diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index d9d42709d84c9a1b4983cb919814da850b8a3206..2cc19a45613210f720cd19807d81924d8ff7cf6c 100644
--- a/src/apps/structure-info/model.ts
+++ b/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);
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index a61efa6771935c8e742d5db03d43883e9b00c67a..d1c183b4c818b6b6de0b9677d2515ea717242a2b 100644
--- a/src/mol-data/db/column.ts
+++ b/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);
}
diff --git a/src/mol-data/db/table.ts b/src/mol-data/db/table.ts
index b68967dfc55f73985b3256beb0f122a733fa4416..1237cba5a7f272778ad5c31fa5c993c8204c1683 100644
--- a/src/mol-data/db/table.ts
+++ b/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;
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 4bd2eee7bd7b4ecd40df07003e83c4a2a670c53c..e944d9c8d93060cb76f250996a056c293040050d 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/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);
});
}
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
index f3bd5ad8113a8cfcf9698e9e45cc38deb65dda9a..db2e86c84014a70e261ec700a16c9c2512cbcfc6 100644
--- a/src/mol-model/structure/model/formats/mmcif/ihm.ts
+++ b/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) };
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index c76964e053f6f63e35f8409f59e64b263281173d..e83ed86d3591283395a1efce657fe0d9a57d0acf 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/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,
diff --git a/src/mol-model/structure/model/properties/coarse/hierarchy.ts b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
index 2bcdabbe815d39d0d62a062e9695796294d9688c..86071cbc54be4e9d8b6968e381202e764d87125f 100644
--- a/src/mol-model/structure/model/properties/coarse/hierarchy.ts
+++ b/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
}
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
index c18dc27ec7d72dc43b3dbab51a4f3e30f80a385f..da591779c8d5c17a111c7686686cd78b2156e127 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-keys.ts
+++ b/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 };
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 943c219c239e6d7a5c04d13fa5cb4f10a2de79da..5a7b9e4d8971e9e1c30781c35d6a72ab87f96667 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/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,