From a69062164158174deb57bcd53aae425662a93441 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 10 Sep 2018 15:18:11 +0200
Subject: [PATCH] Refactored AtomicKeys to AtomicIndex and added more types of
lookups
---
.../pdbe/structure-quality-report.ts | 4 +-
.../structure/model/formats/mmcif/atomic.ts | 6 +-
.../model/formats/mmcif/bonds/struct_conn.ts | 7 +-
.../mmcif/pair-restraints/cross-links.ts | 8 +-
.../model/properties/atomic/hierarchy.ts | 25 ++---
.../structure/model/properties/sequence.ts | 4 +-
.../model/properties/utils/atomic-index.ts | 17 +++-
.../model/properties/utils/atomic-keys.ts | 99 -------------------
src/mol-model/structure/structure/element.ts | 2 +-
9 files changed, 35 insertions(+), 137 deletions(-)
delete mode 100644 src/mol-model/structure/model/properties/utils/atomic-keys.ts
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 4a02a66b2..2d6b11e3f 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -71,7 +71,7 @@ function createIssueMapFromJson(modelData: Model, data: any): IssueMap | undefin
for (const residue of model.residues) {
const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || '';
- const idx = modelData.atomicHierarchy.findResidueKey(entity_id, asym_id, '', auth_seq_id, ins_code);
+ const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code);
ret.set(idx, residue.outlier_types);
}
}
@@ -86,7 +86,7 @@ function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQua
const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, _rowCount } = data;
for (let i = 0; i < _rowCount; i++) {
- const idx = modelData.atomicHierarchy.findResidueKey(label_entity_id.value(i), label_asym_id.value(i), '', auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
+ const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
ret.set(idx, issues.value(i));
}
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index 69327f011..23879400f 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -12,7 +12,7 @@ import { ElementIndex } from '../../../../structure';
import Format from '../../format';
import { Model } from '../../model';
import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../properties/atomic';
-import { getAtomicKeys } from '../../properties/utils/atomic-keys';
+import { getAtomicIndex } from '../../properties/utils/atomic-index';
import { ElementSymbol } from '../../types';
import { Entities } from '../../properties/common';
@@ -98,8 +98,8 @@ export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_sit
chainAtomSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
}
- const hierarchyKeys = getAtomicKeys(hierarchyData, entities, hierarchySegments);
+ const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, formatData.chemicalComponentMap);
- const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments, ...hierarchyRanges };
+ const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, ...hierarchyRanges, index };
return { sameAsPrevious: false, hierarchy, conformation };
}
\ 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
index e3b16f772..75a4afa89 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
@@ -163,7 +163,6 @@ export namespace StructConn {
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,
auth_seq_id: struct_conn.ptnr1_auth_seq_id,
label_atom_id: struct_conn.ptnr1_label_atom_id,
@@ -173,7 +172,6 @@ export namespace StructConn {
};
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,
auth_seq_id: struct_conn.ptnr2_auth_seq_id,
label_atom_id: struct_conn.ptnr2_label_atom_id,
@@ -184,11 +182,10 @@ 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.atomicHierarchy.findResidueKey(
+ const asymId = ps.label_asym_id.value(row);
+ const residueIndex = model.atomicHierarchy.index.findResidue(
findEntityIdByAsymId(model, asymId),
asymId,
- ps.label_comp_id.value(row),
ps.auth_seq_id.value(row),
ps.ins_code.value(row)
);
diff --git a/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
index b16448853..0aebfc74f 100644
--- a/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
+++ b/src/mol-model/structure/model/formats/mmcif/pair-restraints/cross-links.ts
@@ -11,9 +11,9 @@ import { findAtomIndexByLabelName } from '../util';
import { Unit } from '../../../../structure';
import { ElementIndex } from '../../../indexing';
-function findAtomIndex(model: Model, entityId: string, asymId: string, compId: string, seqId: number, atomId: string) {
+function findAtomIndex(model: Model, entityId: string, asymId: string, seqId: number, atomId: string) {
if (!model.atomicHierarchy.atoms.auth_atom_id.isDefined) return -1
- const residueIndex = model.atomicHierarchy.findResidueKey(entityId, compId, asymId, seqId, '')
+ const residueIndex = model.atomicHierarchy.index.findResidue(entityId, asymId, seqId)
if (residueIndex < 0) return -1
return findAtomIndexByLabelName(model, residueIndex, atomId, '') as ElementIndex
}
@@ -35,7 +35,6 @@ export namespace IHMCrossLinkRestraint {
const p1 = {
entity_id: ihm_cross_link_restraint.entity_id_1,
asym_id: ihm_cross_link_restraint.asym_id_1,
- comp_id: ihm_cross_link_restraint.comp_id_1,
seq_id: ihm_cross_link_restraint.seq_id_1,
atom_id: ihm_cross_link_restraint.atom_id_1,
}
@@ -43,7 +42,6 @@ export namespace IHMCrossLinkRestraint {
const p2: typeof p1 = {
entity_id: ihm_cross_link_restraint.entity_id_2,
asym_id: ihm_cross_link_restraint.asym_id_2,
- comp_id: ihm_cross_link_restraint.comp_id_2,
seq_id: ihm_cross_link_restraint.seq_id_2,
atom_id: ihm_cross_link_restraint.atom_id_2,
}
@@ -60,7 +58,7 @@ export namespace IHMCrossLinkRestraint {
const seqId = ps.seq_id.value(row)
if (ihm_cross_link_restraint.model_granularity.value(row) === 'by-atom') {
- const atomicElement = findAtomIndex(model, entityId, asymId, ps.comp_id.value(row), seqId, ps.atom_id.value(row))
+ const atomicElement = findAtomIndex(model, entityId, asymId, seqId, ps.atom_id.value(row))
if (atomicElement >= 0) _add(atomicElementMap, atomicElement as ElementIndex, row)
} else if (model.coarseHierarchy.isDefined) {
const sphereElement = model.coarseHierarchy.spheres.findSequenceKey(entityId, asymId, seqId)
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index e1dce3c6d..bb3fbf514 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -119,22 +119,6 @@ export interface AtomicSegments {
// TODO: include entity segments?
}
-export interface AtomicKeys {
- // TODO: include (lazily computed) "entity/chain/residue" indices?
-
- /** @returns index or -1 if not present. */
- getEntityKey(cI: ChainIndex): EntityIndex,
-
- /** @returns index or -1 if not present. */
- findChainKey(entityId: string, label_asym_id: string): ChainIndex,
-
- /**
- * Unique number for each of the residue. Also the index of the 1st occurence of this residue.
- * @returns index or -1 if not present.
- */
- findResidueKey(entityId: string, label_asym_id: string, label_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code: string): ResidueIndex
-}
-
export interface AtomicIndex {
/** @returns index or -1 if not present. */
getEntityFromChain(cI: ChainIndex): EntityIndex,
@@ -157,6 +141,7 @@ export interface AtomicIndex {
* @returns index or -1 if not present.
*/
findResidue(key: AtomicIndex.ResidueKey): ResidueIndex,
+ findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex,
/**
* Index of the 1st occurence of this residue.
@@ -181,6 +166,8 @@ export namespace AtomicIndex {
export interface ChainAuthKey { auth_asym_id: string }
export interface ResidueKey { label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string }
+ export function EmptyResidueKey(): ResidueKey { return { label_entity_id: '', label_asym_id: '', auth_seq_id: 0, pdbx_PDB_ins_code: void 0 }; }
+
export interface ResidueAuthKey { auth_asym_id: string, auth_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string }
export interface ResidueLabelKey { label_entity_id: string, label_asym_id: string, label_seq_id: number, pdbx_PDB_ins_code?: string }
}
@@ -191,8 +178,10 @@ export interface AtomicRanges {
cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
}
-type _Hierarchy = AtomicData & AtomicSegments & AtomicKeys & AtomicRanges
-export interface AtomicHierarchy extends _Hierarchy { }
+type _Hierarchy = AtomicData & AtomicSegments & AtomicRanges
+export interface AtomicHierarchy extends _Hierarchy {
+ index: AtomicIndex
+}
export namespace AtomicHierarchy {
/** Start residue inclusive */
diff --git a/src/mol-model/structure/model/properties/sequence.ts b/src/mol-model/structure/model/properties/sequence.ts
index 441ffb431..726b9e517 100644
--- a/src/mol-model/structure/model/properties/sequence.ts
+++ b/src/mol-model/structure/model/properties/sequence.ts
@@ -32,13 +32,13 @@ namespace StructureSequence {
const sequences: StructureSequence.Entity[] = [];
for (let cI = 0 as ChainIndex, _cI = hierarchy.chains._rowCount; cI < _cI; cI++) {
- const entityKey = hierarchy.getEntityKey(cI);
+ const entityKey = hierarchy.index.getEntityFromChain(cI);
// Only for polymers, trying to mirror _entity_poly_seq
if (byEntityKey[entityKey] !== void 0 || entities.data.type.value(entityKey) !== 'polymer') continue;
let start = cI;
cI++;
- while (cI < _cI && entityKey === hierarchy.getEntityKey(cI) && entities.data.type.value(entityKey) !== 'polymer') {
+ while (cI < _cI && entityKey === hierarchy.index.getEntityFromChain(cI) && entities.data.type.value(entityKey) !== 'polymer') {
cI++;
}
cI--;
diff --git a/src/mol-model/structure/model/properties/utils/atomic-index.ts b/src/mol-model/structure/model/properties/utils/atomic-index.ts
index 1d554dae3..c98894a4b 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -62,6 +62,7 @@ function createMapping(entities: Entities, data: AtomicData, segments: AtomicSeg
};
}
+const _tempResidueKey = AtomicIndex.EmptyResidueKey();
class Index implements AtomicIndex {
private entityIndex: Entities['getEntityIndex'];
@@ -81,7 +82,19 @@ class Index implements AtomicIndex {
return this.map.auth_asym_id.has(key.auth_asym_id) ? this.map.auth_asym_id.get(key.auth_asym_id)! : -1 as ChainIndex;
}
- findResidue(key: AtomicIndex.ResidueKey): ResidueIndex {
+ findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex
+ findResidue(key: AtomicIndex.ResidueKey): ResidueIndex
+ findResidue(label_entity_id_or_key: string | AtomicIndex.ResidueKey, label_asym_id?: string, auth_seq_id?: number, pdbx_PDB_ins_code?: string): ResidueIndex {
+ let key: AtomicIndex.ResidueKey;
+ if (arguments.length === 1) {
+ key = label_entity_id_or_key as AtomicIndex.ResidueKey
+ } else {
+ _tempResidueKey.label_entity_id = label_entity_id_or_key as string;
+ _tempResidueKey.label_asym_id = label_asym_id!;
+ _tempResidueKey.auth_seq_id = auth_seq_id!;
+ _tempResidueKey.pdbx_PDB_ins_code = pdbx_PDB_ins_code;
+ key = _tempResidueKey;
+ }
const cI = this.findChainLabel(key);
if (cI < 0) return -1 as ResidueIndex;
const rm = this.map.chain_index_auth_seq_id.get(cI)!;
@@ -117,7 +130,7 @@ class Index implements AtomicIndex {
}
}
-export function getAtomicKeys(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicIndex {
+export function getAtomicIndex(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicIndex {
const map = createMapping(entities, data, segments);
const { label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = data.residues;
diff --git a/src/mol-model/structure/model/properties/utils/atomic-keys.ts b/src/mol-model/structure/model/properties/utils/atomic-keys.ts
deleted file mode 100644
index a13469217..000000000
--- a/src/mol-model/structure/model/properties/utils/atomic-keys.ts
+++ /dev/null
@@ -1,99 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { AtomicData, AtomicSegments, AtomicKeys } from '../atomic'
-import { Interval, Segmentation } from 'mol-data/int'
-import { Entities } from '../common'
-import { ChainIndex, ResidueIndex, EntityIndex } from '../../indexing';
-
-function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
- // TODO: add new index that support comp_id again?
- return `${seq_id} ${ins_code}`;
- //return `${comp_id} ${seq_id} ${ins_code}`;
-}
-
-function getElementKey(map: Map<string, number>, key: string, counter: { index: number }) {
- if (map.has(key)) return map.get(key)!;
- const ret = counter.index++;
- map.set(key, ret);
- return ret;
-}
-
-function getElementSubstructureKeyMap(map: Map<number, Map<string, number>>, key: number) {
- if (map.has(key)) return map.get(key)!;
- const ret = new Map<string, number>();
- map.set(key, ret);
- return ret;
-}
-
-function createLookUp(entities: Entities, chain: Map<number, Map<string, number>>, residue: Map<number, Map<string, number>>) {
- const getEntKey = entities.getEntityIndex;
- const findChainKey: AtomicKeys['findChainKey'] = (e, c) => {
- let eKey = getEntKey(e);
- if (eKey < 0) return -1 as ChainIndex;
- const cm = chain.get(eKey)!;
- if (!cm.has(c)) return -1 as ChainIndex;
- return cm.get(c)! as ChainIndex;
- }
- const findResidueKey: AtomicKeys['findResidueKey'] = (e, c, name, seq, ins) => {
- let eKey = getEntKey(e);
- if (eKey < 0) return -1 as ResidueIndex;
- const cm = chain.get(eKey)!;
- if (!cm.has(c)) return -1 as ResidueIndex;
- const rm = residue.get(cm.get(c)!)!
- const id = getResidueId(name, seq, ins);
- if (!rm.has(id)) return -1 as ResidueIndex;
- return rm.get(id)! as ResidueIndex;
- }
- return { findChainKey, findResidueKey };
-}
-
-function missingEntity(k: string) {
- throw new Error(`Missing entity entry for entity id '${k}'.`);
-}
-
-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 };
- const residueMaps = new Map<number, Map<string, number>>(), residueCounter = { index: 0 };
-
- const residueKey = new Int32Array(residues._rowCount);
- const chainKey = new Int32Array(chains._rowCount);
- const entityKey = new Int32Array(chains._rowCount);
-
- const { label_comp_id, auth_seq_id, pdbx_PDB_ins_code } = data.residues;
- const { label_entity_id, label_asym_id } = data.chains;
-
- const atomSet = Interval.ofBounds(0, data.atoms._rowCount);
-
- const chainsIt = Segmentation.transientSegments(segments.chainAtomSegments, atomSet);
- while (chainsIt.hasNext) {
- const chainSegment = chainsIt.move();
- const cI = chainSegment.index;
-
- let eKey = entities.getEntityIndex(label_entity_id.value(cI));
- if (eKey < 0) missingEntity(label_entity_id.value(cI));
- const chainMap = getElementSubstructureKeyMap(chainMaps, eKey);
- const cKey = getElementKey(chainMap, label_asym_id.value(cI), chainCounter);
-
- chainKey[cI] = cKey;
- entityKey[cI] = eKey;
-
- const residueMap = getElementSubstructureKeyMap(residueMaps, cKey);
- const residuesIt = Segmentation.transientSegments(segments.residueAtomSegments, atomSet, chainSegment);
- while (residuesIt.hasNext) {
- const residueSegment = residuesIt.move();
- const rI = residueSegment.index;
- const residueId = getResidueId(label_comp_id.value(rI), auth_seq_id.value(rI), pdbx_PDB_ins_code.value(rI));
- residueKey[rI] = getElementKey(residueMap, residueId, residueCounter);
- }
- }
-
- const { findChainKey, findResidueKey } = createLookUp(entities, chainMaps, residueMaps);
-
- return { getEntityKey: cI => entityKey[cI] as EntityIndex, findChainKey, findResidueKey };
-}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index a8ad08e1a..197ff5cb7 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -99,7 +99,7 @@ namespace StructureElement {
export function entityIndex(l: StructureElement) {
switch (l.unit.kind) {
case Unit.Kind.Atomic:
- return l.unit.model.atomicHierarchy.getEntityKey(l.unit.chainIndex[l.element])
+ return l.unit.model.atomicHierarchy.index.getEntityFromChain(l.unit.chainIndex[l.element])
case Unit.Kind.Spheres:
return l.unit.model.coarseHierarchy.spheres.entityKey[l.element]
case Unit.Kind.Gaussians:
--
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