multimodel IHM is now parsed into separate models

src/apps/structure-info/model.ts

@@ -12,7 +12,6 @@ import { CifFrame } from 'mol-io/reader/cif'
 import { Model, Structure, Element, Unit, Format, StructureProperties } from 'mol-model/structure'
 // import { Run, Progress } from 'mol-task'
 import { OrderedSet } from 'mol-data/int';
-import { Table } from 'mol-data/db';
 import { openCif, downloadCif } from './helpers';
 import { BitFlags } from 'mol-util';
 import { SecondaryStructureType } from 'mol-model/structure/model/types';
@@ -192,12 +191,6 @@ export function printSymmetryInfo(model: Model) {
     console.log(`NCS operators: ${symmetry.ncsOperators && symmetry.ncsOperators.map(a => a.name).join(', ')}`);
 }
 
-export function printIHMModels(model: Model) {
-    if (!model.coarseHierarchy.isDefined) return false;
-    console.log('\nIHM Models\n=============');
-    console.log(Table.formatToString(model.coarseHierarchy.models));
-}
-
 export function printModelStats(models: ReadonlyArray<Model>) {
     console.log('\nModels\n=============');
 
@@ -217,7 +210,6 @@ async function run(frame: CifFrame, args: Args) {
 
     if (args.models) printModelStats(models);
     if (args.seq) printSequence(models[0]);
-    if (args.ihm) printIHMModels(models[0]);
     if (args.units) printUnits(structure);
     if (args.sym) printSymmetryInfo(models[0]);
     if (args.rings) printRings(structure);

src/mol-data/db/column.ts

@@ -270,6 +270,7 @@ function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Colu
 
 function windowColumn<T>(column: Column<T>, start: number, end: number) {
     if (!column.isDefined) return Column.Undefined(end - start, column.schema);
+    if (start === 0 && end === column.rowCount) return column;
     if (!!column['@array'] && ColumnHelpers.isTypedArray(column['@array'])) return windowTyped(column, start, end);
     return windowFull(column, start, end);
 }

src/mol-data/db/table.ts

@@ -102,6 +102,7 @@ namespace Table {
     }
 
     export function window<S extends R, R extends Schema>(table: Table<S>, schema: R, start: number, end: number) {
+        if (start === 0 && end === table._rowCount) return table;
         const ret = Object.create(null);
         const columns = Object.keys(schema);
         ret._rowCount = view.length;

src/mol-model/structure/model/formats/mmcif.ts

@@ -135,11 +135,6 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
     };
 }
 
-// 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);
@@ -216,6 +211,7 @@ 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) };
 
+    // TODO: will IHM require sorting or will we trust it?
     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);
@@ -228,7 +224,6 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
         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),
@@ -240,34 +235,12 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format) {
     }
 
     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 isIHM = format.data.ihm_model_list._rowCount > 0;
-        return isIHM ?  await readIHM(ctx, format) : await readStandard(ctx, format);
+        return isIHM ? await readIHM(ctx, format) : await readStandard(ctx, format);
     });
 }
 

src/mol-model/structure/model/formats/mmcif/ihm.ts

@@ -14,39 +14,31 @@ import { Segmentation, Interval } from 'mol-data/int';
 import { Mat3, Tensor } from 'mol-math/linear-algebra';
 import { Element } from '../../../structure'
 
-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
+    atom_site: mmCIF['atom_site'],
+    ihm_sphere_obj_site: mmCIF['ihm_sphere_obj_site'],
+    ihm_gaussian_obj_site: mmCIF['ihm_gaussian_obj_site']
 }
 
 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 { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;
 
     const sphereData = getData(ihm_sphere_obj_site);
     const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
-    const sphereKeys = getCoarseKeys(sphereData, modelIndex, data.entities);
+    const sphereKeys = getCoarseKeys(sphereData, data.entities);
 
     const gaussianData = getData(ihm_gaussian_obj_site);
     const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
-    const gaussianKeys = getCoarseKeys(gaussianData, modelIndex, data.entities);
+    const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
 
     return {
         hierarchy: {
             isDefined: true,
-            //models: ihm_model_list,
             spheres: { ...sphereData, ...sphereKeys },
             gaussians: { ...gaussianData, ...gaussianKeys },
         },
@@ -96,6 +88,6 @@ function getChainSegments(asym_id: Column<string>) {
 }
 
 function getData(data: mmCIF['ihm_sphere_obj_site'] | mmCIF['ihm_gaussian_obj_site']): CoarseElementData {
-    const { model_id, entity_id, seq_id_begin, seq_id_end, asym_id } = data;
-    return { count: model_id.rowCount, entity_id, model_id, asym_id, seq_id_begin, seq_id_end, chainSegments: getChainSegments(asym_id) };
+    const { entity_id, seq_id_begin, seq_id_end, asym_id } = data;
+    return { count: entity_id.rowCount, entity_id, asym_id, seq_id_begin, seq_id_end, chainSegments: getChainSegments(asym_id) };
 }

src/mol-model/structure/model/model.ts

@@ -25,6 +25,7 @@ interface Model extends Readonly<{
     id: UUID,
     label: string,
 
+    // for IHM, corresponds to ihm_model_list.model_id
     modelNum: number,
 
     sourceData: Format,

src/mol-model/structure/model/properties/coarse/hierarchy.ts

@@ -5,7 +5,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
 import { Column } from 'mol-data/db'
 import { Segmentation } from 'mol-data/int';
 import { Element } from '../../../structure'
@@ -15,9 +14,6 @@ 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>,
 
     /** find index of the residue/feature element where seq_id is included */
     findSequenceKey(entityId: string, asym_id: string, seq_id: number): number
@@ -27,7 +23,6 @@ export interface CoarsedElementKeys {
 export interface CoarseElementData {
     count: number,
     entity_id: Column<string>,
-    model_id: Column<number>,
     asym_id: Column<string>,
     seq_id_begin: Column<number>,
     seq_id_end: Column<number>,
@@ -39,7 +34,6 @@ export type CoarseElements = CoarsedElementKeys & CoarseElementData
 
 export interface CoarseHierarchy {
     isDefined: boolean,
-    //models: mmCIF['ihm_model_list'],
     spheres: CoarseElements,
     gaussians: CoarseElements
 }

src/mol-model/structure/model/properties/utils/coarse-keys.ts

@@ -49,25 +49,18 @@ function missingEntity(k: string) {
     throw new Error(`Missing entity entry for entity id '${k}'.`);
 }
 
-function missingModel(k: string) {
-    throw new Error(`Missing entity entry for model id '${k}'.`);
-}
-
-export function getCoarseKeys(data: CoarseElementData, modelIndex: (id: number) => number, entities: Entities): CoarsedElementKeys {
-    const { model_id, entity_id, asym_id, seq_id_begin, seq_id_end, count, chainSegments } = data;
+export function getCoarseKeys(data: CoarseElementData, entities: Entities): CoarsedElementKeys {
+    const { entity_id, asym_id, seq_id_begin, seq_id_end, count, chainSegments } = data;
 
     const seqMaps = new Map<number, Map<number, number>>();
     const chainMaps = new Map<number, Map<string, number>>(), chainCounter = { index: 0 };
 
     const chainKey = new Int32Array(count);
     const entityKey = new Int32Array(count);
-    const modelKey = new Int32Array(count);
 
     for (let i = 0; i < count; i++) {
         entityKey[i] = entities.getEntityIndex(entity_id.value(i));
         if (entityKey[i] < 0) missingEntity(entity_id.value(i));
-        modelKey[i] = modelIndex(model_id.value(i));
-        if (modelKey[i] < 0) missingModel('' + model_id.value(i));
     }
 
     for (let cI = 0; cI < chainSegments.count; cI++) {
@@ -92,5 +85,5 @@ export function getCoarseKeys(data: CoarseElementData, modelIndex: (id: number)
 
     const { findChainKey, findSequenceKey } = createLookUp(entities, chainMaps, seqMaps);
 
-    return { chainKey, entityKey, /*modelKey,*/ findSequenceKey, findChainKey };
+    return { chainKey, entityKey, findSequenceKey, findChainKey };
 }

src/mol-model/structure/structure/properties.ts

@@ -72,7 +72,6 @@ const chain = {
 
 const coarse = {
     key: atom.key,
-    modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.modelKey[l.element]),
     entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entityKey[l.element]),
 
     x: atom.x,