From c1d54facc6d37c341bd752cae71156016c519606 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 26 Jun 2018 11:30:14 +0200
Subject: [PATCH] moved Queries.props to StructureProperies, wip custom props
---
src/apps/structure-info/model.ts | 4 +-
.../ui/visualization/sequence-view.tsx | 6 +-
src/mol-geo/representation/structure/index.ts | 6 +-
src/mol-geo/theme/structure/color/chain-id.ts | 10 +-
src/mol-geo/theme/structure/size/physical.ts | 6 +-
.../structure/export/categories/atom_site.ts | 54 ++++
.../export/categories/chem_comp_bond.ts | 7 +
src/mol-model/structure/export/mmcif.ts | 60 +---
.../structure/model/formats/mmcif/assembly.ts | 5 +-
.../structure/model/formats/mmcif/bonds.ts | 273 +-----------------
.../model/formats/mmcif/bonds/comp.ts | 93 ++++++
.../model/formats/mmcif/bonds/struct_conn.ts | 192 ++++++++++++
src/mol-model/structure/query.ts | 2 -
src/mol-model/structure/query/generators.ts | 3 +-
src/mol-model/structure/query/predicates.ts | 3 +-
src/mol-model/structure/query/properties.ts | 118 +-------
src/mol-model/structure/structure.ts | 3 +-
.../structure/structure/properties.ts | 126 ++++++++
.../structure/structure/structure.ts | 14 +-
src/mol-view/label.ts | 18 +-
src/perf-tests/structure.ts | 24 +-
src/servers/model/server/api.ts | 20 +-
22 files changed, 543 insertions(+), 504 deletions(-)
create mode 100644 src/mol-model/structure/export/categories/atom_site.ts
create mode 100644 src/mol-model/structure/export/categories/chem_comp_bond.ts
create mode 100644 src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
create mode 100644 src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
create mode 100644 src/mol-model/structure/structure/properties.ts
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index d63913dca..d1252937c 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -10,7 +10,7 @@ require('util.promisify').shim();
// import { Table } from 'mol-data/db'
import { CifFrame } from 'mol-io/reader/cif'
-import { Model, Structure, Element, Unit, Queries, Format } from 'mol-model/structure'
+import { Model, Structure, Element, Unit, Format, StructureProperties } from 'mol-model/structure'
// import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
import { Table } from 'mol-data/db';
@@ -166,7 +166,7 @@ export function printUnits(structure: Structure) {
} else if (Unit.isCoarse(l.unit)) {
console.log(`Coarse unit ${unit.id} ${unit.conformation.operator.name} (${Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
- const props = Queries.props.coarse;
+ const props = StructureProperties.coarse;
const seq = l.unit.model.sequence;
for (let j = 0, _j = Math.min(size, 3); j < _j; j++) {
diff --git a/src/mol-app/ui/visualization/sequence-view.tsx b/src/mol-app/ui/visualization/sequence-view.tsx
index 520505ca2..6025eea22 100644
--- a/src/mol-app/ui/visualization/sequence-view.tsx
+++ b/src/mol-app/ui/visualization/sequence-view.tsx
@@ -7,7 +7,7 @@
import * as React from 'react'
import { View } from '../view';
import { SequenceViewController } from '../../controller/visualization/sequence-view';
-import { Structure, StructureSequence, Queries, Selection } from 'mol-model/structure';
+import { Structure, StructureSequence, Queries, Selection, StructureProperties } from 'mol-model/structure';
import { Context } from '../../context/context';
import { InteractivityEvents } from '../../event/basic';
import { SyncRuntimeContext } from 'mol-task/execution/synchronous';
@@ -27,8 +27,8 @@ export class SequenceView extends View<SequenceViewController, {}, {}> {
function createQuery(entityId: string, label_seq_id: number) {
return Queries.generators.atoms({
- entityTest: l => Queries.props.entity.id(l) === entityId,
- residueTest: l => Queries.props.residue.label_seq_id(l) === label_seq_id
+ entityTest: l => StructureProperties.entity.id(l) === entityId,
+ residueTest: l => StructureProperties.residue.label_seq_id(l) === label_seq_id
});
}
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 9d46deebc..fd8340667 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Structure, StructureSymmetry, Unit } from 'mol-model/structure';
+import { Structure, Unit } from 'mol-model/structure';
import { Task } from 'mol-task'
import { RenderObject } from 'mol-gl/render-object';
import { Representation, RepresentationProps, Visual } from '..';
@@ -43,7 +43,7 @@ export function StructureRepresentation<P extends StructureProps>(unitsVisualCto
return Task.create('Creating StructureRepresentation', async ctx => {
if (!_structure) {
- _groups = structure.symmetryGroups;
+ _groups = structure.unitSymmetryGroups;
for (let i = 0; i < _groups.length; i++) {
const group = _groups[i];
const visual = unitsVisualCtor()
@@ -59,7 +59,7 @@ export function StructureRepresentation<P extends StructureProps>(unitsVisualCto
if (_structure.hashCode === structure.hashCode) {
await update(_props)
} else {
- _groups = structure.symmetryGroups;
+ _groups = structure.unitSymmetryGroups;
const newGroups: Unit.SymmetryGroup[] = []
const oldUnitsVisuals = unitsVisuals
unitsVisuals = new Map()
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index 4c4b9687f..7afe56c46 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, Queries, Element } from 'mol-model/structure';
+import { Unit, StructureProperties, Element } from 'mol-model/structure';
import { StructureColorDataProps } from '.';
import { ColorData, createElementColor } from '../../../util/color-data';
@@ -49,9 +49,9 @@ export function chainIdColorData(props: StructureColorDataProps, locationFn: (l:
let asym_id: Element.Property<string>
if (Unit.isAtomic(unit)) {
- asym_id = Queries.props.chain.label_asym_id
+ asym_id = StructureProperties.chain.label_asym_id
} else if (Unit.isCoarse(unit)) {
- asym_id = Queries.props.coarse.asym_id
+ asym_id = StructureProperties.coarse.asym_id
} else {
throw new Error('unhandled unit kind')
}
@@ -92,9 +92,9 @@ export function chainIdElementColorData(props: StructureColorDataProps, colorDat
// let asym_id: Element.Property<string>
// if (Unit.isAtomic(unit)) {
- // asym_id = Queries.props.chain.label_asym_id
+ // asym_id = StructureProperties.chain.label_asym_id
// } else if (Unit.isCoarse(unit)) {
- // asym_id = Queries.props.coarse.asym_id
+ // asym_id = StructureProperties.coarse.asym_id
// }
// const l = Element.Location()
diff --git a/src/mol-geo/theme/structure/size/physical.ts b/src/mol-geo/theme/structure/size/physical.ts
index 84be4d339..34ac86d0d 100644
--- a/src/mol-geo/theme/structure/size/physical.ts
+++ b/src/mol-geo/theme/structure/size/physical.ts
@@ -4,15 +4,15 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Element, Unit, Queries } from 'mol-model/structure';
+import { Element, Unit, StructureProperties } from 'mol-model/structure';
import { StructureSizeDataProps } from '.';
import { createAttributeSize } from '../../../util/size-data';
export function getPhysicalRadius(unit: Unit): Element.Property<number> {
if (Unit.isAtomic(unit)) {
- return Queries.props.atom.vdw_radius
+ return StructureProperties.atom.vdw_radius
} else if (Unit.isSpheres(unit)) {
- return Queries.props.coarse.sphere_radius
+ return StructureProperties.coarse.sphere_radius
} else {
return () => 0
}
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
new file mode 100644
index 000000000..7ee771645
--- /dev/null
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -0,0 +1,54 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CifWriter } from 'mol-io/writer/cif';
+import { Element, Structure, StructureProperties as P } from '../../structure';
+import { CifExportContext } from '../mmcif';
+import CifField = CifWriter.Field
+import CifCategory = CifWriter.Category
+import E = CifWriter.Encodings
+
+const atom_site_fields: CifField<Element.Location>[] = [
+ CifField.str('group_PDB', P.residue.group_PDB),
+ CifField.int('id', P.atom.id, { encoder: E.deltaRLE }),
+ CifField.str('type_symbol', P.atom.type_symbol as any),
+ CifField.str('label_atom_id', P.atom.label_atom_id),
+ CifField.str('label_alt_id', P.atom.label_alt_id),
+
+ CifField.str('label_comp_id', P.residue.label_comp_id),
+ CifField.int('label_seq_id', P.residue.label_seq_id, { encoder: E.deltaRLE }),
+ CifField.str('pdbx_PDB_ins_code', P.residue.pdbx_PDB_ins_code),
+
+ CifField.str('label_asym_id', P.chain.label_asym_id),
+ CifField.str('label_entity_id', P.chain.label_entity_id),
+
+ CifField.float('Cartn_x', P.atom.x, { digitCount: 3, encoder: E.fixedPoint3 }),
+ CifField.float('Cartn_y', P.atom.y, { digitCount: 3, encoder: E.fixedPoint3 }),
+ CifField.float('Cartn_z', P.atom.z, { digitCount: 3, encoder: E.fixedPoint3 }),
+ CifField.float('occupancy', P.atom.occupancy, { digitCount: 2, encoder: E.fixedPoint2 }),
+ CifField.int('pdbx_formal_charge', P.atom.pdbx_formal_charge, { encoder: E.deltaRLE }),
+
+ CifField.str('auth_atom_id', P.atom.auth_atom_id),
+ CifField.str('auth_comp_id', P.residue.auth_comp_id),
+ CifField.int('auth_seq_id', P.residue.auth_seq_id, { encoder: E.deltaRLE }),
+ CifField.str('auth_asym_id', P.chain.auth_asym_id),
+
+ CifField.int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE }),
+ CifField.str<Element.Location, Structure>('operator_name', P.unit.operator_name, {
+ shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
+ })
+];
+
+export function _atom_site({ structure }: CifExportContext): CifCategory {
+ return {
+ data: structure,
+ name: 'atom_site',
+ fields: atom_site_fields,
+ rowCount: structure.elementCount,
+ keys: () => structure.elementLocations()
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/categories/chem_comp_bond.ts b/src/mol-model/structure/export/categories/chem_comp_bond.ts
new file mode 100644
index 000000000..66298c566
--- /dev/null
+++ b/src/mol-model/structure/export/categories/chem_comp_bond.ts
@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index bf93893f0..4458ef154 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -7,52 +7,18 @@
import { CifWriter } from 'mol-io/writer/cif'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif'
-import { Structure, Element } from '../structure'
+import { Structure } from '../structure'
import { Model } from '../model'
-import P from '../query/properties'
+import { _atom_site } from './categories/atom_site';
export interface CifExportContext {
structure: Structure,
model: Model
}
-import CifField = CifWriter.Field
import CifCategory = CifWriter.Category
-import E = CifWriter.Encodings
-
-const atom_site_fields: CifField<Element.Location>[] = [
- CifField.str('group_PDB', P.residue.group_PDB),
- CifField.int('id', P.atom.id, { encoder: E.deltaRLE }),
- CifField.str('type_symbol', P.atom.type_symbol as any),
- CifField.str('label_atom_id', P.atom.label_atom_id),
- CifField.str('label_alt_id', P.atom.label_alt_id),
-
- CifField.str('label_comp_id', P.residue.label_comp_id),
- CifField.int('label_seq_id', P.residue.label_seq_id, { encoder: E.deltaRLE }),
- CifField.str('pdbx_PDB_ins_code', P.residue.pdbx_PDB_ins_code),
-
- CifField.str('label_asym_id', P.chain.label_asym_id),
- CifField.str('label_entity_id', P.chain.label_entity_id),
-
- CifField.float('Cartn_x', P.atom.x, { digitCount: 3, encoder: E.fixedPoint3 }),
- CifField.float('Cartn_y', P.atom.y, { digitCount: 3, encoder: E.fixedPoint3 }),
- CifField.float('Cartn_z', P.atom.z, { digitCount: 3, encoder: E.fixedPoint3 }),
- CifField.float('occupancy', P.atom.occupancy, { digitCount: 2, encoder: E.fixedPoint2 }),
- CifField.int('pdbx_formal_charge', P.atom.pdbx_formal_charge, { encoder: E.deltaRLE }),
-
- CifField.str('auth_atom_id', P.atom.auth_atom_id),
- CifField.str('auth_comp_id', P.residue.auth_comp_id),
- CifField.int('auth_seq_id', P.residue.auth_seq_id, { encoder: E.deltaRLE }),
- CifField.str('auth_asym_id', P.chain.auth_asym_id),
-
- CifField.int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE }),
- CifField.str<Element.Location, Structure>('operator_name', P.unit.operator_name, {
- shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
- })
-];
-
-function copy_mmCif_cat(name: keyof mmCIF_Schema) {
+function copy_mmCif_category(name: keyof mmCIF_Schema) {
return ({ model }: CifExportContext) => {
if (model.sourceData.kind !== 'mmCIF') return CifCategory.Empty;
const table = model.sourceData.data[name];
@@ -66,27 +32,15 @@ function _entity({ model, structure }: CifExportContext): CifCategory {
return CifCategory.ofTable('entity', model.entities.data, keys);
}
-function _atom_site({ structure }: CifExportContext): CifCategory {
- return {
- data: structure,
- name: 'atom_site',
- fields: atom_site_fields,
- rowCount: structure.elementCount,
- keys: () => structure.elementLocations()
- }
-}
-
const Categories = [
- copy_mmCif_cat('entry'),
- copy_mmCif_cat('exptl'),
- copy_mmCif_cat('cell'),
- copy_mmCif_cat('symmetry'),
+ copy_mmCif_category('entry'),
+ copy_mmCif_category('exptl'),
+ copy_mmCif_category('cell'),
+ copy_mmCif_category('symmetry'),
_entity,
_atom_site
];
-mmCIF_Schema
-
namespace _Filters {
export const AtomSitePositionsFieldNames = new Set<string>(<(keyof typeof mmCIF_Schema.atom_site)[]>['id', 'Cartn_x', 'Cartn_y', 'Cartn_z']);
}
diff --git a/src/mol-model/structure/model/formats/mmcif/assembly.ts b/src/mol-model/structure/model/formats/mmcif/assembly.ts
index 48720596c..c86abd27c 100644
--- a/src/mol-model/structure/model/formats/mmcif/assembly.ts
+++ b/src/mol-model/structure/model/formats/mmcif/assembly.ts
@@ -11,6 +11,7 @@ import { Assembly, OperatorGroup, OperatorGroups } from '../../properties/symmet
import { Queries as Q, Query } from '../../../query'
import mmCIF_Format = Format.mmCIF
+import { StructureProperties } from '../../../structure';
export function createAssemblies(format: mmCIF_Format): ReadonlyArray<Assembly> {
const { pdbx_struct_assembly } = format.data;
@@ -58,8 +59,8 @@ function operatorGroupsProvider(generators: Generator[], matrices: Matrices): ()
const operatorNames = expandOperators(operatorList);
const operators = getAssemblyOperators(matrices, operatorNames, operatorOffset);
const selector = Query(Q.generators.atoms({ chainTest: Q.pred.and(
- Q.pred.eq(Q.props.unit.operator_name, SymmetryOperator.DefaultName),
- Q.pred.inSet(Q.props.chain.label_asym_id, gen.asymIds)
+ Q.pred.eq(StructureProperties.unit.operator_name, SymmetryOperator.DefaultName),
+ Q.pred.inSet(StructureProperties.chain.label_asym_id, gen.asymIds)
)}));
groups[groups.length] = { selector, operators };
operatorOffset += operators.length;
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds.ts b/src/mol-model/structure/model/formats/mmcif/bonds.ts
index 873ccda96..0f6997023 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds.ts
@@ -5,274 +5,5 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import Model from '../../model'
-import { Element } from '../../../structure'
-import { LinkType } from '../../types'
-import { findEntityIdByAsymId, findAtomIndexByLabelName } from './util'
-import { Column } from 'mol-data/db'
-
-// TODO: add dynamic property descriptor for this?
-
-export interface StructConn {
- getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry>
- getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry>
-}
-
-export interface ComponentBond {
- entries: Map<string, ComponentBond.Entry>
-}
-
-export namespace StructConn {
- function _resKey(rA: number, rB: number) {
- if (rA < rB) return `${rA}-${rB}`;
- return `${rB}-${rA}`;
- }
- const _emptyEntry: Entry[] = [];
-
- class StructConnImpl implements StructConn {
- private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
- private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
-
- private getResiduePairIndex() {
- if (this._residuePairIndex) return this._residuePairIndex;
- this._residuePairIndex = new Map();
- for (const e of this.entries) {
- const ps = e.partners;
- const l = ps.length;
- for (let i = 0; i < l - 1; i++) {
- for (let j = i + i; j < l; j++) {
- const key = _resKey(ps[i].residueIndex, ps[j].residueIndex);
- if (this._residuePairIndex.has(key)) {
- this._residuePairIndex.get(key)!.push(e);
- } else {
- this._residuePairIndex.set(key, [e]);
- }
- }
- }
- }
- return this._residuePairIndex;
- }
-
- private getAtomIndex() {
- if (this._atomIndex) return this._atomIndex;
- this._atomIndex = new Map();
- for (const e of this.entries) {
- for (const p of e.partners) {
- const key = p.atomIndex;
- if (this._atomIndex.has(key)) {
- this._atomIndex.get(key)!.push(e);
- } else {
- this._atomIndex.set(key, [e]);
- }
- }
- }
- return this._atomIndex;
- }
-
-
- getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry> {
- return this.getResiduePairIndex().get(_resKey(residueAIndex, residueBIndex)) || _emptyEntry;
- }
-
- getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry> {
- return this.getAtomIndex().get(atomIndex) || _emptyEntry;
- }
-
- constructor(public entries: StructConn.Entry[]) {
- }
- }
-
- export interface Entry {
- distance: number,
- order: number,
- flags: number,
- partners: { residueIndex: number, atomIndex: Element, symmetry: string }[]
- }
-
- type StructConnType =
- | 'covale'
- | 'covale_base'
- | 'covale_phosphate'
- | 'covale_sugar'
- | 'disulf'
- | 'hydrog'
- | 'metalc'
- | 'mismat'
- | 'modres'
- | 'saltbr'
-
- export const PropName = '__StructConn__';
- export function fromModel(model: Model): StructConn | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
-
- if (model.sourceData.kind !== 'mmCIF') return;
- const { struct_conn } = model.sourceData.data;
- if (!struct_conn._rowCount) return void 0;
-
- const { conn_type_id, pdbx_dist_value, pdbx_value_order } = struct_conn;
- const p1 = {
- label_asym_id: struct_conn.ptnr1_label_asym_id,
- label_comp_id: struct_conn.ptnr1_label_comp_id,
- label_seq_id: struct_conn.ptnr1_label_seq_id,
- label_atom_id: struct_conn.ptnr1_label_atom_id,
- label_alt_id: struct_conn.pdbx_ptnr1_label_alt_id,
- ins_code: struct_conn.pdbx_ptnr1_PDB_ins_code,
- symmetry: struct_conn.ptnr1_symmetry
- };
- const p2: typeof p1 = {
- label_asym_id: struct_conn.ptnr2_label_asym_id,
- label_comp_id: struct_conn.ptnr2_label_comp_id,
- label_seq_id: struct_conn.ptnr2_label_seq_id,
- label_atom_id: struct_conn.ptnr2_label_atom_id,
- label_alt_id: struct_conn.pdbx_ptnr2_label_alt_id,
- ins_code: struct_conn.pdbx_ptnr2_PDB_ins_code,
- symmetry: struct_conn.ptnr2_symmetry
- };
-
- 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.atomicHierarchy.findResidueKey(
- findEntityIdByAsymId(model, asymId),
- ps.label_comp_id.value(row),
- asymId,
- ps.label_seq_id.value(row),
- ps.ins_code.value(row)
- );
- if (residueIndex < 0) return void 0;
- const atomName = ps.label_atom_id.value(row);
- // turns out "mismat" records might not have atom name value
- if (!atomName) return void 0;
- const atomIndex = findAtomIndexByLabelName(model, residueIndex, atomName, ps.label_alt_id.value(row));
- if (atomIndex < 0) return void 0;
- return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) || '1_555' };
- }
-
- const _ps = (row: number) => {
- const ret = [];
- let p = _p(row, p1);
- if (p) ret.push(p);
- p = _p(row, p2);
- if (p) ret.push(p);
- return ret;
- }
-
- const entries: StructConn.Entry[] = [];
- for (let i = 0; i < struct_conn._rowCount; i++) {
- const partners = _ps(i);
- if (partners.length < 2) continue;
-
- const type = conn_type_id.value(i)! as StructConnType;
- const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
- let flags = LinkType.Flag.None;
- let order = 1;
-
- switch (orderType) {
- case 'sing': order = 1; break;
- case 'doub': order = 2; break;
- case 'trip': order = 3; break;
- case 'quad': order = 4; break;
- }
-
- switch (type) {
- case 'covale':
- case 'covale_base':
- case 'covale_phosphate':
- case 'covale_sugar':
- case 'modres':
- flags = LinkType.Flag.Covalent;
- break;
- case 'disulf': flags = LinkType.Flag.Covalent | LinkType.Flag.Sulfide; break;
- case 'hydrog': flags = LinkType.Flag.Hydrogen; break;
- case 'metalc': flags = LinkType.Flag.MetallicCoordination; break;
- case 'saltbr': flags = LinkType.Flag.Ion; break;
- }
-
- entries.push({ flags, order, distance: pdbx_dist_value.value(i), partners });
- }
-
- const ret = new StructConnImpl(entries);
- model._staticPropertyData[PropName] = ret;
- return ret;
- }
-}
-
-export namespace ComponentBond {
- export class ComponentBondImpl implements ComponentBond {
- entries: Map<string, ComponentBond.Entry> = new Map();
-
- addEntry(id: string) {
- let e = new Entry(id);
- this.entries.set(id, e);
- return e;
- }
- }
-
- export class Entry implements Entry {
- map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
-
- add(a: string, b: string, order: number, flags: number, swap = true) {
- let e = this.map.get(a);
- if (e !== void 0) {
- let f = e.get(b);
- if (f === void 0) {
- e.set(b, { order, flags });
- }
- } else {
- let map = new Map<string, { order: number, flags: number }>();
- map.set(b, { order, flags });
- this.map.set(a, map);
- }
-
- if (swap) this.add(b, a, order, flags, false);
- }
-
- constructor(public id: string) {
- }
- }
-
- export const PropName = '__ComponentBond__';
- export function fromModel(model: Model): ComponentBond | undefined {
- if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
-
- if (model.sourceData.kind !== 'mmCIF') return
- const { chem_comp_bond } = model.sourceData.data;
- if (!chem_comp_bond._rowCount) return void 0;
-
- let compBond = new ComponentBondImpl();
-
- const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount: rowCount } = chem_comp_bond;
-
- let entry = compBond.addEntry(comp_id.value(0)!);
-
- for (let i = 0; i < rowCount; i++) {
-
- const id = comp_id.value(i)!;
- const nameA = atom_id_1.value(i)!;
- const nameB = atom_id_2.value(i)!;
- const order = value_order.value(i)!;
- const aromatic = pdbx_aromatic_flag.value(i) === 'Y';
-
- if (entry.id !== id) {
- entry = compBond.addEntry(id);
- }
-
- let flags: number = LinkType.Flag.Covalent;
- let ord = 1;
- if (aromatic) flags |= LinkType.Flag.Aromatic;
- switch (order.toLowerCase()) {
- case 'doub':
- case 'delo':
- ord = 2;
- break;
- case 'trip': ord = 3; break;
- case 'quad': ord = 4; break;
- }
-
- entry.add(nameA, nameB, ord, flags);
- }
-
- model._staticPropertyData[PropName] = compBond;
- return compBond;
- }
-}
\ No newline at end of file
+export * from './bonds/comp'
+export * from './bonds/struct_conn'
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
new file mode 100644
index 000000000..4b31456ab
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
@@ -0,0 +1,93 @@
+/**
+ * Copyright (c) 2017-2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import Model from '../../../model'
+import { LinkType } from '../../../types'
+
+export interface ComponentBond {
+ entries: Map<string, ComponentBond.Entry>
+}
+
+export namespace ComponentBond {
+ export class ComponentBondImpl implements ComponentBond {
+ entries: Map<string, ComponentBond.Entry> = new Map();
+
+ addEntry(id: string) {
+ let e = new Entry(id);
+ this.entries.set(id, e);
+ return e;
+ }
+ }
+
+ export class Entry implements Entry {
+ map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
+
+ add(a: string, b: string, order: number, flags: number, swap = true) {
+ let e = this.map.get(a);
+ if (e !== void 0) {
+ let f = e.get(b);
+ if (f === void 0) {
+ e.set(b, { order, flags });
+ }
+ } else {
+ let map = new Map<string, { order: number, flags: number }>();
+ map.set(b, { order, flags });
+ this.map.set(a, map);
+ }
+
+ if (swap) this.add(b, a, order, flags, false);
+ }
+
+ constructor(public id: string) {
+ }
+ }
+
+ export const PropName = '__ComponentBond__';
+ export function fromModel(model: Model): ComponentBond | undefined {
+ if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
+
+ if (model.sourceData.kind !== 'mmCIF') return
+ const { chem_comp_bond } = model.sourceData.data;
+ if (!chem_comp_bond._rowCount) return void 0;
+
+ let compBond = new ComponentBondImpl();
+
+ const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount: rowCount } = chem_comp_bond;
+
+ let entry = compBond.addEntry(comp_id.value(0)!);
+
+ for (let i = 0; i < rowCount; i++) {
+
+ const id = comp_id.value(i)!;
+ const nameA = atom_id_1.value(i)!;
+ const nameB = atom_id_2.value(i)!;
+ const order = value_order.value(i)!;
+ const aromatic = pdbx_aromatic_flag.value(i) === 'Y';
+
+ if (entry.id !== id) {
+ entry = compBond.addEntry(id);
+ }
+
+ let flags: number = LinkType.Flag.Covalent;
+ let ord = 1;
+ if (aromatic) flags |= LinkType.Flag.Aromatic;
+ switch (order.toLowerCase()) {
+ case 'doub':
+ case 'delo':
+ ord = 2;
+ break;
+ case 'trip': ord = 3; break;
+ case 'quad': ord = 4; break;
+ }
+
+ entry.add(nameA, nameB, ord, flags);
+ }
+
+ model._staticPropertyData[PropName] = compBond;
+ return compBond;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
new file mode 100644
index 000000000..d0c0e5f07
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
@@ -0,0 +1,192 @@
+/**
+ * Copyright (c) 2017-2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import Model from '../../../model'
+import { Element } from '../../../../structure'
+import { LinkType } from '../../../types'
+import { findEntityIdByAsymId, findAtomIndexByLabelName } from '../util'
+import { Column } from 'mol-data/db'
+
+export interface StructConn {
+ getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry>
+ getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry>
+}
+
+export namespace StructConn {
+ function _resKey(rA: number, rB: number) {
+ if (rA < rB) return `${rA}-${rB}`;
+ return `${rB}-${rA}`;
+ }
+ const _emptyEntry: Entry[] = [];
+
+ class StructConnImpl implements StructConn {
+ private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
+ private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
+
+ private getResiduePairIndex() {
+ if (this._residuePairIndex) return this._residuePairIndex;
+ this._residuePairIndex = new Map();
+ for (const e of this.entries) {
+ const ps = e.partners;
+ const l = ps.length;
+ for (let i = 0; i < l - 1; i++) {
+ for (let j = i + i; j < l; j++) {
+ const key = _resKey(ps[i].residueIndex, ps[j].residueIndex);
+ if (this._residuePairIndex.has(key)) {
+ this._residuePairIndex.get(key)!.push(e);
+ } else {
+ this._residuePairIndex.set(key, [e]);
+ }
+ }
+ }
+ }
+ return this._residuePairIndex;
+ }
+
+ private getAtomIndex() {
+ if (this._atomIndex) return this._atomIndex;
+ this._atomIndex = new Map();
+ for (const e of this.entries) {
+ for (const p of e.partners) {
+ const key = p.atomIndex;
+ if (this._atomIndex.has(key)) {
+ this._atomIndex.get(key)!.push(e);
+ } else {
+ this._atomIndex.set(key, [e]);
+ }
+ }
+ }
+ return this._atomIndex;
+ }
+
+
+ getResidueEntries(residueAIndex: number, residueBIndex: number): ReadonlyArray<StructConn.Entry> {
+ return this.getResiduePairIndex().get(_resKey(residueAIndex, residueBIndex)) || _emptyEntry;
+ }
+
+ getAtomEntries(atomIndex: number): ReadonlyArray<StructConn.Entry> {
+ return this.getAtomIndex().get(atomIndex) || _emptyEntry;
+ }
+
+ constructor(public entries: StructConn.Entry[]) {
+ }
+ }
+
+ export interface Entry {
+ distance: number,
+ order: number,
+ flags: number,
+ partners: { residueIndex: number, atomIndex: Element, symmetry: string }[]
+ }
+
+ type StructConnType =
+ | 'covale'
+ | 'covale_base'
+ | 'covale_phosphate'
+ | 'covale_sugar'
+ | 'disulf'
+ | 'hydrog'
+ | 'metalc'
+ | 'mismat'
+ | 'modres'
+ | 'saltbr'
+
+ export const PropName = '__StructConn__';
+ export function fromModel(model: Model): StructConn | undefined {
+ if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName];
+
+ if (model.sourceData.kind !== 'mmCIF') return;
+ const { struct_conn } = model.sourceData.data;
+ if (!struct_conn._rowCount) return void 0;
+
+ const { conn_type_id, pdbx_dist_value, pdbx_value_order } = struct_conn;
+ const p1 = {
+ label_asym_id: struct_conn.ptnr1_label_asym_id,
+ label_comp_id: struct_conn.ptnr1_label_comp_id,
+ label_seq_id: struct_conn.ptnr1_label_seq_id,
+ label_atom_id: struct_conn.ptnr1_label_atom_id,
+ label_alt_id: struct_conn.pdbx_ptnr1_label_alt_id,
+ ins_code: struct_conn.pdbx_ptnr1_PDB_ins_code,
+ symmetry: struct_conn.ptnr1_symmetry
+ };
+ const p2: typeof p1 = {
+ label_asym_id: struct_conn.ptnr2_label_asym_id,
+ label_comp_id: struct_conn.ptnr2_label_comp_id,
+ label_seq_id: struct_conn.ptnr2_label_seq_id,
+ label_atom_id: struct_conn.ptnr2_label_atom_id,
+ label_alt_id: struct_conn.pdbx_ptnr2_label_alt_id,
+ ins_code: struct_conn.pdbx_ptnr2_PDB_ins_code,
+ symmetry: struct_conn.ptnr2_symmetry
+ };
+
+ 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.atomicHierarchy.findResidueKey(
+ findEntityIdByAsymId(model, asymId),
+ ps.label_comp_id.value(row),
+ asymId,
+ ps.label_seq_id.value(row),
+ ps.ins_code.value(row)
+ );
+ if (residueIndex < 0) return void 0;
+ const atomName = ps.label_atom_id.value(row);
+ // turns out "mismat" records might not have atom name value
+ if (!atomName) return void 0;
+ const atomIndex = findAtomIndexByLabelName(model, residueIndex, atomName, ps.label_alt_id.value(row));
+ if (atomIndex < 0) return void 0;
+ return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) || '1_555' };
+ }
+
+ const _ps = (row: number) => {
+ const ret = [];
+ let p = _p(row, p1);
+ if (p) ret.push(p);
+ p = _p(row, p2);
+ if (p) ret.push(p);
+ return ret;
+ }
+
+ const entries: StructConn.Entry[] = [];
+ for (let i = 0; i < struct_conn._rowCount; i++) {
+ const partners = _ps(i);
+ if (partners.length < 2) continue;
+
+ const type = conn_type_id.value(i)! as StructConnType;
+ const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
+ let flags = LinkType.Flag.None;
+ let order = 1;
+
+ switch (orderType) {
+ case 'sing': order = 1; break;
+ case 'doub': order = 2; break;
+ case 'trip': order = 3; break;
+ case 'quad': order = 4; break;
+ }
+
+ switch (type) {
+ case 'covale':
+ case 'covale_base':
+ case 'covale_phosphate':
+ case 'covale_sugar':
+ case 'modres':
+ flags = LinkType.Flag.Covalent;
+ break;
+ case 'disulf': flags = LinkType.Flag.Covalent | LinkType.Flag.Sulfide; break;
+ case 'hydrog': flags = LinkType.Flag.Hydrogen; break;
+ case 'metalc': flags = LinkType.Flag.MetallicCoordination; break;
+ case 'saltbr': flags = LinkType.Flag.Ion; break;
+ }
+
+ entries.push({ flags, order, distance: pdbx_dist_value.value(i), partners });
+ }
+
+ const ret = new StructConnImpl(entries);
+ model._staticPropertyData[PropName] = ret;
+ return ret;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/query.ts b/src/mol-model/structure/query.ts
index b5886cbda..428d976d8 100644
--- a/src/mol-model/structure/query.ts
+++ b/src/mol-model/structure/query.ts
@@ -8,13 +8,11 @@ import Selection from './query/selection'
import Query from './query/query'
import * as generators from './query/generators'
import * as modifiers from './query/modifiers'
-import props from './query/properties'
import pred from './query/predicates'
export const Queries = {
generators,
modifiers,
- props,
pred
}
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
index 0650a17ae..290a84341 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -6,8 +6,7 @@
import Query from './query'
import Selection from './selection'
-import P from './properties'
-import { Element, Unit } from '../structure'
+import { Element, Unit, StructureProperties as P } from '../structure'
import { OrderedSet, Segmentation } from 'mol-data/int'
import { LinearGroupingBuilder } from './utils/builders';
diff --git a/src/mol-model/structure/query/predicates.ts b/src/mol-model/structure/query/predicates.ts
index f6e6dfc32..99ef95389 100644
--- a/src/mol-model/structure/query/predicates.ts
+++ b/src/mol-model/structure/query/predicates.ts
@@ -4,8 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Element } from '../structure'
-import P from './properties'
+import { Element, StructureProperties as P } from '../structure'
namespace Predicates {
export interface SetLike<A> { has(v: A): boolean }
diff --git a/src/mol-model/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
index 3299acaae..66298c566 100644
--- a/src/mol-model/structure/query/properties.ts
+++ b/src/mol-model/structure/query/properties.ts
@@ -4,120 +4,4 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Element, Unit } from '../structure'
-import { VdwRadius } from '../model/properties/atomic';
-
-const constant = {
- true: Element.property(l => true),
- false: Element.property(l => false),
- zero: Element.property(l => 0)
-}
-
-function notAtomic(): never {
- throw 'Property only available for atomic models.';
-}
-
-function notCoarse(kind?: string): never {
- if (!!kind) throw `Property only available for coarse models (${kind}).`;
- throw `Property only available for coarse models.`;
-}
-
-const atom = {
- key: Element.property(l => l.element),
-
- // Conformation
- 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.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.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.atomicHierarchy.atoms.type_symbol.value(l.element))),
-}
-
-const residue = {
- 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])),
-
- // Properties
- secondary_structure_type: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
- secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
-}
-
-const chain = {
- 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.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 = {
- key: atom.key,
- modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.modelKey[l.element]),
- entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entityKey[l.element]),
-
- x: atom.x,
- y: atom.y,
- z: atom.z,
-
- 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.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.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.atomicHierarchy.entityKey[l.unit.chainIndex[l.element]]; }
-
-const entity = {
- key: eK,
-
- 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 = {
- operator_name: Element.property(l => l.unit.conformation.operator.name),
- model_num: Element.property(l => l.unit.model.modelNum)
-}
-
-const Properties = {
- constant,
- atom,
- residue,
- chain,
- entity,
- unit,
- coarse
-}
-
-type Properties = typeof Properties
-export default Properties
\ No newline at end of file
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index bed8ae1fd..e64227851 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -9,5 +9,6 @@ import Structure from './structure/structure'
import Unit from './structure/unit'
import StructureSymmetry from './structure/symmetry'
import { Link } from './structure/unit/links'
+import StructureProperties from './structure/properties'
-export { Element, Link, Structure, Unit, StructureSymmetry }
\ No newline at end of file
+export { Element, Link, Structure, Unit, StructureSymmetry, StructureProperties }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
new file mode 100644
index 000000000..943c219c2
--- /dev/null
+++ b/src/mol-model/structure/structure/properties.ts
@@ -0,0 +1,126 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Element from './element'
+import Unit from './unit'
+import { VdwRadius } from '../model/properties/atomic';
+
+const constant = {
+ true: Element.property(l => true),
+ false: Element.property(l => false),
+ zero: Element.property(l => 0)
+}
+
+function notAtomic(): never {
+ throw 'Property only available for atomic models.';
+}
+
+function notCoarse(kind?: string): never {
+ if (!!kind) throw `Property only available for coarse models (${kind}).`;
+ throw `Property only available for coarse models.`;
+}
+
+// TODO: remove the type checks?
+
+const atom = {
+ key: Element.property(l => l.element),
+
+ // Conformation
+ 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.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.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.atomicHierarchy.atoms.type_symbol.value(l.element))),
+}
+
+const residue = {
+ 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])),
+
+ // Properties
+ secondary_structure_type: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
+ secondary_structure_key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
+}
+
+const chain = {
+ 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.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 = {
+ key: atom.key,
+ modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.modelKey[l.element]),
+ entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entityKey[l.element]),
+
+ x: atom.x,
+ y: atom.y,
+ z: atom.z,
+
+ 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.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.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.atomicHierarchy.entityKey[l.unit.chainIndex[l.element]]; }
+
+const entity = {
+ key: eK,
+
+ 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 = {
+ operator_name: Element.property(l => l.unit.conformation.operator.name),
+ model_num: Element.property(l => l.unit.model.modelNum)
+}
+
+const StructureProperties = {
+ constant,
+ atom,
+ residue,
+ chain,
+ entity,
+ unit,
+ coarse
+}
+
+type StructureProperties = typeof StructureProperties
+export default StructureProperties
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index d36ea0a2b..5bca93fff 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -14,9 +14,9 @@ import Unit from './unit'
import { StructureLookup3D } from './util/lookup3d';
import { CoarseElements } from '../model/properties/coarse';
import { StructureSubsetBuilder } from './util/subset-builder';
-import { Queries } from '../query';
import { InterUnitBonds, computeInterUnitBonds } from './unit/links';
import StructureSymmetry from './symmetry';
+import StructureProperties from './properties';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -69,11 +69,11 @@ class Structure {
return this._links;
}
- private _symmetryGroups?: ReadonlyArray<Unit.SymmetryGroup> = void 0;
- get symmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
- if (this._symmetryGroups) return this._symmetryGroups;
- this._symmetryGroups = StructureSymmetry.computeTransformGroups(this);
- return this._symmetryGroups;
+ private _unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup> = void 0;
+ get unitSymmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
+ if (this._unitSymmetryGroups) return this._unitSymmetryGroups;
+ this._unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
+ return this._unitSymmetryGroups;
}
constructor(units: ArrayLike<Unit>) {
@@ -252,7 +252,7 @@ namespace Structure {
const keys = UniqueArray.create<number, number>();
for (const unit of units) {
- const prop = unit.kind === Unit.Kind.Atomic ? Queries.props.entity.key : Queries.props.coarse.entityKey;
+ const prop = unit.kind === Unit.Kind.Atomic ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
l.unit = unit;
const elements = unit.elements;
diff --git a/src/mol-view/label.ts b/src/mol-view/label.ts
index 3107afeb8..1623b27a9 100644
--- a/src/mol-view/label.ts
+++ b/src/mol-view/label.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Unit, Element, Queries } from 'mol-model/structure';
+import { Unit, Element, StructureProperties as Props } from 'mol-model/structure';
import { Loci } from 'mol-model/loci';
import { OrderedSet } from 'mol-data/int';
@@ -49,17 +49,17 @@ export function elementLabel(loc: Element.Location) {
let element = ''
if (Unit.isAtomic(loc.unit)) {
- const asym_id = Queries.props.chain.auth_asym_id(loc)
- const seq_id = Queries.props.residue.auth_seq_id(loc)
- const comp_id = Queries.props.residue.auth_comp_id(loc)
- const atom_id = Queries.props.atom.auth_atom_id(loc)
+ const asym_id = Props.chain.auth_asym_id(loc)
+ const seq_id = Props.residue.auth_seq_id(loc)
+ const comp_id = Props.residue.auth_comp_id(loc)
+ const atom_id = Props.atom.auth_atom_id(loc)
element = `[${comp_id}]${seq_id}:${asym_id}.${atom_id}`
} else if (Unit.isCoarse(loc.unit)) {
- const asym_id = Queries.props.coarse.asym_id(loc)
- const seq_id_begin = Queries.props.coarse.seq_id_begin(loc)
- const seq_id_end = Queries.props.coarse.seq_id_end(loc)
+ const asym_id = Props.coarse.asym_id(loc)
+ const seq_id_begin = Props.coarse.seq_id_begin(loc)
+ const seq_id_end = Props.coarse.seq_id_end(loc)
if (seq_id_begin === seq_id_end) {
- const entityKey = Queries.props.coarse.entityKey(loc)
+ const entityKey = Props.coarse.entityKey(loc)
const seq = loc.unit.model.sequence.byEntityKey[entityKey]
const comp_id = seq.compId.value(seq_id_begin)
element = `[${comp_id}]${seq_id_begin}:${asym_id}`
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 22914398f..ee8cae29c 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,7 +11,7 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry, Query, Format } from 'mol-model/structure'
+import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry, Query, Format, StructureProperties as SP } from 'mol-model/structure'
//import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
@@ -293,7 +293,7 @@ export namespace PropertyAccess {
export async function testAssembly(id: string, s: Structure) {
console.time('assembly')
const a = await StructureSymmetry.buildAssembly(s, '1').run();
- //const auth_comp_id = Q.props.residue.auth_comp_id;
+ //const auth_comp_id = SP.residue.auth_comp_id;
//const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
//const alas = await query(q1, a);
@@ -306,7 +306,7 @@ export namespace PropertyAccess {
export async function testSymmetry(id: string, s: Structure) {
console.time('symmetry')
const a = await StructureSymmetry.buildSymmetryRange(s, Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)).run();
- //const auth_comp_id = Q.props.residue.auth_comp_id;
+ //const auth_comp_id = SP.residue.auth_comp_id;
//const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
//const alas = await query(q1, a);
@@ -322,7 +322,7 @@ export namespace PropertyAccess {
const a = await StructureSymmetry.buildSymmetryRange(s, Vec3.create(-2, -2, -2), Vec3.create(2, 2, 2)).run();
//console.log(printUnits(a));
- const auth_comp_id = Q.props.residue.auth_comp_id, op = Q.props.unit.operator_name;
+ const auth_comp_id = SP.residue.auth_comp_id, op = SP.unit.operator_name;
//const q1 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'REA' });
const q1 = Q.modifiers.includeSurroundings(Q.generators.atoms({
chainTest: l => op(l) === '1_555',
@@ -345,7 +345,7 @@ export namespace PropertyAccess {
// const it = surr.elementLocations();
// while (it.hasNext) {
// const e = it.move();
- // console.log(`${Q.props.unit.operator_name(e)} ${Q.props.atom.id(e)}`);
+ // console.log(`${SP.unit.operator_name(e)} ${SP.atom.id(e)}`);
// }
//fs.writeFileSync(`${DATA_DIR}/${id}_surr.bcif`, to_mmCIF(id, a, true));
fs.writeFileSync(`${DATA_DIR}/${id}_surr.cif`, to_mmCIF(id, surr, false));
@@ -418,7 +418,7 @@ export namespace PropertyAccess {
//console.log('r', sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])));
console.time('atom.x');
- console.log('atom.x', sumProperty(structures[0], Q.props.atom.x));
+ console.log('atom.x', sumProperty(structures[0], SP.atom.x));
console.timeEnd('atom.x');
console.time('__x')
//console.log('__x', sumProperty(structures[0], l => l.unit.conformation.x[l.atom]));
@@ -426,16 +426,16 @@ export namespace PropertyAccess {
//const authSeqId = Element.property(l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom]));
- //const auth_seq_id = Q.props.residue.auth_seq_id;
- const auth_comp_id = Q.props.residue.auth_comp_id;
- //const auth_asym_id = Q.props.chain.auth_asym_id;
+ //const auth_seq_id = SP.residue.auth_seq_id;
+ const auth_comp_id = SP.residue.auth_comp_id;
+ //const auth_asym_id = SP.chain.auth_asym_id;
//const set = new Set(['A', 'B', 'C', 'D']);
//const q = Q.generators.atomGroups({ atomTest: l => auth_seq_id(l) < 3 });
- const q = Query(Q.generators.atoms({ atomTest: Q.pred.eq(Q.props.residue.auth_comp_id, 'ALA') }));
- const P = Q.props
+ const q = Query(Q.generators.atoms({ atomTest: Q.pred.eq(SP.residue.auth_comp_id, 'ALA') }));
+ const P = SP
//const q0 = Q.generators.atoms({ atomTest: l => auth_comp_id(l) === 'ALA' });
const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
- const q2 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: Q.props.residue.key }));
+ const q2 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: SP.residue.key }));
const q3 = Query(Q.generators.atoms({
chainTest: Q.pred.inSet(P.chain.auth_asym_id, ['A', 'B', 'C', 'D']),
residueTest: Q.pred.eq(P.residue.auth_comp_id, 'ALA')
diff --git a/src/servers/model/server/api.ts b/src/servers/model/server/api.ts
index 96820b82d..88830f6cd 100644
--- a/src/servers/model/server/api.ts
+++ b/src/servers/model/server/api.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Query, Queries, Structure, Element, StructureSymmetry } from 'mol-model/structure';
+import { Query, Queries, Structure, Element, StructureSymmetry, StructureProperties as Props } from 'mol-model/structure';
export enum QueryParamType {
String,
@@ -47,23 +47,23 @@ const AtomSiteParameters = {
// function entityTest(params: any): Element.Predicate | undefined {
// if (typeof params.entity_id === 'undefined') return void 0;
-// const p = Queries.props.entity.id, id = '' + params.entityId;
+// const p = Props.entity.id, id = '' + params.entityId;
// return Element.property(l => p(l) === id);
// }
function entityTest1_555(params: any): Element.Predicate | undefined {
if (typeof params.entity_id === 'undefined') return Element.property(l => l.unit.conformation.operator.isIdentity);
- const p = Queries.props.entity.id, id = '' + params.entityId;
+ const p = Props.entity.id, id = '' + params.entityId;
return Element.property(l => l.unit.conformation.operator.isIdentity && p(l) === id);
}
function chainTest(params: any): Element.Predicate | undefined {
if (typeof params.label_asym_id !== 'undefined') {
- const p = Queries.props.chain.label_asym_id, id = '' + params.label_asym_id;
+ const p = Props.chain.label_asym_id, id = '' + params.label_asym_id;
return Element.property(l => p(l) === id);
}
if (typeof params.auth_asym_id !== 'undefined') {
- const p = Queries.props.chain.auth_asym_id, id = '' + params.auth_asym_id;
+ const p = Props.chain.auth_asym_id, id = '' + params.auth_asym_id;
return Element.property(l => p(l) === id);
}
return void 0;
@@ -73,27 +73,27 @@ function residueTest(params: any): Element.Predicate | undefined {
const props: Element.Property<any>[] = [], values: any[] = [];
if (typeof params.label_seq_id !== 'undefined') {
- props.push(Queries.props.residue.label_seq_id);
+ props.push(Props.residue.label_seq_id);
values.push(+params.label_seq_id);
}
if (typeof params.auth_seq_id !== 'undefined') {
- props.push(Queries.props.residue.auth_seq_id);
+ props.push(Props.residue.auth_seq_id);
values.push(+params.auth_seq_id);
}
if (typeof params.label_comp_id !== 'undefined') {
- props.push(Queries.props.residue.label_comp_id);
+ props.push(Props.residue.label_comp_id);
values.push(params.label_comp_id);
}
if (typeof params.auth_comp_id !== 'undefined') {
- props.push(Queries.props.residue.auth_comp_id);
+ props.push(Props.residue.auth_comp_id);
values.push(params.auth_comp_id);
}
if (typeof params.pdbx_PDB_ins_code !== 'undefined') {
- props.push(Queries.props.residue.pdbx_PDB_ins_code);
+ props.push(Props.residue.pdbx_PDB_ins_code);
values.push(params.pdbx_PDB_ins_code);
}
--
GitLab