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Commit 87171e14 authored by David Sehnal's avatar David Sehnal
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wip, refactoring mmCIF parsing for better IHM model support

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src/apps/structure-info/model.ts
+ 16
− 0
View file @ 87171e14
......@@ -198,10 +198,24 @@ export function printIHMModels(model: Model) {
console.log(Table.formatToString(model.coarseHierarchy.models));
}
export function printModelStats(models: ReadonlyArray<Model>) {
console.log('\nModels\n=============');
for (const m of models) {
if (m.coarseHierarchy.isDefined) {
console.log(`${m.label} ${m.modelNum}: ${m.atomicHierarchy.atoms._rowCount} atom(s), ${m.coarseHierarchy.spheres.count} sphere(s), ${m.coarseHierarchy.gaussians.count} gaussian(s)`);
} else {
console.log(`${m.label} ${m.modelNum}: ${m.atomicHierarchy.atoms._rowCount} atom(s)`);
}
}
console.log();
}
async function run(frame: CifFrame, args: Args) {
const models = await Model.create(Format.mmCIF(frame)).run();
const structure = Structure.ofModel(models[0]);
if (args.models) printModelStats(models);
if (args.seq) printSequence(models[0]);
if (args.ihm) printIHMModels(models[0]);
if (args.units) printUnits(structure);
......@@ -230,6 +244,7 @@ const parser = new argparse.ArgumentParser({
parser.addArgument(['--download', '-d'], { help: 'Pdb entry id' });
parser.addArgument(['--file', '-f'], { help: 'filename' });
parser.addArgument(['--models'], { help: 'print models info', action: 'storeTrue' });
parser.addArgument(['--seq'], { help: 'print sequence', action: 'storeTrue' });
parser.addArgument(['--ihm'], { help: 'print IHM', action: 'storeTrue' });
parser.addArgument(['--units'], { help: 'print units', action: 'storeTrue' });
......@@ -243,6 +258,7 @@ interface Args {
download?: string,
file?: string,
models?:boolean,
seq?: boolean,
ihm?: boolean,
units?: boolean,
......
src/mol-data/db/table.ts
+ 12
− 0
View file @ 87171e14
......@@ -101,6 +101,18 @@ namespace Table {
return ret as Table<R>;
}
export function window<S extends R, R extends Schema>(table: Table<S>, schema: R, start: number, end: number) {
const ret = Object.create(null);
const columns = Object.keys(schema);
ret._rowCount = view.length;
ret._columns = columns;
ret._schema = schema;
for (const k of columns) {
(ret as any)[k] = Column.window(table[k], start, end);
}
return ret as Table<R>;
}
export function concat<S extends R, R extends Schema>(tables: Table<S>[], schema: R) {
const ret = Object.create(null);
const columns = Object.keys(schema);
......
src/mol-model/structure/model/formats/mmcif.ts
+ 143
− 128
View file @ 87171e14
......@@ -5,89 +5,27 @@
*/
import { Column, Table } from 'mol-data/db';
import { Interval, Segmentation } from 'mol-data/int';
import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { Spacegroup, SpacegroupCell, SymmetryOperator } from 'mol-math/geometry';
import { Vec3, Tensor } from 'mol-math/linear-algebra';
import { Task } from 'mol-task';
import { Tensor, Vec3 } from 'mol-math/linear-algebra';
import { Task, RuntimeContext } from 'mol-task';
import UUID from 'mol-util/uuid';
import Format from '../format';
import Model from '../model';
import { AtomicConformation, AtomicData, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../properties/atomic';
import { Entities } from '../properties/common';
import { CustomProperties } from '../properties/custom';
import { ModelSymmetry } from '../properties/symmetry';
import { getAtomicKeys } from '../properties/utils/atomic-keys';
import { ElementSymbol } from '../types';
import { createAssemblies } from './mmcif/assembly';
import { getIHMCoarse } from './mmcif/ihm';
import { getAtomicHierarchyAndConformation } from './mmcif/atomic';
import { ComponentBond } from './mmcif/bonds';
import { getIHMCoarse, EmptyIHMCoarse, IHMData } from './mmcif/ihm';
import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
import { getSequence } from './mmcif/sequence';
import { sortAtomSite } from './mmcif/sort';
import { mmCIF_Database, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { Element } from '../../../structure'
import { CustomProperties } from '../properties/custom';
import mmCIF_Format = Format.mmCIF
import { ComponentBond } from './mmcif/bonds';
type AtomSite = mmCIF_Database['atom_site']
function findModelEnd({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
const atomCount = num.rowCount;
if (!num.isDefined) return atomCount;
let endIndex = startIndex + 1;
while (endIndex < atomCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
return endIndex;
}
function findHierarchyOffsets(atom_site: AtomSite) {
if (atom_site._rowCount === 0) return { residues: [], chains: [] };
const start = 0, end = atom_site._rowCount;
const residues = [start as Element], chains = [start as Element];
const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
for (let i = start + 1; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !label_seq_id.areValuesEqual(i - 1, i)
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
|| !label_comp_id.areValuesEqual(i - 1, i);
if (newResidue) residues[residues.length] = i as Element;
if (newChain) chains[chains.length] = i as Element;
}
return { residues, chains };
}
function createHierarchyData(atom_site: AtomSite, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
const atoms = Table.ofColumns(AtomsSchema, {
type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
label_atom_id: atom_site.label_atom_id,
auth_atom_id: atom_site.auth_atom_id,
label_alt_id: atom_site.label_alt_id,
pdbx_formal_charge: atom_site.pdbx_formal_charge
});
const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
// Optimize the numeric columns
Table.columnToArray(residues, 'label_seq_id', Int32Array);
Table.columnToArray(residues, 'auth_seq_id', Int32Array);
const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
return { atoms, residues, chains };
}
function getConformation(atom_site: AtomSite): AtomicConformation {
return {
id: UUID.create(),
atomId: atom_site.id,
occupancy: atom_site.occupancy,
B_iso_or_equiv: atom_site.B_iso_or_equiv,
x: atom_site.Cartn_x.toArray({ array: Float32Array }),
y: atom_site.Cartn_y.toArray({ array: Float32Array }),
z: atom_site.Cartn_z.toArray({ array: Float32Array }),
}
}
type AtomSite = mmCIF_Database['atom_site']
function getSymmetry(format: mmCIF_Format): ModelSymmetry {
const assemblies = createAssemblies(format);
......@@ -129,14 +67,6 @@ function getNcsOperators(format: mmCIF_Format) {
}
return opers;
}
function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
// need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
return Table.areEqual(a.chains as Table<ChainsSchema>, b.chains as Table<ChainsSchema>)
&& Table.areEqual(a.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
function getModifiedResidueNameMap(format: mmCIF_Format) {
const data = format.data.pdbx_struct_mod_residue;
const map = new Map<string, string>();
......@@ -168,35 +98,13 @@ function getAsymIdSerialMap(format: mmCIF_Format) {
return map;
}
// TODO split IHM data into models as well, atomistic ihm models have `atom_site.ihm_model_id`,
// how to handle it in a generic way, i.e. when there is no ihm data, use `atom_site.pdbx_PDB_model_num`
// but if there is use `atom_site.ihm_model_id`, `ihm_sphere_obj_site.model_id` and
// `ihm_gaussian_obj_site.model_id` for splitting
// - PDBDEV_00000002 is an example for an IHM structure with multiple models
function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model): Model {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
return {
...previous,
atomicConformation: getConformation(atom_site)
};
}
const hierarchySegments: AtomicSegments = {
residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, previous?: Model): Model {
const atomic = getAtomicHierarchyAndConformation(format, atom_site, entities, previous);
if (previous && atomic.sameAsPrevious) {
return { ...previous, atomicConformation: atomic.conformation };
}
const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
const atomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
const coarse = getIHMCoarse(format.data, entities);
const coarse = EmptyIHMCoarse;
const label = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
? format.data.entry.id.value(0)
: format.data._name;
......@@ -211,13 +119,47 @@ function createModel(format: mmCIF_Format, atom_site: AtomSite, previous?: Model
modelNum: atom_site.pdbx_PDB_model_num.value(0),
entities,
symmetry: getSymmetry(format),
atomicHierarchy,
sequence: getSequence(format.data, entities, atomicHierarchy, modifiedResidueNameMap),
atomicConformation: getConformation(atom_site),
sequence: getSequence(format.data, entities, atomic.hierarchy, modifiedResidueNameMap),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomicHierarchy),
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
modifiedResidueNameMap,
asymIdSerialMap
},
customProperties: new CustomProperties(),
_staticPropertyData: Object.create(null),
_dynamicPropertyData: Object.create(null)
};
}
// TODO split IHM data into models as well, atomistic ihm models have `atom_site.ihm_model_id`,
// how to handle it in a generic way, i.e. when there is no ihm data, use `atom_site.pdbx_PDB_model_num`
// but if there is use `atom_site.ihm_model_id`, `ihm_sphere_obj_site.model_id` and
// `ihm_gaussian_obj_site.model_id` for splitting
// - PDBDEV_00000002 is an example for an IHM structure with multiple models
function createModelIHM(format: mmCIF_Format, data: IHMData): Model {
const atomic = getAtomicHierarchyAndConformation(format, data.atom_site, data.entities);
const coarse = getIHMCoarse(data);
const modifiedResidueNameMap = getModifiedResidueNameMap(format);
const asymIdSerialMap = getAsymIdSerialMap(format)
return {
id: UUID.create(),
label: data.model_name,
sourceData: format,
modelNum: data.model_id,
entities: data.entities,
symmetry: getSymmetry(format),
sequence: getSequence(format.data, data.entities, atomic.hierarchy, modifiedResidueNameMap),
atomicHierarchy: atomic.hierarchy,
atomicConformation: atomic.conformation,
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomic.hierarchy),
modifiedResidueNameMap,
asymIdSerialMap
},
......@@ -231,28 +173,101 @@ function attachProps(model: Model) {
ComponentBond.attachFromMmCif(model);
}
function findModelEnd(num: Column<number>, startIndex: number) {
const rowCount = num.rowCount;
if (!num.isDefined) return rowCount;
let endIndex = startIndex + 1;
while (endIndex < rowCount && num.areValuesEqual(startIndex, endIndex)) endIndex++;
return endIndex;
}
async function readStandard(ctx: RuntimeContext, format: mmCIF_Format) {
const atomCount = format.data.atom_site._rowCount;
const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
const models: Model[] = [];
let modelStart = 0;
while (modelStart < atomCount) {
const modelEnd = findModelEnd(format.data.atom_site.pdbx_PDB_model_num, modelStart);
const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
const model = createStandardModel(format, atom_site, entities, models.length > 0 ? models[models.length - 1] : void 0);
attachProps(model);
models.push(model);
modelStart = modelEnd;
}
return models;
}
function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
const ret = new Map<number, T>()
const rowCount = table._rowCount;
let modelStart = 0;
while (modelStart < rowCount) {
const modelEnd = findModelEnd(col, modelStart);
const id = col.value(modelStart);
const window = Table.window(table, table._schema, modelStart, modelEnd) as T;
ret.set(id, window);
modelStart = modelEnd;
}
return ret;
}
async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
const { ihm_model_list } = format.data;
const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
const sphere_sites = splitTable(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site.model_id);
const gauss_sites = splitTable(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site.model_id);
const models: Model[] = [];
const { model_id, model_name } = ihm_model_list;
for (let i = 0; i < ihm_model_list._rowCount; i++) {
const id = model_id.value(i);
const data: IHMData = {
model_id: id,
model_name: model_name.value(i),
ihm_model_list,
entities: entities,
atom_site: atom_sites.has(id) ? atom_sites.get(id)! : Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0),
ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)! : Table.window(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site._schema, 0, 0),
ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)! : Table.window(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site._schema, 0, 0)
};
const model = createModelIHM(format, data);
attachProps(model);
models.push(createModelIHM(format, data));
}
return models;
// const atomCount = format.data.atom_site._rowCount;
// const isIHM = format.data.ihm_model_list._rowCount > 0;
// if (atomCount === 0) {
// return isIHM
// ? [createModel(format, format.data.atom_site, void 0)]
// : [];
// }
// const models: Model[] = [];
// let modelStart = 0;
// while (modelStart < atomCount) {
// const modelEnd = findModelEnd(format, modelStart);
// const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
// const model = createModel(format, atom_site, models.length > 0 ? models[models.length - 1] : void 0);
// attachProps(model);
// models.push(model);
// modelStart = modelEnd;
// }
// return models;
}
function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
return Task.create('Create mmCIF Model', async ctx => {
const atomCount = format.data.atom_site._rowCount;
const isIHM = format.data.ihm_model_list._rowCount > 0;
if (atomCount === 0) {
return isIHM
? [createModel(format, format.data.atom_site, void 0)]
: [];
}
const models: Model[] = [];
let modelStart = 0;
while (modelStart < atomCount) {
const modelEnd = findModelEnd(format, modelStart);
const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
const model = createModel(format, atom_site, models.length > 0 ? models[models.length - 1] : void 0);
attachProps(model);
models.push(model);
modelStart = modelEnd;
}
return models;
return isIHM ? await readIHM(ctx, format) : await readStandard(ctx, format);
});
}
......
src/mol-model/structure/model/formats/mmcif/atomic.ts 0 → 100644
+ 104
− 0
View file @ 87171e14
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Column, Table } from 'mol-data/db';
import { Interval, Segmentation } from 'mol-data/int';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import UUID from 'mol-util/uuid';
import { Element } from '../../../../structure';
import Format from '../../format';
import Model from '../../model';
import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../properties/atomic';
import { getAtomicKeys } from '../../properties/utils/atomic-keys';
import { ElementSymbol } from '../../types';
import { Entities } from '../../properties/common';
import mmCIF_Format = Format.mmCIF
type AtomSite = mmCIF_Database['atom_site']
function findHierarchyOffsets(atom_site: AtomSite) {
if (atom_site._rowCount === 0) return { residues: [], chains: [] };
const start = 0, end = atom_site._rowCount;
const residues = [start as Element], chains = [start as Element];
const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
for (let i = start + 1; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !label_seq_id.areValuesEqual(i - 1, i)
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
|| !label_comp_id.areValuesEqual(i - 1, i);
if (newResidue) residues[residues.length] = i as Element;
if (newChain) chains[chains.length] = i as Element;
}
return { residues, chains };
}
function createHierarchyData(atom_site: AtomSite, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
const atoms = Table.ofColumns(AtomsSchema, {
type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
label_atom_id: atom_site.label_atom_id,
auth_atom_id: atom_site.auth_atom_id,
label_alt_id: atom_site.label_alt_id,
pdbx_formal_charge: atom_site.pdbx_formal_charge
});
const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
// Optimize the numeric columns
Table.columnToArray(residues, 'label_seq_id', Int32Array);
Table.columnToArray(residues, 'auth_seq_id', Int32Array);
const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
return { atoms, residues, chains };
}
function getConformation(atom_site: AtomSite): AtomicConformation {
return {
id: UUID.create(),
atomId: atom_site.id,
occupancy: atom_site.occupancy,
B_iso_or_equiv: atom_site.B_iso_or_equiv,
x: atom_site.Cartn_x.toArray({ array: Float32Array }),
y: atom_site.Cartn_y.toArray({ array: Float32Array }),
z: atom_site.Cartn_z.toArray({ array: Float32Array }),
}
}
function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
// need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
return Table.areEqual(a.chains as Table<ChainsSchema>, b.chains as Table<ChainsSchema>)
&& Table.areEqual(a.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, previous?: Model) {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
return {
sameAsPrevious: true,
hierarchy: previous.atomicHierarchy,
conformation: getConformation(atom_site)
};
}
const hierarchySegments: AtomicSegments = {
residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
}
const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
return {
sameAsPrevious: false,
hierarchy,
conformation: getConformation(atom_site)
};
}
\ No newline at end of file
src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
+ 1
− 0
View file @ 87171e14
......@@ -43,6 +43,7 @@ export namespace ComponentBond {
}
export function attachFromMmCif(model: Model): boolean {
if (model.customProperties.has(Descriptor)) return true;
if (model.sourceData.kind !== 'mmCIF') return false;
const { chem_comp_bond } = model.sourceData.data;
if (chem_comp_bond._rowCount === 0) return false;
......
src/mol-model/structure/model/formats/mmcif/ihm.ts
+ 20
− 5
View file @ 87171e14
......@@ -14,24 +14,39 @@ import { Segmentation, Interval } from 'mol-data/int';
import { Mat3, Tensor } from 'mol-math/linear-algebra';
import { Element } from '../../../structure'
export function getIHMCoarse(data: mmCIF, entities: Entities): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
if (data.ihm_model_list._rowCount === 0) return { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any };
type AtomSite = mmCIF['atom_site']
type SphereSite = mmCIF['ihm_sphere_obj_site']
type GaussSite = mmCIF['ihm_gaussian_obj_site']
type IHMModels = mmCIF['ihm_model_list']
export interface IHMData {
model_id: number,
model_name: string,
ihm_model_list: IHMModels,
entities: Entities,
atom_site: AtomSite,
ihm_sphere_obj_site: SphereSite,
ihm_gaussian_obj_site: GaussSite
}
export const EmptyIHMCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any }
export function getIHMCoarse(data: IHMData): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
const { ihm_model_list, ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;
const modelIndex = Column.createIndexer(ihm_model_list.model_id);
const sphereData = getData(ihm_sphere_obj_site);
const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
const sphereKeys = getCoarseKeys(sphereData, modelIndex, entities);
const sphereKeys = getCoarseKeys(sphereData, modelIndex, data.entities);
const gaussianData = getData(ihm_gaussian_obj_site);
const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
const gaussianKeys = getCoarseKeys(gaussianData, modelIndex, entities);
const gaussianKeys = getCoarseKeys(gaussianData, modelIndex, data.entities);
return {
hierarchy: {
isDefined: true,
models: ihm_model_list,
//models: ihm_model_list,
spheres: { ...sphereData, ...sphereKeys },
gaussians: { ...gaussianData, ...gaussianKeys },
},
......
src/mol-model/structure/model/properties/coarse/hierarchy.ts
+ 4
− 3
View file @ 87171e14
......@@ -15,8 +15,9 @@ export interface CoarsedElementKeys {
chainKey: ArrayLike<number>,
// assign a key to each element, index to the Model.entities.data table
entityKey: ArrayLike<number>,
// assign a key to each element, index to the CoarseHierarchy.models table
modelKey: ArrayLike<number>,
// // assign a key to each element, index to the CoarseHierarchy.models table
// modelKey: ArrayLike<number>,
/** find index of the residue/feature element where seq_id is included */
findSequenceKey(entityId: string, asym_id: string, seq_id: number): number
......@@ -38,7 +39,7 @@ export type CoarseElements = CoarsedElementKeys & CoarseElementData
export interface CoarseHierarchy {
isDefined: boolean,
models: mmCIF['ihm_model_list'],
//models: mmCIF['ihm_model_list'],
spheres: CoarseElements,
gaussians: CoarseElements
}
......
src/mol-model/structure/model/properties/utils/coarse-keys.ts
+ 1
− 1
View file @ 87171e14
......@@ -92,5 +92,5 @@ export function getCoarseKeys(data: CoarseElementData, modelIndex: (id: number)
const { findChainKey, findSequenceKey } = createLookUp(entities, chainMaps, seqMaps);
return { chainKey, entityKey, modelKey, findSequenceKey, findChainKey };
return { chainKey, entityKey, /*modelKey,*/ findSequenceKey, findChainKey };
}
\ No newline at end of file
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