<T>> {
+ export function Mapped<T>(defaultKey: string, names: ([string, string] | [string, string, string])[], map: (name: string) => Any, info?: Info): Mapped<NamedParams<T>> {
const name = checkDefaultKey(defaultKey, names);
return setInfo<Mapped<NamedParams<T>>>({
type: 'mapped',
@@ -406,7 +406,7 @@ export namespace ParamDefinition {
return ret;
}
- function checkDefaultKey<T>(k: T, options: readonly (readonly [T, string])[]) {
+ function checkDefaultKey<T>(k: T, options: readonly (readonly [T, string] | readonly [T, string, string])[]) {
for (const o of options) {
if (o[0] === k) return k;
}
diff --git a/src/mol-util/param-mapping.ts b/src/mol-util/param-mapping.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e85731ffa8f14e9ab2f8b69dcf46c57264dd77c7
--- /dev/null
+++ b/src/mol-util/param-mapping.ts
@@ -0,0 +1,37 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { ParamDefinition as PD } from './param-definition';
+import produce from 'immer'
+import { Mutable } from './type-helpers';
+
+export interface ParamMapping<S, T, Ctx> {
+ params(ctx: Ctx): PD.For<S>,
+ getTarget(ctx: Ctx): T,
+ getValues(t: T, ctx: Ctx): S,
+ update(s: S, ctx: Ctx): T,
+ apply(t: T, ctx: Ctx): void | Promise<void>
+}
+
+export function ParamMapping<S, T, Ctx>(def: {
+ params: ((ctx: Ctx) => PD.For<S>) | PD.For<S>,
+ target(ctx: Ctx): T
+}): (options: {
+ values(t: T, ctx: Ctx): S,
+ update(s: S, t: Mutable<T>, ctx: Ctx): void,
+ apply?(t: T, ctx: Ctx): void | Promise<void>
+}) => ParamMapping<S, T, Ctx> {
+ return ({ values, update, apply }) => ({
+ params: typeof def.params === 'function' ? def.params as any : ctx => def.params,
+ getTarget: def.target,
+ getValues: values,
+ update(s, ctx) {
+ const t = def.target(ctx);
+ return produce(t, t1 => update(s, t1 as any, ctx));
+ },
+ apply: apply ? apply : () => { }
+ });
+}
\ No newline at end of file
diff --git a/src/mol-util/set.ts b/src/mol-util/set.ts
index af02d56a3cab789b73612da9c24a48d43c4c461f..9e1f71738511e4ef34547c9aae44f375f635859b 100644
--- a/src/mol-util/set.ts
+++ b/src/mol-util/set.ts
@@ -4,9 +4,15 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
+import { iterableToArray } from '../mol-data/util/array';
+
// TODO use set@@iterator when targeting es6
export namespace SetUtils {
+ export function toArray<T>(set: ReadonlySet<T>) {
+ return iterableToArray(set.values())
+ }
+
/** Test if set a contains all elements of set b. */
export function isSuperset<T>(setA: ReadonlySet<T>, setB: ReadonlySet<T>) {
let flag = true
diff --git a/webpack.config.js b/webpack.config.js
index f33a385636c5aff1423777bb51873a7d60824ddb..9e9aceeaccfddf66f9691890c05f5a854fabdfb7 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -46,7 +46,8 @@ const sharedConfig = {
'node_modules',
path.resolve(__dirname, 'lib/')
],
- }
+ },
+ devtool: ''
}