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@@ -4,24 +4,34 @@
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* @author David Sehnal <david.sehnal@gmail.com>
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*/
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-import { Task } from '../../mol-task';
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import { Column, Table } from '../../mol-data/db';
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-import { MoleculeType } from '../../mol-model/structure/model/types';
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-import { EntityBuilder } from '../../mol-model-formats/structure/common/entity';
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-import { BasicSchema, createBasic } from '../../mol-model-formats/structure/basic/schema';
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import { createModels } from '../../mol-model-formats/structure/basic/parser';
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-import { G3dDataBlock } from './data';
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+import { BasicSchema, createBasic } from '../../mol-model-formats/structure/basic/schema';
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+import { EntityBuilder } from '../../mol-model-formats/structure/common/entity';
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+import { CustomModelProperty } from '../../mol-model-props/common/custom-model-property';
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+import { Model, Trajectory, Unit } from '../../mol-model/structure';
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+import { MoleculeType } from '../../mol-model/structure/model/types';
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+import { CustomPropSymbol } from '../../mol-script/language/symbol';
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+import Type from '../../mol-script/language/type';
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+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
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+import { Task, RuntimeContext } from '../../mol-task';
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import { objectForEach } from '../../mol-util/object';
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-import { Trajectory } from '../../mol-model/structure';
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+import { ParamDefinition } from '../../mol-util/param-definition';
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+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
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+import { G3dDataBlock } from './data';
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+import { Loci } from '../../mol-model/loci';
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+import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
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+import { OrderedSet } from '../../mol-data/int';
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-interface Columns {
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+interface NormalizedData {
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entity_id: string[],
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chromosome: string[],
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+ seq_id_begin: Int32Array,
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+ seq_id_end: Int32Array,
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start: Int32Array,
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- end: Int32Array,
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- x: Float32Array
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- y: Float32Array
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- z: Float32Array
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+ x: Float32Array,
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+ y: Float32Array,
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+ z: Float32Array,
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haplotype: string[]
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}
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@@ -31,11 +41,12 @@ function getColumns(block: G3dDataBlock) {
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objectForEach(data, h => objectForEach(h, g => size += g.start.length));
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- const columns: Columns = {
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+ const normalized: NormalizedData = {
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entity_id: new Array(size),
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chromosome: new Array(size),
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+ seq_id_begin: new Int32Array(size),
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+ seq_id_end: new Int32Array(size),
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start: new Int32Array(size),
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- end: new Int32Array(size),
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x: new Float32Array(size),
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y: new Float32Array(size),
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z: new Float32Array(size),
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@@ -47,56 +58,58 @@ function getColumns(block: G3dDataBlock) {
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objectForEach(hs, (chs, ch) => {
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const entity_id = `${ch}-${h}`;
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for (let i = 0, _i = chs.start.length; i < _i; i++) {
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- columns.entity_id[o] = entity_id;
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- columns.chromosome[o] = ch;
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- columns.start[o] = o + 1;
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- columns.end[o] = o + 2;
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- columns.x[o] = 10 * chs.x[i];
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- columns.y[o] = 10 * chs.y[i];
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- columns.z[o] = 10 * chs.z[i];
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- columns.haplotype[o] = h;
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+ normalized.entity_id[o] = entity_id;
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+ normalized.chromosome[o] = ch;
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+ normalized.start[o] = chs.start[i];
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+ normalized.seq_id_begin[o] = o;
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+ normalized.seq_id_end[o] = o;
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+ normalized.x[o] = 10 * chs.x[i];
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+ normalized.y[o] = 10 * chs.y[i];
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+ normalized.z[o] = 10 * chs.z[i];
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+ normalized.haplotype[o] = h;
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o++;
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}
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});
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});
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- return columns;
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+ return normalized;
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}
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-function getBasic(data: G3dDataBlock) {
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- const columns = getColumns(data);
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+async function getTraj(ctx: RuntimeContext, data: G3dDataBlock) {
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+ const normalized = getColumns(data);
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- const rowCount = columns.start.length;
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+ const rowCount = normalized.seq_id_begin.length;
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const entityIds = new Array<string>(rowCount);
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const entityBuilder = new EntityBuilder();
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- const stride = columns.start[1] - columns.start[0];
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-
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+ const stride = normalized.seq_id_begin[1] - normalized.seq_id_begin[0];
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const objectRadius = stride / 3500;
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+ const eName = { customName: '' };
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for (let i = 0; i < rowCount; ++i) {
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- const e = columns.entity_id[i];
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- const entityId = entityBuilder.getEntityId(e, MoleculeType.DNA, e);
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+ const e = normalized.entity_id[i];
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+ eName.customName = e;
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+ const entityId = entityBuilder.getEntityId(e, MoleculeType.DNA, e, eName);
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entityIds[i] = entityId;
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}
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const ihm_sphere_obj_site = Table.ofPartialColumns(BasicSchema.ihm_sphere_obj_site, {
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id: Column.range(0, rowCount),
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entity_id: Column.ofStringArray(entityIds),
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- seq_id_begin: Column.ofIntArray(columns.start),
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- seq_id_end: Column.ofIntArray(columns.end),
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- asym_id: Column.ofStringArray(columns.chromosome),
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+ seq_id_begin: Column.ofIntArray(normalized.seq_id_begin),
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+ seq_id_end: Column.ofIntArray(normalized.seq_id_end),
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+ asym_id: Column.ofStringArray(normalized.chromosome),
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- Cartn_x: Column.ofFloatArray(columns.x),
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- Cartn_y: Column.ofFloatArray(columns.y),
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- Cartn_z: Column.ofFloatArray(columns.z),
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+ Cartn_x: Column.ofFloatArray(normalized.x),
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+ Cartn_y: Column.ofFloatArray(normalized.y),
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+ Cartn_z: Column.ofFloatArray(normalized.z),
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object_radius: Column.ofConst(objectRadius, rowCount, Column.Schema.float),
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rmsf: Column.ofConst(0, rowCount, Column.Schema.float),
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model_id: Column.ofConst(1, rowCount, Column.Schema.int),
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}, rowCount);
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- return createBasic({
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+ const basic = createBasic({
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entity: entityBuilder.getEntityTable(),
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ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
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model_id: Column.ofIntArray([1]),
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@@ -104,11 +117,74 @@ function getBasic(data: G3dDataBlock) {
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}, 1),
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ihm_sphere_obj_site
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});
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+
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+ const models = await createModels(basic, { kind: 'g3d', name: 'G3D', data }, ctx);
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+
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+ await G3dInfoPropertyProvider.attach({ runtime: ctx, assetManager: void 0 as any }, models.representative, {
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+ resolution: data.resolution,
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+ haplotype: normalized.haplotype,
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+ start: normalized.start
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+ });
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+
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+ return models;
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}
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export function trajectoryFromG3D(data: G3dDataBlock): Task<Trajectory> {
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return Task.create('Parse G3D', async ctx => {
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- const basic = getBasic(data);
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- return createModels(basic, { kind: 'g3d', name: 'G3D', data }, ctx);
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+ return getTraj(ctx, data);
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+ });
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+}
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+
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+export const G3dSymbols = {
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+ haplotype: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'haplotype', Type.Str),
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+ ctx => {
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+ if (Unit.isAtomic(ctx.element.unit)) return '';
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+ const info = G3dInfoPropertyProvider.get(ctx.element.unit.model);
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+ const seqId = ctx.element.unit.model.coarseHierarchy.spheres.seq_id_begin.value(ctx.element.element);
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+ return info.value?.haplotype[seqId] || '';
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+ }
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+ )
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+};
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+
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+export function g3dHaplotypeQuery(haplotype: 'maternal' | 'paternal') {
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+ return MS.struct.generator.atomGroups({
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+ 'chain-test': MS.core.rel.eq([G3dSymbols.haplotype.symbol(), haplotype]),
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});
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-}
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+}
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+
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+export const G3dInfoPropertyParams = {
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+ haplotype: ParamDefinition.Value<string[]>([]),
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+ start: ParamDefinition.Value<Int32Array>(new Int32Array(0)),
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+ resolution: ParamDefinition.Numeric(0)
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+};
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+
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+export type G3dInfoPropertyParams = typeof G3dInfoPropertyParams
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+export type G3dInfoPropertyParamsProps = ParamDefinition.Values<G3dInfoPropertyParams>
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+
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+export const G3dInfoPropertyProvider: CustomModelProperty.Provider<G3dInfoPropertyParams, G3dInfoPropertyParamsProps> = CustomModelProperty.createProvider({
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+ label: 'G3d Info',
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+ type: 'static',
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+ isHidden: true,
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+ defaultParams: G3dInfoPropertyParams,
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+ descriptor: { name: 'g3d_info', symbols: G3dSymbols },
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+ getParams: (data: Model) => G3dInfoPropertyParams,
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+ isApplicable: (data: Model) => true,
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+ obtain: async (ctx, data, props) => {
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+ return { value: props as any };
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+ }
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+});
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+
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+export const G3dLabelProvider: LociLabelProvider = {
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+ label: (e: Loci): string | undefined => {
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+ if (e.kind !== 'element-loci' || Loci.isEmpty(e)) return;
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+
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+ const first = e.elements[0];
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+ if (e.elements.length !== 1 || Unit.isAtomic(first.unit)) return;
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+ const info = G3dInfoPropertyProvider.get(first.unit.model);
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+ if (!info) return;
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+
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+ const eI = first.unit.elements[OrderedSet.getAt(first.indices, 0)];
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+ const seqId = first.unit.model.coarseHierarchy.spheres.seq_id_begin.value(eI);
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+ return `<b>Start:</b> ${info.value?.start[seqId]} <small>| resolution ${info.value?.resolution}<small>`;
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+ }
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+};
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Alexander Rose