From ba2a4f3a99ae98b4b9dae3ee9f476f290f67d056 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 10 May 2018 16:10:54 +0200
Subject: [PATCH] More refactoring of mol-model
---
package-lock.json | Bin 478290 -> 489768 bytes
package.json | 2 +-
src/apps/structure-info/model.ts | 12 +-
.../representation/structure/spacefill.ts | 2 +-
src/mol-geo/theme/structure/color/chain-id.ts | 10 +-
.../theme/structure/color/element-symbol.ts | 2 +-
src/mol-geo/theme/structure/size/element.ts | 2 +-
src/mol-math/linear-algebra/3d/mat3.ts | 4 +
src/mol-math/linear-algebra/tensor.ts | 12 +-
src/mol-model/structure/export/mmcif.ts | 2 +-
src/mol-model/structure/model/format.ts | 6 +-
src/mol-model/structure/model/formats/gro.ts | 307 +++++++++---------
.../structure/model/formats/mmcif.ts | 52 +--
.../structure/model/formats/mmcif/assembly.ts | 2 +-
.../structure/model/formats/mmcif/bonds.ts | 2 +-
.../structure/model/formats/mmcif/ihm.ts | 87 +++--
.../structure/model/formats/mmcif/util.ts | 4 +-
src/mol-model/structure/model/model.ts | 26 +-
.../model/properties/atomic/hierarchy.ts | 17 +-
.../properties/coarse-grained/conformation.ts | 0
.../properties/coarse-grained/hierarchy.ts | 53 ---
.../structure/model/properties/coarse.ts | 8 +
.../model/properties/coarse/conformation.ts | 30 ++
.../model/properties/coarse/hierarchy.ts | 49 +++
.../structure/model/properties/common.ts | 16 -
.../utils/atomic-keys.ts} | 17 +-
.../model/properties/utils/coarse-keys.ts | 84 +++++
.../{ => properties}/utils/guess-element.ts | 0
src/mol-model/structure/query/generators.ts | 8 +-
src/mol-model/structure/query/properties.ts | 66 ++--
.../structure/structure/structure.ts | 19 +-
src/mol-model/structure/structure/unit.ts | 54 +--
.../structure/unit/bonds/intra-compute.ts | 6 +-
src/perf-tests/structure.ts | 4 +-
34 files changed, 560 insertions(+), 405 deletions(-)
delete mode 100644 src/mol-model/structure/model/properties/coarse-grained/conformation.ts
delete mode 100644 src/mol-model/structure/model/properties/coarse-grained/hierarchy.ts
create mode 100644 src/mol-model/structure/model/properties/coarse.ts
create mode 100644 src/mol-model/structure/model/properties/coarse/conformation.ts
create mode 100644 src/mol-model/structure/model/properties/coarse/hierarchy.ts
rename src/mol-model/structure/model/{utils/hierarchy-keys.ts => properties/utils/atomic-keys.ts} (90%)
create mode 100644 src/mol-model/structure/model/properties/utils/coarse-keys.ts
rename src/mol-model/structure/model/{ => properties}/utils/guess-element.ts (100%)
diff --git a/package-lock.json b/package-lock.json
index 2d93002f4e7b77be351e8e4eb333e62b3f5807b4..c1e108171140e7de69fdc590f15d660d717faef1 100644
GIT binary patch
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diff --git a/package.json b/package.json
index fc7b94070..23e18880b 100644
--- a/package.json
+++ b/package.json
@@ -85,7 +85,7 @@
"argparse": "^1.0.10",
"express": "^4.16.3",
"gl": "^4.0.4",
- "material-ui": "^1.0.0-beta.46",
+ "material-ui": "~1.0.0-beta.43",
"node-fetch": "^2.1.2",
"react": "^16.3.2",
"react-dom": "^16.3.2",
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 1bc3b500b..15ee55fd8 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -30,7 +30,7 @@ async function readPdbFile(path: string) {
}
export function atomLabel(model: Model, aI: number) {
- const { atoms, residues, chains, residueSegments, chainSegments } = model.hierarchy
+ const { atoms, residues, chains, residueSegments, chainSegments } = model.atomicHierarchy
const { label_atom_id } = atoms
const { label_comp_id, label_seq_id } = residues
const { label_asym_id } = chains
@@ -92,10 +92,10 @@ export function printUnits(structure: Structure) {
} else if (Unit.isCoarse(l.unit)) {
console.log(`Coarse unit ${unit.id} (${Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
- const props = Queries.props.coarse_grained;
+ const props = Queries.props.coarse;
const seq = l.unit.model.sequence;
- for (let j = 0, _j = Math.min(size, 10); j < _j; j++) {
+ for (let j = 0, _j = Math.min(size, 3); j < _j; j++) {
l.element = OrderedSet.getAt(elements, j);
const residues: string[] = [];
@@ -104,16 +104,16 @@ export function printUnits(structure: Structure) {
for (let e = start; e <= end; e++) residues.push(compId(e));
console.log(`${props.asym_id(l)}:${start}-${end} (${residues.join('-')}) ${props.asym_id(l)} [${props.x(l).toFixed(2)}, ${props.y(l).toFixed(2)}, ${props.z(l).toFixed(2)}]`);
}
- if (size > 10) console.log(`...`);
+ if (size > 3) console.log(`...`);
}
}
}
export function printIHMModels(model: Model) {
- if (!model.coarseGrained.isDefined) return false;
+ if (!model.coarseHierarchy.isDefined) return false;
console.log('IHM Models\n=============');
- console.log(Table.formatToString(model.coarseGrained.modelList));
+ console.log(Table.formatToString(model.coarseHierarchy.models));
}
async function run(mmcif: mmCIF_Database) {
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 1946f8103..db8240514 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -39,7 +39,7 @@ function createSpacefillMesh(unit: Unit, detail: number) {
if (Unit.isAtomic(unit)) {
radius = Queries.props.atom.vdw_radius
} else if (Unit.isSpheres(unit)) {
- radius = Queries.props.coarse_grained.sphere_radius
+ radius = Queries.props.coarse.sphere_radius
} else {
console.warn('Unsupported unit type')
return meshBuilder.getMesh()
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index 95e305be3..d521d6036 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -18,11 +18,11 @@ function createChainIdMap(unit: Unit) {
let count: number
let asym_id: Column<string>
if (Unit.isAtomic(unit)) {
- asym_id = unit.model.hierarchy.chains.label_asym_id
- count = unit.model.hierarchy.chains._rowCount
+ asym_id = unit.model.atomicHierarchy.chains.label_asym_id
+ count = unit.model.atomicHierarchy.chains._rowCount
} else if (Unit.isCoarse(unit)) {
- asym_id = unit.sites.asym_id
- count = unit.sites.count
+ asym_id = unit.coarseElements.asym_id
+ count = unit.coarseElements.count
} else {
console.warn('Unknown unit type')
return { map, count: index }
@@ -51,7 +51,7 @@ export function chainIdColorData(props: StructureColorDataProps) {
if (Unit.isAtomic(unit)) {
asym_id = Queries.props.chain.label_asym_id
} else if (Unit.isCoarse(unit)) {
- asym_id = Queries.props.coarse_grained.asym_id
+ asym_id = Queries.props.coarse.asym_id
}
const l = Element.Location()
diff --git a/src/mol-geo/theme/structure/color/element-symbol.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
index 815985b33..affedfac0 100644
--- a/src/mol-geo/theme/structure/color/element-symbol.ts
+++ b/src/mol-geo/theme/structure/color/element-symbol.ts
@@ -23,7 +23,7 @@ export function elementSymbolColor(element: ElementSymbol): Color {
export function elementSymbolColorData(props: StructureColorDataProps) {
const { group: { units, elements }, vertexMap } = props
- const { type_symbol } = units[0].model.hierarchy.atoms
+ const { type_symbol } = units[0].model.atomicHierarchy.atoms
return createAttributeOrElementColor(vertexMap, {
colorFn: (elementIdx: number) => {
const e = elements[elementIdx]
diff --git a/src/mol-geo/theme/structure/size/element.ts b/src/mol-geo/theme/structure/size/element.ts
index 8bf99acc0..741ba136f 100644
--- a/src/mol-geo/theme/structure/size/element.ts
+++ b/src/mol-geo/theme/structure/size/element.ts
@@ -17,7 +17,7 @@ export function elementSizeData(props: StructureSizeDataProps) {
if (Unit.isAtomic(unit)) {
radius = Queries.props.atom.vdw_radius
} else if (Unit.isSpheres(unit)) {
- radius = Queries.props.coarse_grained.sphere_radius
+ radius = Queries.props.coarse.sphere_radius
}
const l = Element.Location()
l.unit = unit
diff --git a/src/mol-math/linear-algebra/3d/mat3.ts b/src/mol-math/linear-algebra/3d/mat3.ts
index cd577776b..c72dc713d 100644
--- a/src/mol-math/linear-algebra/3d/mat3.ts
+++ b/src/mol-math/linear-algebra/3d/mat3.ts
@@ -104,6 +104,10 @@ namespace Mat3 {
return Mat3.copy(Mat3.zero(), a);
}
+ export function setValue(a: Mat3, i: number, j: number, value: number) {
+ a[3 * j + i] = value;
+ }
+
/**
* Copy the values from one Mat3 to another
*/
diff --git a/src/mol-math/linear-algebra/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
index 976e410e1..4bcae46f7 100644
--- a/src/mol-math/linear-algebra/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Mat4, Vec3, Vec4 } from './3d'
+import { Mat4, Vec3, Vec4, Mat3 } from './3d'
export interface Tensor { data: Tensor.Data, space: Tensor.Space }
@@ -65,6 +65,16 @@ export namespace Tensor {
return mat;
}
+ export function toMat3(space: Space, data: Tensor.Data): Mat3 {
+ if (space.rank !== 2) throw new Error('Invalid tensor rank');
+ const mat = Mat3.zero();
+ const d0 = Math.min(3, space.dimensions[0]), d1 = Math.min(3, space.dimensions[1]);
+ for (let i = 0; i < d0; i++) {
+ for (let j = 0; j < d1; j++) Mat3.setValue(mat, i, j, space.get(data, i, j));
+ }
+ return mat;
+ }
+
export function toVec3(space: Space, data: Tensor.Data): Vec3 {
if (space.rank !== 1) throw new Error('Invalid tensor rank');
const vec = Vec3.zero();
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 65ded0cbb..d7f4491a6 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -96,7 +96,7 @@ const atom_site: Encoder.CategoryDefinition<Element.Location> = {
str('auth_asym_id', P.chain.auth_asym_id),
int('pdbx_PDB_model_num', P.unit.model_num),
- str('pdbx_operator_name', P.unit.operator_name)
+ str('operator_name', P.unit.operator_name)
]
};
diff --git a/src/mol-model/structure/model/format.ts b/src/mol-model/structure/model/format.ts
index d463c30d7..2fa1f8ae1 100644
--- a/src/mol-model/structure/model/format.ts
+++ b/src/mol-model/structure/model/format.ts
@@ -4,15 +4,15 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { File as GroFile } from 'mol-io/reader/gro/schema'
+// import { File as GroFile } from 'mol-io/reader/gro/schema'
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif'
type Format =
- | Format.gro
+ // | Format.gro
| Format.mmCIF
namespace Format {
- export interface gro { kind: 'gro', data: GroFile }
+ // export interface gro { kind: 'gro', data: GroFile }
export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database }
}
diff --git a/src/mol-model/structure/model/formats/gro.ts b/src/mol-model/structure/model/formats/gro.ts
index 46a9cd165..5e5350974 100644
--- a/src/mol-model/structure/model/formats/gro.ts
+++ b/src/mol-model/structure/model/formats/gro.ts
@@ -1,153 +1,154 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import UUID from 'mol-util/uuid'
-import { Column, Table } from 'mol-data/db'
-import { Interval, Segmentation } from 'mol-data/int'
-import { Atoms } from 'mol-io/reader/gro/schema'
-import Format from '../format'
-import Model from '../model'
-import { AtomicConformation, AtomicData, AtomsSchema, ResiduesSchema, ChainsSchema, AtomicSegments } from '../properties/atomic'
-import { CoarseGrainedHierarchy } from '../properties/coarse-grained/hierarchy'
-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';
-import { ModelSymmetry } from '../properties/symmetry';
-
-type HierarchyOffsets = { residues: ArrayLike<number>, chains: ArrayLike<number> }
-
-function findHierarchyOffsets(atomsData: Atoms, bounds: Interval) {
- const start = Interval.start(bounds), end = Interval.end(bounds);
- const residues = [start], chains = [start];
-
- const { residueName, residueNumber } = atomsData;
-
- for (let i = start + 1; i < end; i++) {
- const newResidue = !residueNumber.areValuesEqual(i - 1, i)
- || !residueName.areValuesEqual(i - 1, i);
- console.log(residueName.value(i - 1), residueName.value(i), residueNumber.value(i - 1), residueNumber.value(i), newResidue)
- if (newResidue) residues[residues.length] = i;
- }
- console.log(residues, residues.length)
- return { residues, chains };
-}
-
-function guessElementSymbol (value: string) {
- return ElementSymbol(guessElement(value));
-}
-
-function createHierarchyData(atomsData: Atoms, offsets: HierarchyOffsets): AtomicData {
- console.log(atomsData.atomName)
- const atoms = Table.ofColumns(AtomsSchema, {
- type_symbol: Column.ofArray({ array: Column.mapToArray(atomsData.atomName, guessElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
- label_atom_id: atomsData.atomName,
- auth_atom_id: atomsData.atomName,
- label_alt_id: Column.Undefined(atomsData.count, Column.Schema.str),
- pdbx_formal_charge: Column.Undefined(atomsData.count, Column.Schema.int)
- });
-
- const residues = Table.view(Table.ofColumns(ResiduesSchema, {
- group_PDB: Column.Undefined(atomsData.count, Column.Schema.Aliased<'ATOM' | 'HETATM'>(Column.Schema.str)),
- label_comp_id: atomsData.residueName,
- auth_comp_id: atomsData.residueName,
- label_seq_id: atomsData.residueNumber,
- auth_seq_id: atomsData.residueNumber,
- pdbx_PDB_ins_code: Column.Undefined(atomsData.count, Column.Schema.str),
- }), ResiduesSchema, offsets.residues);
- // Optimize the numeric columns
- Table.columnToArray(residues, 'label_seq_id', Int32Array);
- Table.columnToArray(residues, 'auth_seq_id', Int32Array);
-
- // const chains = Table.ofColumns(Hierarchy.ChainsSchema, {
- // label_asym_id: Column.ofConst('A', atomsData.count, Column.Schema.str),
- // auth_asym_id: Column.ofConst('A', atomsData.count, Column.Schema.str),
- // label_entity_id: Column.Undefined(atomsData.count, Column.Schema.str)
- // });
-
- const chains = Table.ofUndefinedColumns(ChainsSchema, 0);
-
- return { atoms, residues, chains };
-}
-
-function getConformation(atoms: Atoms): AtomicConformation {
- return {
- id: UUID.create(),
- atomId: atoms.atomNumber,
- occupancy: Column.Undefined(atoms.count, Column.Schema.int),
- B_iso_or_equiv: Column.Undefined(atoms.count, Column.Schema.float),
- x: Column.mapToArray(atoms.x, x => x * 10, Float32Array),
- y: Column.mapToArray(atoms.y, y => y * 10, Float32Array),
- z: Column.mapToArray(atoms.z, z => z * 10, 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.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
- && Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
-}
-
-function createModel(format: gro_Format, modelNum: number, previous?: Model): Model {
- const structure = format.data.structures[modelNum];
- const bounds = Interval.ofBounds(0, structure.atoms.count);
-
- const hierarchyOffsets = findHierarchyOffsets(structure.atoms, bounds);
- const hierarchyData = createHierarchyData(structure.atoms, hierarchyOffsets);
-
- if (previous && isHierarchyDataEqual(previous.hierarchy, hierarchyData)) {
- return {
- ...previous,
- atomSiteConformation: getConformation(structure.atoms)
- };
- }
-
- const hierarchySegments: AtomicSegments = {
- residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, bounds),
- chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
- }
-
- // 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.fromAtomicHierarchy(hierarchy),
- atomSiteConformation: getConformation(structure.atoms),
- coarseGrained: CoarseGrainedHierarchy.Empty,
- symmetry: ModelSymmetry.Default,
- atomCount: structure.atoms.count
- };
-}
-
-function buildModels(format: gro_Format): ReadonlyArray<Model> {
- const models: Model[] = [];
-
- format.data.structures.forEach((_, i) => {
- const model = createModel(format, i, models.length > 0 ? models[models.length - 1] : void 0);
- models.push(model);
- });
- return models;
-}
-
-export default buildModels;
\ No newline at end of file
+// TODO: make this work when the time comes.
+// /**
+// * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author Alexander Rose <alexander.rose@weirdbyte.de>
+// */
+
+// import { Column, Table } from 'mol-data/db';
+// import { Interval, Segmentation } from 'mol-data/int';
+// import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif';
+// import { Atoms } from 'mol-io/reader/gro/schema';
+// 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 { CoarseHierarchy } from '../properties/coarse';
+// import { Entities } from '../properties/common';
+// import Sequence from '../properties/sequence';
+// import { ModelSymmetry } from '../properties/symmetry';
+// import { guessElement } from '../properties/utils/guess-element';
+// import { getAtomicKeys } from '../properties/utils/keys';
+// import { ElementSymbol } from '../types';
+
+// import gro_Format = Format.gro
+
+// type HierarchyOffsets = { residues: ArrayLike<number>, chains: ArrayLike<number> }
+
+// function findHierarchyOffsets(atomsData: Atoms, bounds: Interval) {
+// const start = Interval.start(bounds), end = Interval.end(bounds);
+// const residues = [start], chains = [start];
+
+// const { residueName, residueNumber } = atomsData;
+
+// for (let i = start + 1; i < end; i++) {
+// const newResidue = !residueNumber.areValuesEqual(i - 1, i)
+// || !residueName.areValuesEqual(i - 1, i);
+// console.log(residueName.value(i - 1), residueName.value(i), residueNumber.value(i - 1), residueNumber.value(i), newResidue)
+// if (newResidue) residues[residues.length] = i;
+// }
+// console.log(residues, residues.length)
+// return { residues, chains };
+// }
+
+// function guessElementSymbol (value: string) {
+// return ElementSymbol(guessElement(value));
+// }
+
+// function createHierarchyData(atomsData: Atoms, offsets: HierarchyOffsets): AtomicData {
+// console.log(atomsData.atomName)
+// const atoms = Table.ofColumns(AtomsSchema, {
+// type_symbol: Column.ofArray({ array: Column.mapToArray(atomsData.atomName, guessElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
+// label_atom_id: atomsData.atomName,
+// auth_atom_id: atomsData.atomName,
+// label_alt_id: Column.Undefined(atomsData.count, Column.Schema.str),
+// pdbx_formal_charge: Column.Undefined(atomsData.count, Column.Schema.int)
+// });
+
+// const residues = Table.view(Table.ofColumns(ResiduesSchema, {
+// group_PDB: Column.Undefined(atomsData.count, Column.Schema.Aliased<'ATOM' | 'HETATM'>(Column.Schema.str)),
+// label_comp_id: atomsData.residueName,
+// auth_comp_id: atomsData.residueName,
+// label_seq_id: atomsData.residueNumber,
+// auth_seq_id: atomsData.residueNumber,
+// pdbx_PDB_ins_code: Column.Undefined(atomsData.count, Column.Schema.str),
+// }), ResiduesSchema, offsets.residues);
+// // Optimize the numeric columns
+// Table.columnToArray(residues, 'label_seq_id', Int32Array);
+// Table.columnToArray(residues, 'auth_seq_id', Int32Array);
+
+// // const chains = Table.ofColumns(Hierarchy.ChainsSchema, {
+// // label_asym_id: Column.ofConst('A', atomsData.count, Column.Schema.str),
+// // auth_asym_id: Column.ofConst('A', atomsData.count, Column.Schema.str),
+// // label_entity_id: Column.Undefined(atomsData.count, Column.Schema.str)
+// // });
+
+// const chains = Table.ofUndefinedColumns(ChainsSchema, 0);
+
+// return { atoms, residues, chains };
+// }
+
+// function getConformation(atoms: Atoms): AtomicConformation {
+// return {
+// id: UUID.create(),
+// atomId: atoms.atomNumber,
+// occupancy: Column.Undefined(atoms.count, Column.Schema.int),
+// B_iso_or_equiv: Column.Undefined(atoms.count, Column.Schema.float),
+// x: Column.mapToArray(atoms.x, x => x * 10, Float32Array),
+// y: Column.mapToArray(atoms.y, y => y * 10, Float32Array),
+// z: Column.mapToArray(atoms.z, z => z * 10, 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.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
+// && Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
+// }
+
+// function createModel(format: gro_Format, modelNum: number, previous?: Model): Model {
+// const structure = format.data.structures[modelNum];
+// const bounds = Interval.ofBounds(0, structure.atoms.count);
+
+// const hierarchyOffsets = findHierarchyOffsets(structure.atoms, bounds);
+// const hierarchyData = createHierarchyData(structure.atoms, hierarchyOffsets);
+
+// if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
+// return {
+// ...previous,
+// atomicConformation: getConformation(structure.atoms)
+// };
+// }
+
+// const hierarchySegments: AtomicSegments = {
+// residueSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, bounds),
+// chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
+// }
+
+// // 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 = getAtomicKeys(hierarchyData, entities, hierarchySegments);
+// const atomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
+// return {
+// id: UUID.create(),
+// sourceData: format,
+// modelNum,
+// atomicHierarchy,
+// entities,
+// sequence: Sequence.fromAtomicHierarchy(atomicHierarchy),
+// atomicConformation: getConformation(structure.atoms),
+// coarseHierarchy: CoarseHierarchy.Empty,
+// coarseConformation: void 0 as any,
+// symmetry: ModelSymmetry.Default
+// };
+// }
+
+// function buildModels(format: gro_Format): ReadonlyArray<Model> {
+// const models: Model[] = [];
+
+// format.data.structures.forEach((_, i) => {
+// const model = createModel(format, i, models.length > 0 ? models[models.length - 1] : void 0);
+// models.push(model);
+// });
+// return models;
+// }
+
+// export default buildModels;
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 22644e2fa..3f68d5444 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -4,23 +4,23 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import UUID from 'mol-util/uuid'
-import { Column, Table } from 'mol-data/db'
-import { Interval, Segmentation } from 'mol-data/int'
-import Format from '../format'
-import Model from '../model'
-import { AtomsSchema, ResiduesSchema, ChainsSchema, AtomicData, AtomicSegments, AtomicConformation } from '../properties/atomic'
-import { ModelSymmetry } from '../properties/symmetry'
-import findHierarchyKeys from '../utils/hierarchy-keys'
-import { ElementSymbol} from '../types'
-import createAssemblies from './mmcif/assembly'
-
-import mmCIF_Format = Format.mmCIF
-import { getSequence } from './mmcif/sequence';
-import { Entities } from '../properties/common';
-import { coarseGrainedFromIHM } from './mmcif/ihm';
+import { Column, Table } from 'mol-data/db';
+import { Interval, Segmentation } from 'mol-data/int';
import { Spacegroup, SpacegroupCell } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
+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 { 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 { getSequence } from './mmcif/sequence';
+
+import mmCIF_Format = Format.mmCIF
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -120,10 +120,10 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
const hierarchyOffsets = findHierarchyOffsets(format, bounds);
const hierarchyData = createHierarchyData(format, bounds, hierarchyOffsets);
- if (previous && isHierarchyDataEqual(previous.hierarchy, hierarchyData)) {
+ if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
return {
...previous,
- atomSiteConformation: getConformation(format, bounds)
+ atomicConformation: getConformation(format, bounds)
};
}
@@ -134,21 +134,23 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
const entities: Entities = { data: format.data.entity, getEntityIndex: Column.createIndexer(format.data.entity.id) };
- const hierarchyKeys = findHierarchyKeys(hierarchyData, entities, hierarchySegments);
+ const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
+
+ const atomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
- const hierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments };
+ const coarse = getIHMCoarse(format.data, entities);
return {
id: UUID.create(),
sourceData: format,
modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
entities,
- hierarchy,
- sequence: getSequence(format.data, entities, hierarchy),
- atomSiteConformation: getConformation(format, bounds),
- coarseGrained: coarseGrainedFromIHM(format.data, entities),
- symmetry: getSymmetry(format),
- atomCount: Interval.size(bounds)
+ atomicHierarchy,
+ sequence: getSequence(format.data, entities, atomicHierarchy),
+ atomicConformation: getConformation(format, bounds),
+ coarseHierarchy: coarse.hierarchy,
+ coarseConformation: coarse.conformation,
+ symmetry: getSymmetry(format)
};
}
diff --git a/src/mol-model/structure/model/formats/mmcif/assembly.ts b/src/mol-model/structure/model/formats/mmcif/assembly.ts
index 2315133d4..48720596c 100644
--- a/src/mol-model/structure/model/formats/mmcif/assembly.ts
+++ b/src/mol-model/structure/model/formats/mmcif/assembly.ts
@@ -12,7 +12,7 @@ import { Queries as Q, Query } from '../../../query'
import mmCIF_Format = Format.mmCIF
-export default function create(format: mmCIF_Format): ReadonlyArray<Assembly> {
+export function createAssemblies(format: mmCIF_Format): ReadonlyArray<Assembly> {
const { pdbx_struct_assembly } = format.data;
if (!pdbx_struct_assembly._rowCount) return [];
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds.ts b/src/mol-model/structure/model/formats/mmcif/bonds.ts
index 7bd6ec6f9..95ac32d4d 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds.ts
@@ -118,7 +118,7 @@ export namespace StructConn {
const _p = (row: number, ps: typeof p1) => {
if (ps.label_asym_id.valueKind(row) !== Column.ValueKind.Present) return void 0;
const asymId = ps.label_asym_id.value(row)
- const residueIndex = model.hierarchy.findResidueKey(
+ const residueIndex = model.atomicHierarchy.findResidueKey(
findEntityIdByAsymId(model, asymId),
ps.label_comp_id.value(row),
asymId,
diff --git a/src/mol-model/structure/model/formats/mmcif/ihm.ts b/src/mol-model/structure/model/formats/mmcif/ihm.ts
index 5eab89ab0..1dfdc1c1d 100644
--- a/src/mol-model/structure/model/formats/mmcif/ihm.ts
+++ b/src/mol-model/structure/model/formats/mmcif/ihm.ts
@@ -5,50 +5,81 @@
*/
import { mmCIF_Database as mmCIF, mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif'
-import { CoarseGrainedHierarchy } from '../../properties/coarse-grained/hierarchy'
+import { CoarseHierarchy, CoarseConformation, CoarseElementData, CoarseSphereConformation, CoarseGaussianConformation } from '../../properties/coarse'
import { Entities } from '../../properties/common';
import { Column } from 'mol-data/db';
+import { getCoarseKeys } from '../../properties/utils/coarse-keys';
+import { UUID } from 'mol-util';
+import { Segmentation, Interval } from 'mol-data/int';
+import { Mat3, Tensor } from 'mol-math/linear-algebra';
-function coarseGrainedFromIHM(data: mmCIF, entities: Entities): CoarseGrainedHierarchy {
- if (data.ihm_model_list._rowCount === 0) return CoarseGrainedHierarchy.Empty;
+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 };
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 gaussianData = getData(ihm_gaussian_obj_site);
+ const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
+ const gaussianKeys = getCoarseKeys(gaussianData, modelIndex, entities);
+
return {
- isDefined: true,
- modelList: ihm_model_list,
- spheres: getSpheres(ihm_sphere_obj_site, entities, modelIndex),
- gaussians: getGaussians(ihm_gaussian_obj_site, entities, modelIndex)
+ hierarchy: {
+ isDefined: true,
+ models: ihm_model_list,
+ spheres: { ...sphereData, ...sphereKeys },
+ gaussians: { ...gaussianData, ...gaussianKeys },
+ },
+ conformation: {
+ id: UUID.create(),
+ spheres: sphereConformation,
+ gaussians: gaussianConformation
+ }
};
}
-function getSpheres(data: mmCIF['ihm_sphere_obj_site'], entities: Entities, modelIndex: (id: number) => number): CoarseGrainedHierarchy.Spheres {
- const { Cartn_x, Cartn_y, Cartn_z, object_radius: radius, rmsf } = data;
- const x = Cartn_x.toArray({ array: Float32Array });
- const y = Cartn_y.toArray({ array: Float32Array });
- const z = Cartn_z.toArray({ array: Float32Array });
- return { count: x.length, ...getCommonColumns(data, entities, modelIndex), x, y, z, radius, rmsf };
+function getSphereConformation(data: mmCIF['ihm_sphere_obj_site']): CoarseSphereConformation {
+ return {
+ x: data.Cartn_x.toArray({ array: Float32Array }),
+ y: data.Cartn_y.toArray({ array: Float32Array }),
+ z: data.Cartn_z.toArray({ array: Float32Array }),
+ radius: data.object_radius.toArray({ array: Float32Array }),
+ rmsf: data.rmsf.toArray({ array: Float32Array })
+ };
}
-function getGaussians(data: mmCIF['ihm_gaussian_obj_site'], entities: Entities, modelIndex: (id: number) => number): CoarseGrainedHierarchy.Gaussians {
- const { mean_Cartn_x, mean_Cartn_y, mean_Cartn_z, weight, covariance_matrix } = data;
- const x = mean_Cartn_x.toArray({ array: Float32Array });
- const y = mean_Cartn_y.toArray({ array: Float32Array });
- const z = mean_Cartn_z.toArray({ array: Float32Array });
- return { count: x.length, ...getCommonColumns(data, entities, modelIndex), x, y, z, weight, covariance_matrix, matrix_space: mmCIF_Schema.ihm_gaussian_obj_site.covariance_matrix.space };
-}
+function getGaussianConformation(data: mmCIF['ihm_gaussian_obj_site']): CoarseGaussianConformation {
+ const matrix_space = mmCIF_Schema.ihm_gaussian_obj_site.covariance_matrix.space;
+ const covariance_matrix: Mat3[] = [];
+ const { covariance_matrix: cm } = data;
-function getCommonColumns(data: mmCIF['ihm_sphere_obj_site'] | mmCIF['ihm_gaussian_obj_site'], entities: Entities, modelIndex: (id: number) => number) {
- const { model_id, entity_id, seq_id_begin, seq_id_end, asym_id } = data;
+ for (let i = 0, _i = cm.rowCount; i < _i; i++) {
+ covariance_matrix[i] = Tensor.toMat3(matrix_space, cm.value(i));
+ }
return {
- entityKey: Column.mapToArray(entity_id, id => entities.getEntityIndex(id), Int32Array),
- modelKey: Column.mapToArray(model_id, modelIndex, Int32Array),
- asym_id,
- seq_id_begin,
- seq_id_end
+ x: data.mean_Cartn_x.toArray({ array: Float32Array }),
+ y: data.mean_Cartn_y.toArray({ array: Float32Array }),
+ z: data.mean_Cartn_z.toArray({ array: Float32Array }),
+ weight: data.weight.toArray({ array: Float32Array }),
+ covariance_matrix
};
}
-export { coarseGrainedFromIHM }
\ No newline at end of file
+function getChainSegments(asym_id: Column<string>) {
+ const offsets = [0];
+ for (let i = 1, _i = asym_id.rowCount; i < _i; i++) {
+ if (!asym_id.areValuesEqual(i - 1, i)) offsets[offsets.length] = i;
+ }
+
+ return Segmentation.ofOffsets(offsets, Interval.ofBounds(0, asym_id.rowCount));
+}
+
+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) };
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif/util.ts b/src/mol-model/structure/model/formats/mmcif/util.ts
index a03d511f5..1817e1c22 100644
--- a/src/mol-model/structure/model/formats/mmcif/util.ts
+++ b/src/mol-model/structure/model/formats/mmcif/util.ts
@@ -16,9 +16,9 @@ export function findEntityIdByAsymId(model: Model, asymId: string) {
}
export function findAtomIndexByLabelName(model: Model, residueIndex: number, atomName: string, altLoc: string | null) {
- const { segmentMap, segments } = model.hierarchy.residueSegments
+ const { segmentMap, segments } = model.atomicHierarchy.residueSegments
const idx = segmentMap[residueIndex]
- const { label_atom_id, label_alt_id } = model.hierarchy.atoms;
+ const { label_atom_id, label_alt_id } = model.atomicHierarchy.atoms;
for (let i = segments[idx], n = segments[idx + 1]; i <= n; ++i) {
if (label_atom_id.value(i) === atomName && (!altLoc || label_alt_id.value(i) === altLoc)) return i;
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index eb7d5024a..0a1725d48 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -9,10 +9,10 @@ import Format from './format'
import Sequence from './properties/sequence'
import { AtomicHierarchy, AtomicConformation } from './properties/atomic'
import { ModelSymmetry } from './properties/symmetry'
-import { CoarseGrainedHierarchy } from './properties/coarse-grained/hierarchy'
+import { CoarseHierarchy, CoarseConformation } from './properties/coarse'
import { Entities } from './properties/common';
-import from_gro from './formats/gro'
+//import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
/**
@@ -31,11 +31,11 @@ interface Model extends Readonly<{
entities: Entities,
sequence: Sequence,
- hierarchy: AtomicHierarchy,
- atomSiteConformation: AtomicConformation,
- coarseGrained: CoarseGrainedHierarchy,
+ atomicHierarchy: AtomicHierarchy,
+ atomicConformation: AtomicConformation,
- atomCount: number,
+ coarseHierarchy: CoarseHierarchy,
+ coarseConformation: CoarseConformation
}> {
} { }
@@ -43,22 +43,10 @@ interface Model extends Readonly<{
namespace Model {
export function create(format: Format) {
switch (format.kind) {
- case 'gro': return from_gro(format);
+ //case 'gro': return from_gro(format);
case 'mmCIF': return from_mmCIF(format);
}
}
- // export function spatialLookup(model: Model): GridLookup {
- // if (model['@spatialLookup']) return model['@spatialLookup']!;
- // const lookup = GridLookup(model.conformation);
- // model['@spatialLookup'] = lookup;
- // return lookup;
- // }
- // export function bonds(model: Model): Bonds {
- // if (model['@bonds']) return model['@bonds']!;
- // const bonds = computeBonds(model);
- // model['@bonds'] = bonds;
- // return bonds;
- // }
}
export default Model
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index 02ef4dd5d..fe50e990b 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -8,7 +8,6 @@ import { Column, Table } from 'mol-data/db'
import { Segmentation } from 'mol-data/int'
import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol} from '../../types'
-import { Keys } from '../common';
export const AtomsSchema = {
type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
@@ -52,9 +51,21 @@ export interface AtomicSegments {
chainSegments: Segmentation
}
-export interface AtomicKeys extends Keys {
+export interface AtomicKeys {
+ // indicate whether the keys form an increasing sequence and within each chain, sequence numbers
+ // are in increasing order.
+ // monotonous sequences enable for example faster secondary structure assignment.
+ isMonotonous: boolean,
+
// assign a key to each residue index.
- residueKey: Column<number>,
+ residueKey: ArrayLike<number>,
+ // assign a key to each chain index
+ chainKey: ArrayLike<number>,
+ // assigne a key to each chain index
+ // also index to the Entities table.
+ entityKey: ArrayLike<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/properties/coarse-grained/conformation.ts b/src/mol-model/structure/model/properties/coarse-grained/conformation.ts
deleted file mode 100644
index e69de29bb..000000000
diff --git a/src/mol-model/structure/model/properties/coarse-grained/hierarchy.ts b/src/mol-model/structure/model/properties/coarse-grained/hierarchy.ts
deleted file mode 100644
index 12dd042cd..000000000
--- a/src/mol-model/structure/model/properties/coarse-grained/hierarchy.ts
+++ /dev/null
@@ -1,53 +0,0 @@
-/**
- * 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'
-import { Tensor } from 'mol-math/linear-algebra';
-import { Column } from 'mol-data/db';
-
-interface CoarseGrainedHierarchy {
- isDefined: boolean,
- modelList: mmCIF['ihm_model_list'],
- spheres: CoarseGrainedHierarchy.Spheres,
- gaussians: CoarseGrainedHierarchy.Gaussians
-}
-
-namespace CoarseGrainedHierarchy {
- export const Empty: CoarseGrainedHierarchy = { isDefined: false } as any;
-
- export const enum ElementType { Sphere, Gaussian }
-
- export interface SiteBase {
- asym_id: string,
- seq_id_begin: number,
- seq_id_end: number
- }
-
- export interface Sphere extends SiteBase {
- radius: number,
- rmsf: number
- }
-
- export interface Gaussian extends SiteBase {
- weight: number,
- covariance_matrix: Tensor.Data
- }
-
- type Common = {
- count: number,
- x: ArrayLike<number>,
- y: ArrayLike<number>,
- z: ArrayLike<number>,
- modelKey: ArrayLike<number>,
- entityKey: ArrayLike<number>
- }
-
- export type SitesBase = Common & { [P in keyof SiteBase]: Column<SiteBase[P]> }
- export type Spheres = Common & { [P in keyof Sphere]: Column<Sphere[P]> }
- export type Gaussians = Common & { matrix_space: Tensor.Space } & { [P in keyof Gaussian]: Column<Gaussian[P]> }
-}
-
-export { CoarseGrainedHierarchy }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/coarse.ts b/src/mol-model/structure/model/properties/coarse.ts
new file mode 100644
index 000000000..d1fc3decf
--- /dev/null
+++ b/src/mol-model/structure/model/properties/coarse.ts
@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './coarse/conformation'
+export * from './coarse/hierarchy'
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/coarse/conformation.ts b/src/mol-model/structure/model/properties/coarse/conformation.ts
new file mode 100644
index 000000000..4298b80bd
--- /dev/null
+++ b/src/mol-model/structure/model/properties/coarse/conformation.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import UUID from 'mol-util/uuid'
+import { Mat3 } from 'mol-math/linear-algebra';
+
+export interface CoarseConformation {
+ id: UUID,
+ spheres: CoarseSphereConformation,
+ gaussians: CoarseGaussianConformation
+}
+
+export interface CoarseSphereConformation {
+ x: ArrayLike<number>,
+ y: ArrayLike<number>,
+ z: ArrayLike<number>,
+ radius: ArrayLike<number>,
+ rmsf: ArrayLike<number>
+}
+
+export interface CoarseGaussianConformation {
+ x: ArrayLike<number>,
+ y: ArrayLike<number>,
+ z: ArrayLike<number>,
+ weight: ArrayLike<number>,
+ covariance_matrix: ArrayLike<Mat3>
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/coarse/hierarchy.ts b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
new file mode 100644
index 000000000..fedb463c9
--- /dev/null
+++ b/src/mol-model/structure/model/properties/coarse/hierarchy.ts
@@ -0,0 +1,49 @@
+/**
+ * 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'
+import { Column } from 'mol-data/db'
+import { Segmentation } from 'mol-data/int';
+
+export interface CoarsedElementKeys {
+ // indicate whether the keys form an increasing sequence and within each chain, sequence numbers
+ // are in increasing order.
+ // monotonous sequences enable for example faster secondary structure assignment.
+ isMonotonous: boolean,
+
+ // assign a key to each element
+ 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>,
+
+ findChainKey(entityId: string, asym_id: string): number
+}
+
+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>,
+
+ chainSegments: Segmentation
+}
+
+export type CoarseElements = CoarsedElementKeys & CoarseElementData
+
+export interface CoarseHierarchy {
+ isDefined: boolean,
+ models: mmCIF['ihm_model_list'],
+ spheres: CoarseElements,
+ gaussians: CoarseElements
+}
+
+export namespace CoarseHierarchy {
+ export const Empty: CoarseHierarchy = { isDefined: false } as any;
+}
\ 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
index e70712cbb..9dadbc95a 100644
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -5,24 +5,8 @@
*/
import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
-import { Column } from 'mol-data/db';
export interface Entities {
data: mmCIF['entity'],
getEntityIndex(id: string): number
-}
-
-export interface Keys {
- // indicate whether the keys form an increasing sequence and within each chain, sequence numbers
- // are in increasing order.
- // monotonous sequences enable for example faster secondary structure assignment.
- isMonotonous: boolean,
-
- // assign a key to each chain index
- chainKey: Column<number>,
- // assigne a key to each chain index
- // also index to the Entities table.
- entityKey: Column<number>,
-
- findChainKey(entityId: string, label_asym_id: string): number
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/utils/hierarchy-keys.ts b/src/mol-model/structure/model/properties/utils/atomic-keys.ts
similarity index 90%
rename from src/mol-model/structure/model/utils/hierarchy-keys.ts
rename to src/mol-model/structure/model/properties/utils/atomic-keys.ts
index aabfe1b4a..1cfec2f03 100644
--- a/src/mol-model/structure/model/utils/hierarchy-keys.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-keys.ts
@@ -4,10 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-data/db'
-import { AtomicData, AtomicSegments, AtomicKeys } from '../properties/atomic'
+import { AtomicData, AtomicSegments, AtomicKeys } from '../atomic'
import { Interval, Segmentation } from 'mol-data/int'
-import { Entities } from '../properties/common';
+import { Entities } from '../common'
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
@@ -62,7 +61,7 @@ function missingEntity(k: string) {
throw new Error(`Missing entity entry for entity id '${k}'.`);
}
-function create(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicKeys {
+export function getAtomicKeys(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicKeys {
const { chains, residues } = data;
const chainMaps = new Map<number, Map<string, number>>(), chainCounter = { index: 0 };
@@ -110,12 +109,10 @@ function create(data: AtomicData, entities: Entities, segments: AtomicSegments):
return {
isMonotonous: isMonotonous && checkMonotonous(entityKey) && checkMonotonous(chainKey) && checkMonotonous(residueKey),
- residueKey: Column.ofIntArray(residueKey),
- chainKey: Column.ofIntArray(chainKey),
- entityKey: Column.ofIntArray(entityKey),
+ residueKey: residueKey,
+ chainKey: chainKey,
+ entityKey: entityKey,
findChainKey,
findResidueKey
};
-}
-
-export default create;
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
new file mode 100644
index 000000000..6ef72039a
--- /dev/null
+++ b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
@@ -0,0 +1,84 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Entities } from '../common';
+import { CoarseElementData, CoarsedElementKeys } from '../coarse';
+
+function getElementKey(map: Map<string, number>, key: string, counter: { index: number }) {
+ if (map.has(key)) return map.get(key)!;
+ const ret = counter.index++;
+ map.set(key, ret);
+ return ret;
+}
+
+function getElementSubstructureKeyMap(map: Map<number, Map<string, number>>, key: number) {
+ if (map.has(key)) return map.get(key)!;
+ const ret = new Map<string, number>();
+ map.set(key, ret);
+ return ret;
+}
+
+function createLookUp(entities: Entities, chain: Map<number, Map<string, number>>) {
+ const getEntKey = entities.getEntityIndex;
+ const findChainKey: CoarsedElementKeys['findChainKey'] = (e, c) => {
+ let eKey = getEntKey(e);
+ if (eKey < 0) return -1;
+ const cm = chain.get(eKey)!;
+ if (!cm.has(c)) return -1;
+ return cm.get(c)!;
+ }
+ return { findChainKey };
+}
+
+function checkMonotonous(xs: ArrayLike<number>) {
+ for (let i = 1, _i = xs.length; i < _i; i++) {
+ if (xs[i] < xs[i - 1]) {
+ return false;
+ }
+ }
+ return true;
+}
+
+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, count, chainSegments } = data;
+
+ 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++) {
+ const start = chainSegments.segments[cI], end = chainSegments.segments[cI + 1];
+ const map = getElementSubstructureKeyMap(chainMaps, entityKey[start]);
+ const key = getElementKey(map, asym_id.value(start), chainCounter);
+ for (let i = start; i < end; i++) chainKey[i] = key;
+ }
+
+ const { findChainKey } = createLookUp(entities, chainMaps);
+
+ return {
+ isMonotonous: checkMonotonous(entityKey) && checkMonotonous(chainKey),
+ chainKey: chainKey,
+ entityKey: entityKey,
+ modelKey: modelKey,
+ findChainKey
+ };
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/utils/guess-element.ts b/src/mol-model/structure/model/properties/utils/guess-element.ts
similarity index 100%
rename from src/mol-model/structure/model/utils/guess-element.ts
rename to src/mol-model/structure/model/properties/utils/guess-element.ts
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
index ac9df8509..01445a1da 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -80,8 +80,8 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const elements = unit.elements;
builder.beginUnit(unit.id);
- const chainsIt = Segmentation.transientSegments(unit.model.hierarchy.chainSegments, elements);
- const residuesIt = Segmentation.transientSegments(unit.model.hierarchy.residueSegments, elements);
+ const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainSegments, elements);
+ const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueSegments, elements);
while (chainsIt.hasNext) {
const chainSegment = chainsIt.move();
l.element = OrderedSet.getAt(elements, chainSegment.start);
@@ -174,8 +174,8 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
l.unit = unit;
const elements = unit.elements;
- const chainsIt = Segmentation.transientSegments(unit.model.hierarchy.chainSegments, elements);
- const residuesIt = Segmentation.transientSegments(unit.model.hierarchy.residueSegments, elements);
+ const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainSegments, elements);
+ const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueSegments, elements);
while (chainsIt.hasNext) {
const chainSegment = chainsIt.move();
l.element = OrderedSet.getAt(elements, chainSegment.start);
diff --git a/src/mol-model/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
index fc2a066ad..a4d4ad5b3 100644
--- a/src/mol-model/structure/query/properties.ts
+++ b/src/mol-model/structure/query/properties.ts
@@ -29,61 +29,61 @@ const atom = {
x: Element.property(l => l.unit.conformation.x(l.element)),
y: Element.property(l => l.unit.conformation.y(l.element)),
z: Element.property(l => l.unit.conformation.z(l.element)),
- id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomSiteConformation.atomId.value(l.element)),
- occupancy: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomSiteConformation.occupancy.value(l.element)),
- B_iso_or_equiv: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomSiteConformation.B_iso_or_equiv.value(l.element)),
+ id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.atomId.value(l.element)),
+ occupancy: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.occupancy.value(l.element)),
+ B_iso_or_equiv: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicConformation.B_iso_or_equiv.value(l.element)),
// Hierarchy
- type_symbol: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.atoms.type_symbol.value(l.element)),
- label_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.atoms.label_atom_id.value(l.element)),
- auth_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.atoms.auth_atom_id.value(l.element)),
- label_alt_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.atoms.label_alt_id.value(l.element)),
- pdbx_formal_charge: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.atoms.pdbx_formal_charge.value(l.element)),
+ type_symbol: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.type_symbol.value(l.element)),
+ label_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.label_atom_id.value(l.element)),
+ auth_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.auth_atom_id.value(l.element)),
+ label_alt_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.label_alt_id.value(l.element)),
+ pdbx_formal_charge: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.atoms.pdbx_formal_charge.value(l.element)),
// Derived
- vdw_radius: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : VdwRadius(l.unit.model.hierarchy.atoms.type_symbol.value(l.element))),
+ vdw_radius: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : VdwRadius(l.unit.model.atomicHierarchy.atoms.type_symbol.value(l.element))),
}
const residue = {
- key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residueKey.value(l.unit.residueIndex[l.element])),
-
- group_PDB: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.group_PDB.value(l.unit.residueIndex[l.element])),
- label_comp_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])),
- auth_comp_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.auth_comp_id.value(l.unit.residueIndex[l.element])),
- label_seq_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.label_seq_id.value(l.unit.residueIndex[l.element])),
- auth_seq_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.element])),
- pdbx_PDB_ins_code: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element]))
+ key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residueKey[l.unit.residueIndex[l.element]]),
+
+ group_PDB: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.group_PDB.value(l.unit.residueIndex[l.element])),
+ label_comp_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])),
+ auth_comp_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_comp_id.value(l.unit.residueIndex[l.element])),
+ label_seq_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.value(l.unit.residueIndex[l.element])),
+ auth_seq_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.element])),
+ pdbx_PDB_ins_code: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element]))
}
const chain = {
- key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.chainKey.value(l.unit.chainIndex[l.element])),
+ key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chainKey[l.unit.chainIndex[l.element]]),
- label_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.chains.label_asym_id.value(l.unit.chainIndex[l.element])),
- auth_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.chains.auth_asym_id.value(l.unit.chainIndex[l.element])),
- label_entity_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.chains.label_entity_id.value(l.unit.chainIndex[l.element]))
+ label_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chains.label_asym_id.value(l.unit.chainIndex[l.element])),
+ auth_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chains.auth_asym_id.value(l.unit.chainIndex[l.element])),
+ label_entity_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chains.label_entity_id.value(l.unit.chainIndex[l.element]))
}
-const coarse_grained = {
+const coarse = {
key: atom.key,
- modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.modelKey[l.element]),
- entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.entityKey[l.element]),
+ 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,
y: atom.y,
z: atom.z,
- asym_id: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.asym_id.value(l.element)),
- seq_id_begin: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.seq_id_begin.value(l.element)),
- seq_id_end: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.seq_id_end.value(l.element)),
+ asym_id: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element)),
+ seq_id_begin: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element)),
+ seq_id_end: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element)),
- sphere_radius: Element.property(l => !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.sites.radius.value(l.element)),
- sphere_rmsf: Element.property(l => !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.sites.rmsf.value(l.element)),
+ sphere_radius: Element.property(l => !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.coarseConformation.radius[l.element]),
+ sphere_rmsf: Element.property(l => !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.coarseConformation.rmsf[l.element]),
- gaussian_weight: Element.property(l => !Unit.isGaussians(l.unit) ? notCoarse('gaussians') : l.unit.sites.weight.value(l.element)),
- gaussian_covariance_matrix: Element.property(l => !Unit.isGaussians(l.unit) ? notCoarse('gaussians') : l.unit.sites.covariance_matrix.value(l.element))
+ gaussian_weight: Element.property(l => !Unit.isGaussians(l.unit) ? notCoarse('gaussians') : l.unit.coarseConformation.weight[l.element]),
+ gaussian_covariance_matrix: Element.property(l => !Unit.isGaussians(l.unit) ? notCoarse('gaussians') : l.unit.coarseConformation.covariance_matrix[l.element])
}
-function eK(l: Element.Location) { return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.hierarchy.entityKey.value(l.unit.chainIndex[l.element]); }
+function eK(l: Element.Location) { return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.entityKey[l.unit.chainIndex[l.element]]; }
const entity = {
key: eK,
@@ -112,7 +112,7 @@ const Properties = {
chain,
entity,
unit,
- coarse_grained
+ coarse
}
type Properties = typeof Properties
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index c2a2ecd38..efe4e8bde 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -13,6 +13,7 @@ import Element from './element'
import Unit from './unit'
import { StructureLookup3D } from './util/lookup3d';
import StructureSymmetry from './symmetry';
+import { CoarseElements } from '../model/properties/coarse';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -90,7 +91,7 @@ namespace Structure {
}
export function ofModel(model: Model): Structure {
- const chains = model.hierarchy.chainSegments;
+ const chains = model.atomicHierarchy.chainSegments;
const builder = new StructureBuilder();
for (let c = 0; c < chains.count; c++) {
@@ -98,21 +99,27 @@ namespace Structure {
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
}
- const cs = model.coarseGrained;
+ const cs = model.coarseHierarchy;
if (cs.isDefined) {
if (cs.spheres.count > 0) {
- const elements = SortedArray.ofBounds(0, cs.spheres.count);
- builder.addUnit(Unit.Kind.Spheres, model, SymmetryOperator.Default, elements);
+ addCoarseUnits(builder, model, model.coarseHierarchy.spheres, Unit.Kind.Spheres);
}
if (cs.gaussians.count > 0) {
- const elements = SortedArray.ofBounds(0, cs.spheres.count);
- builder.addUnit(Unit.Kind.Gaussians, model, SymmetryOperator.Default, elements);
+ addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, Unit.Kind.Gaussians);
}
}
return builder.getStructure();
}
+ function addCoarseUnits(builder: StructureBuilder, model: Model, elements: CoarseElements, kind: Unit.Kind) {
+ const { chainSegments } = elements;
+ for (let cI = 0; cI < chainSegments.count; cI++) {
+ const elements = SortedArray.ofBounds(chainSegments.segments[cI], chainSegments.segments[cI + 1]);
+ builder.addUnit(kind, model, SymmetryOperator.Default, elements);
+ }
+ }
+
export class StructureBuilder {
private units: Unit[] = [];
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 7ede3f8a7..4ea70f014 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -7,10 +7,10 @@
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { Model } from '../model'
import { GridLookup3D, Lookup3D } from 'mol-math/geometry'
-import { CoarseGrainedHierarchy } from '../model/properties/coarse-grained/hierarchy';
import { SortedArray } from 'mol-data/int';
import { idFactory } from 'mol-util/id-factory';
import { IntraUnitBonds, computeIntraUnitBonds } from './unit/bonds'
+import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -26,9 +26,9 @@ namespace Unit {
export function create(id: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: SortedArray): Unit {
switch (kind) {
- case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomSiteConformation));
- case Kind.Spheres: return createCoarse(id, unitIdFactory(), model, Kind.Spheres, model.coarseGrained.spheres, elements, SymmetryOperator.createMapping(operator, model.atomSiteConformation));
- case Kind.Gaussians: return createCoarse(id, unitIdFactory(), model, Kind.Gaussians, model.coarseGrained.gaussians, elements, SymmetryOperator.createMapping(operator, model.atomSiteConformation));
+ case Kind.Atomic: return new Atomic(id, unitIdFactory(), model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation));
+ case Kind.Spheres: return createCoarse(id, unitIdFactory(), model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres));
+ case Kind.Gaussians: return createCoarse(id, unitIdFactory(), model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians));
}
}
@@ -78,13 +78,13 @@ namespace Unit {
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomSiteConformation));
+ return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation));
}
private _lookup3d?: Lookup3D = void 0;
get lookup3d() {
if (this._lookup3d) return this._lookup3d;
- const { x, y, z } = this.model.atomSiteConformation;
+ const { x, y, z } = this.model.atomicConformation;
this._lookup3d = GridLookup3D({ x, y, z, indices: this.elements });
return this._lookup3d;
}
@@ -103,62 +103,64 @@ namespace Unit {
this.elements = elements;
this.conformation = conformation;
- this.residueIndex = model.hierarchy.residueSegments.segmentMap;
- this.chainIndex = model.hierarchy.chainSegments.segmentMap;
+ this.residueIndex = model.atomicHierarchy.residueSegments.segmentMap;
+ this.chainIndex = model.atomicHierarchy.chainSegments.segmentMap;
}
}
- // Coarse grained representations.
- export interface CoarseBase<S extends CoarseGrainedHierarchy.SitesBase> extends Base {
- readonly sites: S
- }
-
- class Coarse<S extends CoarseGrainedHierarchy.SitesBase> implements CoarseBase<S> {
- readonly kind: Kind;
+ class Coarse<K extends Kind.Gaussians | Kind.Spheres, C extends CoarseSphereConformation | CoarseGaussianConformation> implements Base {
+ readonly kind: K;
readonly id: number;
readonly invariantId: number;
readonly elements: SortedArray;
readonly model: Model;
readonly conformation: SymmetryOperator.ArrayMapping;
- readonly sites: S;
+
+ readonly coarseElements: CoarseElements;
+ readonly coarseConformation: C;
getChild(elements: SortedArray): Unit {
if (elements.length === this.elements.length) return this as any as Unit /** lets call this an ugly temporary hack */;
- return createCoarse(this.id, this.invariantId, this.model, this.kind, this.sites, elements, this.conformation);
+ return createCoarse(this.id, this.invariantId, this.model, this.kind, elements, this.conformation);
}
applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
- return createCoarse(id, this.invariantId, this.model, this.kind, this.sites, this.elements, SymmetryOperator.createMapping(op, this.sites));
+ return createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseElements()));
}
private _lookup3d?: Lookup3D = void 0;
get lookup3d() {
if (this._lookup3d) return this._lookup3d;
- const { x, y, z } = this.sites;
- // TODO: support sphere radius
+ const { x, y, z } = this.getCoarseElements();
+ // TODO: support sphere radius?
this._lookup3d = GridLookup3D({ x, y, z, indices: this.elements });
return this._lookup3d;
}
- constructor(id: number, invariantId: number, model: Model, kind: Kind, sites: S, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
+ private getCoarseElements() {
+ return this.kind === Kind.Spheres ? this.model.coarseConformation.spheres : this.model.coarseConformation.gaussians;
+ }
+
+ constructor(id: number, invariantId: number, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping) {
this.kind = kind;
this.id = id;
this.invariantId = invariantId;
this.model = model;
this.elements = elements;
this.conformation = conformation;
- this.sites = sites;
+ this.coarseElements = kind === Kind.Spheres ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
+ this.coarseConformation = (kind === Kind.Spheres ? model.coarseConformation.spheres : model.coarseConformation.gaussians) as C;
}
}
- function createCoarse<S extends CoarseGrainedHierarchy.SitesBase>(id: number, invariantId: number, model: Model, kind: Kind, sites: S, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping): Unit {
- return new Coarse(id, invariantId, model, kind, sites, elements, conformation) as any as Unit /** lets call this an ugly temporary hack */;
+ function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, model: Model, kind: K, elements: SortedArray, conformation: SymmetryOperator.ArrayMapping): Unit {
+ return new Coarse(id, invariantId, model, kind, elements, conformation) as any as Unit /** lets call this an ugly temporary hack */;
}
- export interface Spheres extends CoarseBase<CoarseGrainedHierarchy.Spheres> { kind: Kind.Spheres }
- export interface Gaussians extends CoarseBase<CoarseGrainedHierarchy.Gaussians> { kind: Kind.Gaussians }
+ export class Spheres extends Coarse<Kind.Spheres, CoarseSphereConformation> { }
+ export class Gaussians extends Coarse<Kind.Gaussians, CoarseGaussianConformation> { }
}
export default Unit;
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 2d8f9af02..9cd4a9ed1 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -109,11 +109,11 @@ function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[],
function _computeBonds(unit: Unit.Atomic, params: BondComputationParameters): IntraUnitBonds {
const MAX_RADIUS = 3;
- const { x, y, z } = unit.model.atomSiteConformation;
+ const { x, y, z } = unit.model.atomicConformation;
const atomCount = unit.elements.length;
const { elements: atoms, residueIndex } = unit;
- const { type_symbol, label_atom_id, label_alt_id } = unit.model.hierarchy.atoms;
- const { label_comp_id } = unit.model.hierarchy.residues;
+ const { type_symbol, label_atom_id, label_alt_id } = unit.model.atomicHierarchy.atoms;
+ const { label_comp_id } = unit.model.atomicHierarchy.residues;
const query3d = unit.lookup3d;
const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.create(unit.model) : void 0
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 4070cca0b..92831adec 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -371,7 +371,7 @@ export namespace PropertyAccess {
// return;
console.log('bs', baseline(models[0]));
- console.log('sp', sumProperty(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
+ console.log('sp', sumProperty(structures[0], l => l.unit.model.atomicConformation.atomId.value(l.element)));
//console.log(sumPropertySegmented(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
//console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.element));
@@ -418,7 +418,7 @@ export namespace PropertyAccess {
console.log(Selection.structureCount(q2r));
//console.log(q1(structures[0]));
- const col = models[0].atomSiteConformation.atomId.value;
+ const col = models[0].atomicConformation.atomId.value;
const suite = new B.Suite();
suite
//.add('test q', () => q1(structures[0]))
--
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