diff --git a/src/mol-canvas3d/helper/postprocessing.ts b/src/mol-canvas3d/helper/postprocessing.ts
index e47c803b8e3e1167bf5f8d6da1370ba3d0aeeeaa..3b476365a228b3ac3c2e0c3d446d1e6546671c37 100644
--- a/src/mol-canvas3d/helper/postprocessing.ts
+++ b/src/mol-canvas3d/helper/postprocessing.ts
@@ -33,7 +33,7 @@ const PostprocessingSchema = {
export const PostprocessingParams = {
occlusionEnable: PD.Boolean(false),
- occlusionKernelSize: PD.Numeric(4, { min: 1, max: 100, step: 1 }),
+ occlusionKernelSize: PD.Numeric(4, { min: 1, max: 32, step: 1 }),
occlusionBias: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
occlusionRadius: PD.Numeric(64, { min: 0, max: 256, step: 1 }),
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index 335e7b462eab27cad098c3ce20ce381e8cbdea98..ed77c0c6ca5f65cff27ac3771107ecf831f8563f 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -1021,8 +1021,8 @@ namespace Mat4 {
}
const xAxis = Vec3.create(1, 0, 0)
- const yAxis = Vec3.create(1, 0, 0)
- const zAxis = Vec3.create(1, 0, 0)
+ const yAxis = Vec3.create(0, 1, 0)
+ const zAxis = Vec3.create(0, 0, 1)
/** Rotation matrix for 90deg around x-axis */
export const rotX90: ReadonlyMat4 = Mat4.fromRotation(Mat4(), degToRad(90), xAxis)
diff --git a/src/mol-model-formats/structure/mmcif/ihm.ts b/src/mol-model-formats/structure/mmcif/ihm.ts
index 405fec8cf0fab7b019f477e41ac0dea1d61a9716..e6b86f11b6d6f8982c0495f95f4ef02a7811e560 100644
--- a/src/mol-model-formats/structure/mmcif/ihm.ts
+++ b/src/mol-model-formats/structure/mmcif/ihm.ts
@@ -19,6 +19,7 @@ import { FormatData } from './parser';
export interface IHMData {
model_id: number,
model_name: string,
+ model_group_name: string,
entities: Entities,
atom_site: mmCIF['atom_site'],
atom_site_sourceIndex: Column<number>,
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index b7e9d1ef07f3af0c82a1d63dcb7e870c88d60fa1..eee752fd2ab941c65d818a9a7548012121ba0b37 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -190,6 +190,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
return {
id: UUID.create22(),
label,
+ entry: label,
sourceData: format,
modelNum: atom_site.pdbx_PDB_model_num.value(0),
entities,
@@ -212,10 +213,15 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
const atomic = getAtomicHierarchyAndConformation(data.atom_site, data.atom_site_sourceIndex, data.entities, formatData);
const coarse = getIHMCoarse(data, formatData);
+ const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
+ ? format.data.entry.id.value(0)
+ : format.data._name;
+ const label = data.model_group_name ? `${data.model_name}: ${data.model_group_name}` : data.model_name
return {
id: UUID.create22(),
- label: data.model_name,
+ label,
+ entry,
sourceData: format,
modelNum: data.model_id,
entities: data.entities,
@@ -324,14 +330,13 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
}
async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
- if (format.data.atom_site._rowCount && !format.data.atom_site.ihm_model_id.isDefined) {
- throw new Error('expected _atom_site.ihm_model_id to be defined')
- }
+ // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
+ const atom_sites_modelColumn = format.data.atom_site.ihm_model_id.isDefined ? format.data.atom_site.ihm_model_id : format.data.atom_site.pdbx_PDB_model_num
const { ihm_model_list } = format.data;
const entities = getEntities(format)
- const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
+ const atom_sites = splitTable(format.data.atom_site, atom_sites_modelColumn);
// TODO: will coarse IHM records require sorting or will we trust it?
// ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
// If the sorting is implemented, updated mol-model/structure/properties: atom.sourceIndex
@@ -340,14 +345,15 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
const models: Model[] = [];
- const { model_id, model_name } = ihm_model_list;
+ const { model_id, model_name, model_group_name } = ihm_model_list;
for (let i = 0; i < ihm_model_list._rowCount; i++) {
const id = model_id.value(i);
let atom_site, atom_site_sourceIndex;
if (atom_sites.has(id)) {
const e = atom_sites.get(id)!;
- const { atom_site: sorted, sourceIndex } = await sortAtomSite(ctx, e.table, e.start, e.end);
+ // need to sort `format.data.atom_site` as `e.start` and `e.end` are indices into that
+ const { atom_site: sorted, sourceIndex } = await sortAtomSite(ctx, format.data.atom_site, e.start, e.end);
atom_site = sorted;
atom_site_sourceIndex = sourceIndex;
} else {
@@ -358,6 +364,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
const data: IHMData = {
model_id: id,
model_name: model_name.value(i),
+ model_group_name: model_group_name.value(i),
entities: entities,
atom_site,
atom_site_sourceIndex,
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 303048fdde6740ec47502a9c3baee05a0d927dc7..cad6d07e895cae6c8b3a3ebcfa1e2e0433441ff9 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import UUID from 'mol-util/uuid';
@@ -25,7 +26,10 @@ export interface Model extends Readonly<{
id: UUID,
label: string,
- // for IHM, corresponds to ihm_model_list.model_id
+ /** the name of the entry/file/collection the model is part of */
+ entry: string,
+
+ /** for IHM, corresponds to ihm_model_list.model_id */
modelNum: number,
sourceData: ModelFormat,
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 75bec96914943b8ef01d6627bc188d49ad823d37..64cb0bac27a6606abc1fb1b836444bbf2b4c117f 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -576,4 +576,38 @@ export namespace LinkType {
export function isCovalent(flags: LinkType.Flag) {
return (flags & LinkType.Flag.Covalent) !== 0;
}
-}
\ No newline at end of file
+}
+
+/**
+ * "Experimentally determined hydrophobicity scale for proteins at membrane interfaces"
+ * by Wimely and White (doi:10.1038/nsb1096-842)
+ * http://blanco.biomol.uci.edu/Whole_residue_HFscales.txt
+ * https://www.nature.com/articles/nsb1096-842
+ */
+export const ResidueHydrophobicity = {
+ // AA DGwif DGwoct Oct-IF
+ 'ALA': [ 0.17, 0.50, 0.33 ],
+ 'ARG': [ 0.81, 1.81, 1.00 ],
+ 'ASN': [ 0.42, 0.85, 0.43 ],
+ 'ASP': [ 1.23, 3.64, 2.41 ],
+ 'ASH': [ -0.07, 0.43, 0.50 ],
+ 'CYS': [ -0.24, -0.02, 0.22 ],
+ 'GLN': [ 0.58, 0.77, 0.19 ],
+ 'GLU': [ 2.02, 3.63, 1.61 ],
+ 'GLH': [ -0.01, 0.11, 0.12 ],
+ 'GLY': [ 0.01, 1.15, 1.14 ],
+ // "His+": [ 0.96, 2.33, 1.37 ],
+ 'HIS': [ 0.17, 0.11, -0.06 ],
+ 'ILE': [ -0.31, -1.12, -0.81 ],
+ 'LEU': [ -0.56, -1.25, -0.69 ],
+ 'LYS': [ 0.99, 2.80, 1.81 ],
+ 'MET': [ -0.23, -0.67, -0.44 ],
+ 'PHE': [ -1.13, -1.71, -0.58 ],
+ 'PRO': [ 0.45, 0.14, -0.31 ],
+ 'SER': [ 0.13, 0.46, 0.33 ],
+ 'THR': [ 0.14, 0.25, 0.11 ],
+ 'TRP': [ -1.85, -2.09, -0.24 ],
+ 'TYR': [ -0.94, -0.71, 0.23 ],
+ 'VAL': [ 0.07, -0.46, -0.53 ]
+ }
+ export const DefaultResidueHydrophobicity = [ 0.00, 0.00, 0.00 ]
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 8fc4688a561036e71c7ed334667dd531c8b3996f..342175438faa61d36f8595fa42f7945a66317f66 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -421,16 +421,22 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return `${unit.id}|${residueIndex}`
}
- const anomericCarbonMap = new Map<string, ElementIndex>()
+ const anomericCarbonMap = new Map<string, ElementIndex[]>()
for (let i = 0, il = elements.length; i < il; ++i) {
const { unit, anomericCarbon } = elements[i]
const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index[anomericCarbon]
- anomericCarbonMap.set(anomericCarbonKey(unit, residueIndex), anomericCarbon)
+ const k = anomericCarbonKey(unit, residueIndex)
+ if (anomericCarbonMap.has(k)) {
+ anomericCarbonMap.get(k)!.push(anomericCarbon)
+ } else {
+ anomericCarbonMap.set(k, [anomericCarbon])
+ }
}
- function getAnomericCarbon(unit: Unit, residueIndex: ResidueIndex) {
- return anomericCarbonMap.get(anomericCarbonKey(unit, residueIndex))
+ const EmptyArray: ReadonlyArray<any> = []
+ function getAnomericCarbons(unit: Unit, residueIndex: ResidueIndex) {
+ return anomericCarbonMap.get(anomericCarbonKey(unit, residueIndex)) || EmptyArray
}
- return { getElementIndex, getLinkIndex, getLinkIndices, getTerminalLinkIndex, getTerminalLinkIndices, getAnomericCarbon }
+ return { getElementIndex, getLinkIndex, getLinkIndices, getTerminalLinkIndex, getTerminalLinkIndices, getAnomericCarbons }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index 1eaae487ca98d877dd19d5fa592a2a76e5365151..a753378370aae16424a947f0714d07d7a8a32622 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -49,7 +49,7 @@ export interface Carbohydrates {
getLinkIndices: (unit: Unit, anomericCarbon: ElementIndex) => ReadonlyArray<number>
getTerminalLinkIndex: (unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) => number | undefined
getTerminalLinkIndices: (unit: Unit, element: ElementIndex) => ReadonlyArray<number>
- getAnomericCarbon: (unit: Unit, residueIndex: ResidueIndex) => ElementIndex | undefined
+ getAnomericCarbons: (unit: Unit, residueIndex: ResidueIndex) => ReadonlyArray<ElementIndex>
}
const EmptyArray: ReadonlyArray<any> = []
@@ -63,5 +63,5 @@ export const EmptyCarbohydrates: Carbohydrates = {
getLinkIndices: () => EmptyArray,
getTerminalLinkIndex: () => undefined,
getTerminalLinkIndices: () => EmptyArray,
- getAnomericCarbon: () => undefined,
+ getAnomericCarbons: () => [],
}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index e7b357d9b7e3987edd704fcdd98559c4eed7bd73..6dbc53ea78ca7a90e2e4dd9afc17c94f0ccb0e0d 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -99,7 +99,7 @@ export namespace VolumeStreaming {
channels: Channels = {}
private async queryData(box?: Box3D) {
- let url = urlCombine(this.info.serverUrl, `${this.info.kind}/${this.info.dataId}`);
+ let url = urlCombine(this.info.serverUrl, `${this.info.kind}/${this.info.dataId.toLowerCase()}`);
if (box) {
const { min: a, max: b } = box;
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index aa98aeff147ac90f77973a1dab5f16b2bbb7d56a..8dd2be858575fc55f058fc4b57c166d963e22468 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -115,7 +115,7 @@ const CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
const dataId = params.dataId;
const emDefaultContourLevel = params.source.name === 'em' ? params.source.params.isoValue : VolumeIsoValue.relative(1);
await taskCtx.update('Getting server header...');
- const header = await plugin.fetch<VolumeServerHeader>({ url: urlCombine(params.serverUrl, `${params.source.name}/${dataId}`), type: 'json' }).runInContext(taskCtx);
+ const header = await plugin.fetch<VolumeServerHeader>({ url: urlCombine(params.serverUrl, `${params.source.name}/${dataId.toLocaleLowerCase()}`), type: 'json' }).runInContext(taskCtx);
const data: VolumeServerInfo.Data = {
serverUrl: params.serverUrl,
dataId,
diff --git a/src/mol-plugin/state/actions/data-format.ts b/src/mol-plugin/state/actions/data-format.ts
index 3cb8a05da5a2fae2722df766e895f691050b2d53..9a0ffd829f3fb6808703f6ee63f8028c72b6f3a3 100644
--- a/src/mol-plugin/state/actions/data-format.ts
+++ b/src/mol-plugin/state/actions/data-format.ts
@@ -150,6 +150,8 @@ type cifVariants = 'dscif' | -1
export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
if (info.ext === 'bcif') {
try {
+ // TODO find a way to run msgpackDecode only once
+ // now it is run twice, here and during file parsing
if (msgpackDecode(data as Uint8Array).encoder.startsWith('VolumeServer')) return 'dscif'
} catch { }
} else if (info.ext === 'cif') {
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index e8f8bfb09532de95672039efcd5215046e474232..d6ba75abdf75e930a23e905b800cfb4ca63126c5 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -91,6 +91,10 @@ const DownloadStructure = StateAction.build({
id: PD.Text('1tqn', { label: 'Id' }),
options: DownloadStructurePdbIdSourceOptions
}, { isFlat: true }),
+ 'pdb-dev': PD.Group({
+ id: PD.Text('PDBDEV_00000001', { label: 'Id' }),
+ options: DownloadStructurePdbIdSourceOptions
+ }, { isFlat: true }),
'bcif-static': PD.Group({
id: PD.Text('1tqn', { label: 'Id' }),
options: DownloadStructurePdbIdSourceOptions
@@ -107,6 +111,7 @@ const DownloadStructure = StateAction.build({
options: [
['pdbe-updated', 'PDBe Updated'],
['rcsb', 'RCSB'],
+ ['pdb-dev', 'PDBDEV'],
['bcif-static', 'BinaryCIF (static PDBe Updated)'],
['url', 'URL']
]
@@ -133,6 +138,18 @@ const DownloadStructure = StateAction.build({
supportProps = !!src.params.options.supportProps;
asTrajectory = !!src.params.options.asTrajectory;
break;
+ case 'pdb-dev':
+ downloadParams = getDownloadParams(src.params.id,
+ id => {
+ const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`
+ return `https://pdb-dev.wwpdb.org/static/cif/${nId.toUpperCase()}.cif`
+ },
+ id => id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`,
+ false
+ );
+ supportProps = !!src.params.options.supportProps;
+ asTrajectory = !!src.params.options.asTrajectory;
+ break;
case 'bcif-static':
downloadParams = getDownloadParams(src.params.id, id => `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${id.toLowerCase()}`, id => `BinaryCIF: ${id}`, true);
supportProps = !!src.params.options.supportProps;
@@ -155,7 +172,7 @@ const DownloadStructure = StateAction.build({
});
function getDownloadParams(src: string, url: (id: string) => string, label: (id: string) => string, isBinary: boolean): StateTransformer.Params<Download>[] {
- const ids = src.split(',').map(id => id.trim()).filter(id => !!id && id.length >= 4);
+ const ids = src.split(',').map(id => id.trim()).filter(id => !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)));
const ret: StateTransformer.Params<Download>[] = [];
for (const id of ids) {
ret.push({ url: url(id), isBinary, label: label(id) })
@@ -228,7 +245,7 @@ export function complexRepresentation(
if (!params || !params.hideCoarse) {
root.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' })
.apply(StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'spacefill'));
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'spacefill', {}, 'polymer-id'));
}
}
diff --git a/src/mol-plugin/state/transforms/helpers.ts b/src/mol-plugin/state/transforms/helpers.ts
index 730f140e5e979cf3c4aff7c65504379c46ec73f9..2a72f7a52fdb7e631e41519fa8fca721dc389c09 100644
--- a/src/mol-plugin/state/transforms/helpers.ts
+++ b/src/mol-plugin/state/transforms/helpers.ts
@@ -42,7 +42,7 @@ export function getStructureTransparency(structure: Structure, script: Script, v
* Attaches ComputedSecondaryStructure property when unavailable in sourceData
*/
export async function ensureSecondaryStructure(s: Structure) {
- if (s.model.sourceData.kind === 'mmCIF') {
+ if (s.model && s.model.sourceData.kind === 'mmCIF') {
if (!s.model.sourceData.data.struct_conf.id.isDefined && !s.model.sourceData.data.struct_sheet_range.id.isDefined) {
await ComputedSecondaryStructure.attachFromCifOrCompute(s)
}
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index a8fb3fe99d0ff52d1bf0e7579a59b5acefae08f9..a5edcfbfc80ed6a4ba604f956bf741b92e3f0246 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -153,10 +153,9 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
apply({ a, params }) {
if (params.modelIndex < 0 || params.modelIndex >= a.data.length) throw new Error(`Invalid modelIndex ${params.modelIndex}`);
const model = a.data[params.modelIndex];
- const props = a.data.length === 1
- ? { label: `${model.label}` }
- : { label: `${model.label}:${model.modelNum}`, description: `Model ${params.modelIndex + 1} of ${a.data.length}` };
- return new SO.Molecule.Model(model, props);
+ const label = a.data.length === 1 ? model.entry : `${model.entry}: ${model.modelNum}`
+ const description = a.data.length === 1 ? undefined : `Model ${params.modelIndex + 1} of ${a.data.length}`
+ return new SO.Molecule.Model(model, { label, description });
}
});
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index f0873a69e5a3589938802a013ea1faaf89d58cba..127a50758decff275db4f14da3d144103e3d0016 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -108,13 +108,14 @@ namespace StructureRepresentation3DHelpers {
})
}
- export function getDefaultParamsStatic(ctx: PluginContext, name: BuiltInStructureRepresentationsName, structureParams?: Partial<PD.Values<StructureParams>>): StateTransformer.Params<StructureRepresentation3D> {
+ export function getDefaultParamsStatic(ctx: PluginContext, name: BuiltInStructureRepresentationsName, structureParams?: Partial<PD.Values<StructureParams>>, colorName?: BuiltInColorThemeName): StateTransformer.Params<StructureRepresentation3D> {
const type = ctx.structureRepresentation.registry.get(name);
- const colorParams = ctx.structureRepresentation.themeCtx.colorThemeRegistry.get(type.defaultColorTheme).defaultValues;
+ const color = colorName || type.defaultColorTheme;
+ const colorParams = ctx.structureRepresentation.themeCtx.colorThemeRegistry.get(color).defaultValues;
const sizeParams = ctx.structureRepresentation.themeCtx.sizeThemeRegistry.get(type.defaultSizeTheme).defaultValues
return ({
type: { name, params: structureParams ? { ...type.defaultValues, ...structureParams } : type.defaultValues },
- colorTheme: { name: type.defaultColorTheme, params: colorParams },
+ colorTheme: { name: color, params: colorParams },
sizeTheme: { name: type.defaultSizeTheme, params: sizeParams }
})
}
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index c1c2b046f1d908e78c76dd2a27e102733a026ecd..10a0042d8b2c39b363ee647e52d1b8d767c141d4 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -25,7 +25,7 @@ import { OrderedSet, Interval } from 'mol-data/int';
import { EmptyLoci, Loci } from 'mol-model/loci';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
-import { getResidueLoci } from './util/common';
+import { getAltResidueLoci } from './util/common';
const t = Mat4.identity()
const sVec = Vec3.zero()
@@ -82,7 +82,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
Mat4.scaleUniformly(t, t, side)
MeshBuilder.addPrimitive(builderState, t, perforatedBox)
Mat4.mul(t, t, Mat4.rotZ90X180)
- builderState.currentGroup = i * 2 + 1
+ builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedBox)
break;
case SaccharideShapes.FilledCone:
@@ -93,7 +93,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
Mat4.scaleUniformly(t, t, side * 1.2)
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid)
Mat4.mul(t, t, Mat4.rotZ90)
- builderState.currentGroup = i * 2 + 1
+ builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid)
break
case SaccharideShapes.FlatBox:
@@ -116,7 +116,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron)
Mat4.mul(t, t, Mat4.rotY90)
- builderState.currentGroup = i * 2 + 1
+ builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron)
break
case SaccharideShapes.FlatDiamond:
@@ -186,28 +186,28 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
const { objectId, groupId } = pickingId
if (id === objectId) {
const carb = structure.carbohydrates.elements[Math.floor(groupId / 2)]
- return getResidueLoci(structure, carb.unit, carb.anomericCarbon)
+ return getAltResidueLoci(structure, carb.unit, carb.anomericCarbon)
}
return EmptyLoci
}
/** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
- const { getElementIndex, getAnomericCarbon } = structure.carbohydrates
+ const { getElementIndex, getAnomericCarbons } = structure.carbohydrates
let changed = false
if (!StructureElement.isLoci(loci)) return false
if (!Structure.areEquivalent(loci.structure, structure)) return false
for (const e of loci.elements) {
+ // TODO make more efficient by handling/grouping `e.indices` by residue index
+ // TODO only call apply when the full alt-residue of the unit is part of `e`
OrderedSet.forEach(e.indices, v => {
const { model, elements } = e.unit
- const { index, offsets } = model.atomicHierarchy.residueAtomSegments
+ const { index } = model.atomicHierarchy.residueAtomSegments
const rI = index[elements[v]]
- const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
- const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
- const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
- if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
- const eI = getAnomericCarbon(e.unit, rI)
- if (eI !== undefined) {
+ const eIndices = getAnomericCarbons(e.unit, rI)
+ for (let i = 0, il = eIndices.length; i < il; ++i) {
+ const eI = eIndices[i]
+ if (!OrderedSet.has(e.indices, OrderedSet.indexOf(elements, eI))) continue
const idx = getElementIndex(e.unit, eI)
if (idx !== undefined) {
if (apply(Interval.ofBounds(idx * 2, idx * 2 + 2))) changed = true
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index f2f8faa6da167c06383549f84056fc1af8ee163a..7aaa308dafc2f6dc70d7c765279d3e684caedb77 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -28,6 +28,33 @@ export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementI
return EmptyLoci
}
+/**
+ * Return a Loci for the elements of a whole residue the elementIndex belongs to but
+ * restrict to elements that have the same label_alt_id or none
+ */
+export function getAltResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
+ const { elements, model } = unit
+ const { label_alt_id } = model.atomicHierarchy.atoms
+ const elementAltId = label_alt_id.value(elementIndex)
+ if (OrderedSet.indexOf(elements, elementIndex) !== -1) {
+ const { index, offsets } = model.atomicHierarchy.residueAtomSegments
+ const rI = index[elementIndex]
+ const _indices: number[] = []
+ for (let i = offsets[rI], il = offsets[rI + 1]; i < il; ++i) {
+ const unitIndex = OrderedSet.indexOf(elements, i)
+ if (unitIndex !== -1) {
+ const altId = label_alt_id.value(i)
+ if (elementAltId === altId || altId === '') {
+ _indices.push(unitIndex)
+ }
+ }
+ }
+ const indices = OrderedSet.ofSortedArray<StructureElement.UnitIndex>(SortedArray.ofSortedArray(_indices))
+ return StructureElement.Loci(structure, [{ unit, indices }])
+ }
+ return EmptyLoci
+}
+
//
export function createUnitsTransform({ units }: Unit.SymmetryGroup, transformData?: TransformData) {
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 4ddbdb8b1945619c723c187001858a952a489ad8..ca269c8b679b911795fe653ba7706b5b493655a9 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -187,7 +187,25 @@ const symbols = [
// C(MolScript.structureQuery.slot.elementSetReduce, (ctx, _) => ctx.element),
// ============= FILTERS ================
+ D(MolScript.structureQuery.filter.pick, (ctx, xs) => Queries.filters.pick(xs[0] as any, xs['test'])(ctx)),
D(MolScript.structureQuery.filter.first, (ctx, xs) => Queries.filters.first(xs[0] as any)(ctx)),
+ D(MolScript.structureQuery.filter.withSameAtomProperties, (ctx, xs) => Queries.filters.withSameAtomProperties(xs[0] as any, xs['source'] as any, xs['property'] as any)(ctx)),
+ D(MolScript.structureQuery.filter.intersectedBy, (ctx, xs) => Queries.filters.areIntersectedBy(xs[0] as any, xs['by'] as any)(ctx)),
+ D(MolScript.structureQuery.filter.within, (ctx, xs) => Queries.filters.within({
+ query: xs[0] as any,
+ target: xs['target'] as any,
+ minRadius: xs['min-radius'] as any,
+ maxRadius: xs['max-radius'] as any,
+ elementRadius: xs['atom-radius'] as any,
+ invert: xs['invert'] as any
+ })(ctx)),
+ D(MolScript.structureQuery.filter.isConnectedTo, (ctx, xs) => Queries.filters.isConnectedTo({
+ query: xs[0] as any,
+ target: xs['target'] as any,
+ disjunct: xs['disjunct'] as any,
+ invert: xs['invert'] as any,
+ bondTest: xs['bond-test']
+ })(ctx)),
// ============= GENERATORS ================
D(MolScript.structureQuery.generator.atomGroups, (ctx, xs) => Queries.generators.atoms({
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 5d49660e57af6b6b08dd31a2b7253b7f31e7edb7..b82996be6a92aa90ee0bd5101e55c1ca462fb3a2 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -28,6 +28,8 @@ import { ScaleLegend } from 'mol-util/color/scale';
import { TableLegend } from 'mol-util/color/tables';
import { UncertaintyColorThemeProvider } from './color/uncertainty';
import { GeneColorThemeProvider } from './color/gene';
+import { IllustrativeColorThemeProvider } from './color/illustrative';
+import { HydrophobicityColorThemeProvider } from './color/hydrophobicity';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -75,6 +77,8 @@ export const BuiltInColorThemes = {
'element-index': ElementIndexColorThemeProvider,
'element-symbol': ElementSymbolColorThemeProvider,
'gene': GeneColorThemeProvider,
+ 'hydrophobicity': HydrophobicityColorThemeProvider,
+ 'illustrative': IllustrativeColorThemeProvider,
'molecule-type': MoleculeTypeColorThemeProvider,
'polymer-id': PolymerIdColorThemeProvider,
'polymer-index': PolymerIndexColorThemeProvider,
diff --git a/src/mol-theme/color/carbohydrate-symbol.ts b/src/mol-theme/color/carbohydrate-symbol.ts
index a92d183e0f4fa61d5aa0837c14793b8c2455e32a..f76bd90ed1ee75561453df525509489effc11fb7 100644
--- a/src/mol-theme/color/carbohydrate-symbol.ts
+++ b/src/mol-theme/color/carbohydrate-symbol.ts
@@ -27,13 +27,13 @@ export function CarbohydrateSymbolColorTheme(ctx: ThemeDataContext, props: PD.Va
let color: LocationColor
if (ctx.structure) {
- const { elements, getElementIndex, getAnomericCarbon } = ctx.structure.carbohydrates
+ const { elements, getElementIndex, getAnomericCarbons } = ctx.structure.carbohydrates
const getColor = (unit: Unit, index: ElementIndex) => {
const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index[index]
- const anomericCarbon = getAnomericCarbon(unit, residueIndex)
- if (anomericCarbon !== undefined) {
- const idx = getElementIndex(unit, anomericCarbon)
+ const anomericCarbons = getAnomericCarbons(unit, residueIndex)
+ if (anomericCarbons.length > 0) {
+ const idx = getElementIndex(unit, anomericCarbons[0])
if (idx !== undefined) return elements[idx].component.color
}
return DefaultColor
diff --git a/src/mol-theme/color/hydrophobicity.ts b/src/mol-theme/color/hydrophobicity.ts
new file mode 100644
index 0000000000000000000000000000000000000000..60be994f3888c64b8518d901bb95901de6cc353c
--- /dev/null
+++ b/src/mol-theme/color/hydrophobicity.ts
@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Color, ColorScale } from 'mol-util/color';
+import { StructureElement, Unit, Link, ElementIndex } from 'mol-model/structure';
+import { Location } from 'mol-model/location';
+import { ColorTheme } from '../color';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
+import { ThemeDataContext } from '../theme';
+import { ResidueHydrophobicity } from 'mol-model/structure/model/types';
+import { ColorListName, ColorListOptions } from 'mol-util/color/scale';
+
+const Description = 'Assigns a color to every amino acid according to the "Experimentally determined hydrophobicity scale for proteins at membrane interfaces" by Wimely and White (doi:10.1038/nsb1096-842).'
+
+export const HydrophobicityColorThemeParams = {
+ list: PD.ColorScale<ColorListName>('RedYellowGreen', ColorListOptions),
+ scale: PD.Select('DGwif', [['DGwif', 'DG water-membrane'], ['DGwoct', 'DG water-octanol'], ['Oct-IF', 'DG difference']])
+}
+export type HydrophobicityColorThemeParams = typeof HydrophobicityColorThemeParams
+export function getHydrophobicityColorThemeParams(ctx: ThemeDataContext) {
+ return HydrophobicityColorThemeParams // TODO return copy
+}
+
+const scaleIndexMap = { 'DGwif': 0, 'DGwoct': 1, 'Oct-IF': 2 }
+
+export function hydrophobicity(compId: string, scaleIndex: number): number {
+ const c = (ResidueHydrophobicity as { [k: string]: number[] })[compId];
+ return c === undefined ? 0 : c[scaleIndex]
+}
+
+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
+}
+
+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]
+ let compId = seq.compId.value(seqIdBegin - 1) // 1-indexed
+ const parentId = modifiedResidues.parentId.get(compId)
+ return parentId === undefined ? compId : parentId
+ }
+}
+
+export function HydrophobicityColorTheme(ctx: ThemeDataContext, props: PD.Values<HydrophobicityColorThemeParams>): ColorTheme<HydrophobicityColorThemeParams> {
+ const scaleIndex = scaleIndexMap[props.scale]
+
+ // get domain
+ let min = Infinity
+ let max = -Infinity
+ for (const name in ResidueHydrophobicity) {
+ const val = (ResidueHydrophobicity as { [k: string]: number[] })[name][scaleIndex]
+ min = Math.min(min, val)
+ max = Math.max(max, val)
+ }
+
+ const scale = ColorScale.create({
+ listOrName: props.list,
+ domain: [ max, min ],
+ minLabel: 'Hydrophobic',
+ maxLabel: 'Hydrophilic'
+ })
+
+ function color(location: Location): Color {
+ let compId: string | undefined
+ if (StructureElement.isLocation(location)) {
+ if (Unit.isAtomic(location.unit)) {
+ compId = getAtomicCompId(location.unit, location.element)
+ } else {
+ compId = getCoarseCompId(location.unit, location.element)
+ }
+ } else if (Link.isLocation(location)) {
+ if (Unit.isAtomic(location.aUnit)) {
+ compId = getAtomicCompId(location.aUnit, location.aUnit.elements[location.aIndex])
+ } else {
+ compId = getCoarseCompId(location.aUnit, location.aUnit.elements[location.aIndex])
+ }
+ }
+ return scale.color(compId ? hydrophobicity(compId, scaleIndex) : 0)
+ }
+
+ return {
+ factory: HydrophobicityColorTheme,
+ granularity: 'group',
+ color,
+ props,
+ description: Description,
+ legend: scale ? scale.legend : undefined
+ }
+}
+
+export const HydrophobicityColorThemeProvider: ColorTheme.Provider<HydrophobicityColorThemeParams> = {
+ label: 'Hydrophobicity',
+ factory: HydrophobicityColorTheme,
+ getParams: getHydrophobicityColorThemeParams,
+ defaultValues: PD.getDefaultValues(HydrophobicityColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}
\ No newline at end of file
diff --git a/src/mol-theme/color/illustrative.ts b/src/mol-theme/color/illustrative.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b25da5db4b549023d8b638a1239d5b92e749bdea
--- /dev/null
+++ b/src/mol-theme/color/illustrative.ts
@@ -0,0 +1,80 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ElementSymbol, isNucleic, isProtein, MoleculeType } from 'mol-model/structure/model/types';
+import { Color } from 'mol-util/color';
+import { StructureElement, Unit, Link } from 'mol-model/structure';
+import { Location } from 'mol-model/location';
+import { ColorTheme } from '../color';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
+import { ThemeDataContext } from '../theme';
+import { elementSymbolColor } from './element-symbol';
+
+const DefaultIllustrativeColor = Color(0xFFFFFF)
+const Description = `Assigns an illustrative color similar to David Goodsell's Molecule of the Month style.`
+
+export const IllustrativeColorThemeParams = {}
+export type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams
+export function getIllustrativeColorThemeParams(ctx: ThemeDataContext) {
+ return IllustrativeColorThemeParams // TODO return copy
+}
+
+function illustrativeColor(typeSymbol: ElementSymbol, moleculeType: MoleculeType) {
+ if (isNucleic(moleculeType)) {
+ if (typeSymbol === 'O') {
+ return Color(0xFF8C8C)
+ } else if (typeSymbol === 'P') {
+ return Color(0xFF7D7D)
+ } else {
+ return Color(0xFFA6A6)
+ }
+ } else if (isProtein(moleculeType)) {
+ if (typeSymbol === 'C') {
+ return Color(0x7FB2FF)
+ } else {
+ return Color(0x6699FF)
+ }
+ } else {
+ return elementSymbolColor(typeSymbol)
+ }
+}
+
+export function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<IllustrativeColorThemeParams>): ColorTheme<IllustrativeColorThemeParams> {
+ function color(location: Location): Color {
+ if (StructureElement.isLocation(location)) {
+ if (Unit.isAtomic(location.unit)) {
+ const moleculeType = location.unit.model.atomicHierarchy.derived.residue.moleculeType[location.unit.residueIndex[location.element]]
+ const typeSymbol = location.unit.model.atomicHierarchy.atoms.type_symbol.value(location.element)
+ return illustrativeColor(typeSymbol, moleculeType)
+ }
+ } else if (Link.isLocation(location)) {
+ if (Unit.isAtomic(location.aUnit)) {
+ const elementIndex = location.aUnit.elements[location.aIndex]
+ const moleculeType = location.aUnit.model.atomicHierarchy.derived.residue.moleculeType[location.aUnit.residueIndex[elementIndex]]
+ const typeSymbol = location.aUnit.model.atomicHierarchy.atoms.type_symbol.value(elementIndex)
+ return illustrativeColor(typeSymbol, moleculeType)
+ }
+ }
+ return DefaultIllustrativeColor
+ }
+
+ return {
+ factory: IllustrativeColorTheme,
+ granularity: 'group',
+ color,
+ props,
+ description: Description,
+ // TODO add legend
+ }
+}
+
+export const IllustrativeColorThemeProvider: ColorTheme.Provider<IllustrativeColorThemeParams> = {
+ label: 'Illustrative',
+ factory: IllustrativeColorTheme,
+ getParams: getIllustrativeColorThemeParams,
+ defaultValues: PD.getDefaultValues(IllustrativeColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}
\ No newline at end of file
diff --git a/src/mol-util/color/scale.ts b/src/mol-util/color/scale.ts
index 39f1b716c2511002c81578c45ac8fdb7742c3281..73de47668c1a9093493c9d5386cc418f8a1caa06 100644
--- a/src/mol-util/color/scale.ts
+++ b/src/mol-util/color/scale.ts
@@ -55,7 +55,7 @@ export interface ColorScale {
}
export const DefaultColorScaleProps = {
- domain: [0, 1],
+ domain: [0, 1] as [number, number],
reverse: false,
listOrName: ColorBrewer.RedYellowBlue as Color[] | ColorListName,
minLabel: '' as string | undefined,
diff --git a/src/mol-util/string.ts b/src/mol-util/string.ts
index 62ebf10cf0c16383d93237f2e008d1d1fb48bf5a..dfc8f03bb1e7925389e341edc9b44521bfa6484d 100644
--- a/src/mol-util/string.ts
+++ b/src/mol-util/string.ts
@@ -52,4 +52,25 @@ export function interpolate(str: string, params: { [k: string]: any }) {
const names = Object.keys(params);
const values = Object.values(params);
return new Function(...names, `return \`${str}\`;`)(...values);
+}
+
+export function trimChar(str: string, char: string) {
+ let start = 0;
+ let end = str.length;
+ while (start < end && str[start] === char) ++start;
+ while (end > start && str[end - 1] === char) --end;
+ return (start > 0 || end < str.length) ? str.substring(start, end) : str;
+}
+
+export function trimCharStart(str: string, char: string) {
+ let start = 0;
+ const end = str.length;
+ while (start < end && str[start] === char) ++start;
+ return (start > 0) ? str.substring(start, end) : str;
+}
+
+export function trimCharEnd(str: string, char: string) {
+ let end = str.length;
+ while (end > 0 && str[end - 1] === char) --end;
+ return (end < str.length) ? str.substring(0, end) : str;
}
\ No newline at end of file