From 57f1aa51f32cd4be831bc8cff09f3e26c59b9657 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 26 Apr 2018 19:12:35 +0200
Subject: [PATCH] Model.entities is now a standalone property, updated
CoraseGrained,
---
src/apps/domain-annotation-server/mapping.ts | 2 +-
src/mol-data/db/column.ts | 13 +++++++
src/mol-data/db/table.ts | 4 +--
src/mol-model/structure/export/mmcif.ts | 8 ++---
src/mol-model/structure/model/formats/gro.ts | 19 +++++++++--
.../structure/model/formats/mmcif.ts | 11 ++++--
.../structure/model/formats/mmcif/ihm.ts | 6 ++++
.../structure/model/formats/mmcif/sequence.ts | 5 +--
src/mol-model/structure/model/model.ts | 3 ++
.../model/properties/coarse-grained.ts | 34 +++++++++++++++++--
.../structure/model/properties/common.ts | 14 ++++++++
.../structure/model/properties/hierarchy.ts | 9 +++--
.../structure/model/utils/hierarchy-keys.ts | 32 ++++++++++-------
src/mol-model/structure/query/properties.ts | 20 +++++------
14 files changed, 135 insertions(+), 45 deletions(-)
create mode 100644 src/mol-model/structure/model/formats/mmcif/ihm.ts
create mode 100644 src/mol-model/structure/model/properties/common.ts
diff --git a/src/apps/domain-annotation-server/mapping.ts b/src/apps/domain-annotation-server/mapping.ts
index da87d9b46..0ab03c359 100644
--- a/src/apps/domain-annotation-server/mapping.ts
+++ b/src/apps/domain-annotation-server/mapping.ts
@@ -112,6 +112,6 @@ function getDomain(name: string, schema: any, allData: any) {
return domains.length > 0 ? {
name,
domains: Table.ofRows({ ...S.Base, ...schema }, domains),
- mappings: Table.ofRows(S.mapping, mappings)
+ mappings: Table.ofRows<S.mapping>(S.mapping, mappings)
} : void 0;
}
\ No newline at end of file
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index 93461e8a8..b50672afb 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -132,6 +132,10 @@ namespace Column {
return createFirstIndexMapOfColumn(column);
}
+ export function createIndexer<T>(column: Column<T>) {
+ return createIndexerOfColumn(column);
+ }
+
export function mapToArray<T, S>(column: Column<T>, f: (v: T) => S, ctor?: ArrayCtor<S>): ArrayLike<S> {
return mapToArrayImpl<T, S>(column, f, ctor || Array);
}
@@ -174,6 +178,15 @@ function createFirstIndexMapOfColumn<T>(c: Column<T>): Map<T, number> {
return map;
}
+function createIndexerOfColumn<T>(c: Column<T>): (value: T) => number {
+ const map = new Map<T, number>();
+ for (let i = 0, _i = c.rowCount; i < _i; i++) {
+ const v = c.value(i);
+ if (!map.has(v)) map.set(c.value(i), i);
+ }
+ return v => map.has(v) ? map.get(v)! : -1;
+}
+
function constColumn<T extends Column.Schema>(v: T['T'], rowCount: number, schema: T, valueKind: Column.ValueKind): Column<T['T']> {
const value: Column<T['T']>['value'] = row => v;
return {
diff --git a/src/mol-data/db/table.ts b/src/mol-data/db/table.ts
index cac162233..df96dacbe 100644
--- a/src/mol-data/db/table.ts
+++ b/src/mol-data/db/table.ts
@@ -58,7 +58,7 @@ namespace Table {
return ret;
}
- export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, rows: ArrayLike<Row<S>>): R {
+ export function ofRows<S extends Schema, R extends Table<S> = Table<S>>(schema: Schema, rows: ArrayLike<Partial<Row<S>>>): R {
const ret = Object.create(null);
const rowCount = rows.length;
const columns = Object.keys(schema);
@@ -83,7 +83,7 @@ namespace Table {
ret._columns = columns;
ret._schema = schema;
for (const k of columns) {
- (ret as any)[k] = Column.ofArray({ array: arrays[k], schema: schema[k] })
+ (ret as any)[k] = typeof arrays[k] !== 'undefined' ? Column.ofArray({ array: arrays[k], schema: schema[k] }) : Column.Undefined(ret._rowCount, schema[k]);
}
return ret as R;
}
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 9635dd78b..3958a39fa 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -102,10 +102,10 @@ const atom_site: Encoder.CategoryDefinition<Element.Location> = {
function entityProvider({ model }: Context): Encoder.CategoryInstance {
return {
- data: model.hierarchy.entities,
- definition: Encoder.CategoryDefinition.ofTable('entity', model.hierarchy.entities),
- keys: () => Iterator.Range(0, model.hierarchy.entities._rowCount - 1),
- rowCount: model.hierarchy.entities._rowCount
+ data: model.entities.data,
+ definition: Encoder.CategoryDefinition.ofTable('entity', model.entities.data),
+ keys: () => Iterator.Range(0, model.entities.data._rowCount - 1),
+ rowCount: model.entities.data._rowCount
}
}
diff --git a/src/mol-model/structure/model/formats/gro.ts b/src/mol-model/structure/model/formats/gro.ts
index 84b30517e..cad8c441a 100644
--- a/src/mol-model/structure/model/formats/gro.ts
+++ b/src/mol-model/structure/model/formats/gro.ts
@@ -16,9 +16,11 @@ import CoarseGrained from '../properties/coarse-grained'
import findHierarchyKeys from '../utils/hierarchy-keys'
import { guessElement } from '../utils/guess-element'
import { ElementSymbol} from '../types'
+import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import gro_Format = Format.gro
import Sequence from '../properties/sequence';
+import { Entities } from '../properties/common';
type HierarchyOffsets = { residues: ArrayLike<number>, chains: ArrayLike<number> }
@@ -71,9 +73,8 @@ function createHierarchyData(atomsData: Atoms, offsets: HierarchyOffsets): Hiera
// });
const chains = Table.ofUndefinedColumns(Hierarchy.ChainsSchema, 0);
- const entities = Table.ofUndefinedColumns(Hierarchy.EntitySchema, 0);
- return { atoms, residues, chains, entities };
+ return { atoms, residues, chains };
}
function getConformation(atoms: Atoms): Conformation {
@@ -112,13 +113,25 @@ function createModel(format: gro_Format, modelNum: number, previous?: Model): Mo
residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, bounds),
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
}
- const hierarchyKeys = findHierarchyKeys(hierarchyData, hierarchySegments);
+
+ // TODO: create a better mock entity
+ const entityTable = Table.ofRows<mmCIF['entity']>(mmCIF.entity, [{
+ id: '0',
+ src_method: 'syn',
+ type: 'polymer',
+ pdbx_number_of_molecules: 1
+ }]);
+
+ const entities: Entities = { data: entityTable, getEntityIndex: Column.createIndexer(entityTable.id) };
+
+ const hierarchyKeys = findHierarchyKeys(hierarchyData, entities, hierarchySegments);
const hierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
return {
id: UUID.create(),
sourceData: format,
modelNum,
hierarchy,
+ entities,
sequence: Sequence.fromHierarchy(hierarchy),
conformation: getConformation(structure.atoms),
coarseGrained: CoarseGrained.Empty,
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index b06ed9ef2..d88ca8ac7 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -19,6 +19,7 @@ import createAssemblies from './mmcif/assembly'
import mmCIF_Format = Format.mmCIF
import { getSequence } from './mmcif/sequence';
+import { Entities } from '../properties/common';
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -63,7 +64,7 @@ function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets:
Table.columnToArray(residues, 'label_seq_id', Int32Array);
Table.columnToArray(residues, 'auth_seq_id', Int32Array);
const chains = Table.view(atom_site, Hierarchy.ChainsSchema, offsets.chains);
- return { atoms, residues, chains, entities: data.entity };
+ return { atoms, residues, chains };
}
function getConformation({ data }: mmCIF_Format, bounds: Interval): Conformation {
@@ -106,7 +107,10 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, bounds),
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
}
- const hierarchyKeys = findHierarchyKeys(hierarchyData, hierarchySegments);
+
+ const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
+
+ const hierarchyKeys = findHierarchyKeys(hierarchyData, entities, hierarchySegments);
const hierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
@@ -114,8 +118,9 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
id: UUID.create(),
sourceData: format,
modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
+ entities,
hierarchy,
- sequence: getSequence(format.data, hierarchy),
+ sequence: getSequence(format.data, entities, hierarchy),
conformation: getConformation(format, bounds),
coarseGrained: CoarseGrained.Empty,
symmetry: getSymmetry(format),
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
new file mode 100644
index 000000000..879b4fb84
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/ihm.ts
@@ -0,0 +1,6 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
diff --git a/src/mol-model/structure/model/formats/mmcif/sequence.ts b/src/mol-model/structure/model/formats/mmcif/sequence.ts
index 85bb572ba..ccba6849b 100644
--- a/src/mol-model/structure/model/formats/mmcif/sequence.ts
+++ b/src/mol-model/structure/model/formats/mmcif/sequence.ts
@@ -8,8 +8,9 @@ import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import Sequence from '../../properties/sequence'
import { Column } from 'mol-data/db';
import { Hierarchy } from '../../properties/hierarchy';
+import { Entities } from '../../properties/common';
-export function getSequence(cif: mmCIF, hierarchy: Hierarchy): Sequence {
+export function getSequence(cif: mmCIF, entities: Entities, hierarchy: Hierarchy): Sequence {
if (!cif.entity_poly_seq._rowCount) return Sequence.fromHierarchy(hierarchy);
const { entity_id, num, mon_id } = cif.entity_poly_seq;
@@ -24,7 +25,7 @@ export function getSequence(cif: mmCIF, hierarchy: Hierarchy): Sequence {
i++;
const id = entity_id.value(start);
- byEntityKey[hierarchy.findEntityKey(id)] = { entityId: id, compId: Column.window(mon_id, start, i), num: Column.window(num, start, i) }
+ byEntityKey[entities.getEntityIndex(id)] = { entityId: id, compId: Column.window(mon_id, start, i), num: Column.window(num, start, i) }
}
return { byEntityKey };
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index daf777734..9652cf5b1 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -11,6 +11,7 @@ import Hierarchy from './properties/hierarchy'
import Conformation from './properties/conformation'
import Symmetry from './properties/symmetry'
import CoarseGrained from './properties/coarse-grained'
+import { Entities } from './properties/common';
import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
@@ -27,7 +28,9 @@ interface Model extends Readonly<{
sourceData: Format,
+ entities: Entities,
sequence: Sequence,
+
hierarchy: Hierarchy,
conformation: Conformation,
symmetry: Symmetry,
diff --git a/src/mol-model/structure/model/properties/coarse-grained.ts b/src/mol-model/structure/model/properties/coarse-grained.ts
index 725493ff1..730724114 100644
--- a/src/mol-model/structure/model/properties/coarse-grained.ts
+++ b/src/mol-model/structure/model/properties/coarse-grained.ts
@@ -4,12 +4,42 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
+import { Tensor } from 'mol-math/linear-algebra';
+import { Column } from 'mol-data/db';
+
interface CoarseGrained {
- // TODO
+ modelList: mmCIF['ihm_model_list'],
+ spheres: { [P in keyof CoarseGrained.Sphere]: Column<CoarseGrained.Sphere[P]> },
+ gaussians: { [P in keyof CoarseGrained.Gaussian]: Column<CoarseGrained.Gaussian[P]> }
}
namespace CoarseGrained {
- export const Empty: CoarseGrained = { };
+ export const Empty: CoarseGrained = { } as any;
+
+ interface Site {
+ // index to the Model.hierarchy.entities table
+ entityKey: number,
+ // index to the CoarseGrained.modelList table
+ modelKey: number,
+
+ asym_id: string,
+ seq_id_begin: number,
+ seq_id_end: number,
+ x: number,
+ y: number,
+ z: number
+ }
+
+ export interface Sphere extends Site {
+ radius: number,
+ rmsf: number
+ }
+
+ export interface Gaussian extends Site {
+ weight: number,
+ covarianceMatrix: Tensor.Data
+ }
}
export default CoarseGrained;
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/common.ts b/src/mol-model/structure/model/properties/common.ts
new file mode 100644
index 000000000..aa5d93aae
--- /dev/null
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
+
+interface Entities {
+ data: mmCIF['entity'],
+ getEntityIndex(id: string): number
+}
+
+export { Entities }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/hierarchy.ts b/src/mol-model/structure/model/properties/hierarchy.ts
index 773e091d8..8987e070d 100644
--- a/src/mol-model/structure/model/properties/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/hierarchy.ts
@@ -40,15 +40,15 @@ export const ChainsSchema = {
export type ChainsSchema = typeof ChainsSchema
export interface Chains extends Table<ChainsSchema> { }
-export const EntitySchema = mmCIF['entity']
-export type EntitySchema = typeof EntitySchema
-export interface Entities extends Table<EntitySchema> { }
+// export const EntitySchema = mmCIF['entity']
+// export type EntitySchema = typeof EntitySchema
+// export interface Entities extends Table<EntitySchema> { }
export interface Data {
atoms: Atoms,
residues: Residues,
chains: Chains,
- entities: Entities
+ //entities: Entities
}
export interface Segments {
@@ -70,7 +70,6 @@ export interface Keys {
// also index to the Entities table.
entityKey: Column<number>,
- findEntityKey(id: string): number,
findChainKey(entityId: string, label_asym_id: string): number,
findResidueKey(entityId: string, label_asym_id: string, label_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code: string): number
}
diff --git a/src/mol-model/structure/model/utils/hierarchy-keys.ts b/src/mol-model/structure/model/utils/hierarchy-keys.ts
index c09484245..d70a26a94 100644
--- a/src/mol-model/structure/model/utils/hierarchy-keys.ts
+++ b/src/mol-model/structure/model/utils/hierarchy-keys.ts
@@ -7,6 +7,7 @@
import { Column } from 'mol-data/db'
import { Data, Segments, Keys } from '../properties/hierarchy'
import { Interval, Segmentation } from 'mol-data/int'
+import { Entities } from '../properties/common';
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
@@ -26,24 +27,26 @@ function getElementSubstructureKeyMap(map: Map<number, Map<string, number>>, key
return ret;
}
-function createLookUp(entity: Map<string, number>, chain: Map<number, Map<string, number>>, residue: Map<number, Map<string, number>>) {
- const findEntityKey: Keys['findEntityKey'] = (id) => entity.has(id) ? entity.get(id)! : -1;
+function createLookUp(entities: Entities, chain: Map<number, Map<string, number>>, residue: Map<number, Map<string, number>>) {
+ const getEntKey = entities.getEntityIndex;
const findChainKey: Keys['findChainKey'] = (e, c) => {
- if (!entity.has(e)) return -1;
- const cm = chain.get(entity.get(e)!)!;
+ let eKey = getEntKey(e);
+ if (eKey < 0) return -1;
+ const cm = chain.get(eKey)!;
if (!cm.has(c)) return -1;
return cm.get(c)!;
}
const findResidueKey: Keys['findResidueKey'] = (e, c, name, seq, ins) => {
- if (!entity.has(e)) return -1;
- const cm = chain.get(entity.get(e)!)!;
+ let eKey = getEntKey(e);
+ if (eKey < 0) return -1;
+ const cm = chain.get(eKey)!;
if (!cm.has(c)) return -1;
const rm = residue.get(cm.get(c)!)!
const id = getResidueId(name, seq, ins);
if (!rm.has(id)) return -1;
return rm.get(id)!;
}
- return { findEntityKey, findChainKey, findResidueKey };
+ return { findChainKey, findResidueKey };
}
function checkMonotonous(xs: ArrayLike<number>) {
@@ -55,10 +58,13 @@ function checkMonotonous(xs: ArrayLike<number>) {
return true;
}
-function create(data: Data, segments: Segments): Keys {
- const { chains, residues, entities } = data;
+function missingEntity(k: string) {
+ throw new Error(`Missing entity entry for entity id '${k}'.`);
+}
+
+function create(data: Data, entities: Entities, segments: Segments): Keys {
+ const { chains, residues } = data;
- const entityMap = Column.createFirstIndexMap(entities.id);
const chainMaps = new Map<number, Map<string, number>>(), chainCounter = { index: 0 };
const residueMaps = new Map<number, Map<string, number>>(), residueCounter = { index: 0 };
@@ -78,7 +84,8 @@ function create(data: Data, segments: Segments): Keys {
const chainSegment = chainsIt.move();
const cI = chainSegment.index;
- const eKey = entityMap.get(label_entity_id.value(cI)) || 0;
+ let eKey = entities.getEntityIndex(label_entity_id.value(cI));
+ if (eKey < 0) missingEntity(label_entity_id.value(cI));
const chainMap = getElementSubstructureKeyMap(chainMaps, eKey);
const cKey = getElementKey(chainMap, label_asym_id.value(cI), chainCounter);
@@ -99,14 +106,13 @@ function create(data: Data, segments: Segments): Keys {
}
}
- const { findEntityKey, findChainKey, findResidueKey } = createLookUp(entityMap, chainMaps, residueMaps);
+ const { findChainKey, findResidueKey } = createLookUp(entities, chainMaps, residueMaps);
return {
isMonotonous: isMonotonous && checkMonotonous(entityKey) && checkMonotonous(chainKey) && checkMonotonous(residueKey),
residueKey: Column.ofIntArray(residueKey),
chainKey: Column.ofIntArray(chainKey),
entityKey: Column.ofIntArray(entityKey),
- findEntityKey,
findChainKey,
findResidueKey
};
diff --git a/src/mol-model/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
index 2ed1ac4e4..811c64a89 100644
--- a/src/mol-model/structure/query/properties.ts
+++ b/src/mol-model/structure/query/properties.ts
@@ -59,16 +59,16 @@ function eK(l: Element.Location) { return !Unit.isAtomic(l.unit) ? notAtomic() :
const entity = {
key: eK,
- id: Element.property(l => l.unit.hierarchy.entities.id.value(eK(l))),
- type: Element.property(l => l.unit.hierarchy.entities.type.value(eK(l))),
- src_method: Element.property(l => l.unit.hierarchy.entities.src_method.value(eK(l))),
- pdbx_description: Element.property(l => l.unit.hierarchy.entities.pdbx_description.value(eK(l))),
- formula_weight: Element.property(l => l.unit.hierarchy.entities.formula_weight.value(eK(l))),
- pdbx_number_of_molecules: Element.property(l => l.unit.hierarchy.entities.pdbx_number_of_molecules.value(eK(l))),
- details: Element.property(l => l.unit.hierarchy.entities.details.value(eK(l))),
- pdbx_mutation: Element.property(l => l.unit.hierarchy.entities.pdbx_mutation.value(eK(l))),
- pdbx_fragment: Element.property(l => l.unit.hierarchy.entities.pdbx_fragment.value(eK(l))),
- pdbx_ec: Element.property(l => l.unit.hierarchy.entities.pdbx_ec.value(eK(l)))
+ id: Element.property(l => l.unit.model.entities.data.id.value(eK(l))),
+ type: Element.property(l => l.unit.model.entities.data.type.value(eK(l))),
+ src_method: Element.property(l => l.unit.model.entities.data.src_method.value(eK(l))),
+ pdbx_description: Element.property(l => l.unit.model.entities.data.pdbx_description.value(eK(l))),
+ formula_weight: Element.property(l => l.unit.model.entities.data.formula_weight.value(eK(l))),
+ pdbx_number_of_molecules: Element.property(l => l.unit.model.entities.data.pdbx_number_of_molecules.value(eK(l))),
+ details: Element.property(l => l.unit.model.entities.data.details.value(eK(l))),
+ pdbx_mutation: Element.property(l => l.unit.model.entities.data.pdbx_mutation.value(eK(l))),
+ pdbx_fragment: Element.property(l => l.unit.model.entities.data.pdbx_fragment.value(eK(l))),
+ pdbx_ec: Element.property(l => l.unit.model.entities.data.pdbx_ec.value(eK(l)))
}
const unit = {
--
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