diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/mmcif/atomic.ts
index bbb3889a36870fdc6640b802086fb52b6f3ec8c4..ec4ea2191d133e82a21ff9e939f0c88f920a1a6c 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/mmcif/atomic.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 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 { Column, Table } from '../../../mol-data/db';
@@ -26,15 +27,15 @@ function findHierarchyOffsets(atom_site: AtomSite) {
const start = 0, end = atom_site._rowCount;
const residues = [start as ElementIndex], chains = [start as ElementIndex];
- const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
+ const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = atom_site;
for (let i = start + 1 as ElementIndex; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !label_seq_id.areValuesEqual(i - 1, i)
|| !auth_seq_id.areValuesEqual(i - 1, i)
- || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
- || !label_comp_id.areValuesEqual(i - 1, i);
+ || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i);
+ // not checking label_comp_id to allow for MICROHETEROGENEITY
if (newResidue) residues[residues.length] = i as ElementIndex;
if (newChain) chains[chains.length] = i as ElementIndex;
diff --git a/src/mol-model/sequence/sequence.ts b/src/mol-model/sequence/sequence.ts
index 962e7b80cb97ec037374cc28835afc9ed0f1c460..20776def8b5b1e52101e21bce263a95f295ffbd6 100644
--- a/src/mol-model/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 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 { AminoAlphabet, NuclecicAlphabet, getProteinOneLetterCode, getRnaOneLetterCode, getDnaOneLetterCode } from './constants';
@@ -24,6 +25,9 @@ namespace Sequence {
readonly kind: K,
readonly offset: number,
readonly sequence: ArrayLike<Alphabet>
+ readonly labels: ArrayLike<string>
+ /** maps seqId to list of compIds */
+ readonly microHet: ReadonlyMap<number, string[]>
}
export interface Protein extends Base<Kind.Protein, AminoAlphabet> { }
@@ -31,8 +35,8 @@ namespace Sequence {
export interface DNA extends Base<Kind.DNA, NuclecicAlphabet> { }
export interface Generic extends Base<Kind.Generic, 'X' | '-'> { }
- export function create(kind: Kind, sequence: string, offset: number = 0): Sequence {
- return { kind: kind as any, sequence: sequence as any, offset };
+ export function create<K extends Kind, Alphabet extends string>(kind: K, sequence: Alphabet[], labels: string[], microHet: Map<number, string[]>, offset: number = 0): Base<K, Alphabet> {
+ return { kind: kind, sequence: sequence, labels, microHet, offset };
}
export function getSequenceString(seq: Sequence) {
@@ -62,13 +66,17 @@ namespace Sequence {
const { kind, code } = determineKind(residueName);
- if (!modifiedMap || modifiedMap.size === 0) return new Impl(kind, residueName, seqId, code) as Sequence;
+ if (!modifiedMap || modifiedMap.size === 0) {
+ return new Impl(kind, residueName, seqId, code) as Sequence;
+ }
return new Impl(kind, residueName, seqId, modCode(code, modifiedMap)) as Sequence;
}
- class Impl implements Base<any, any> {
+ class Impl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
private _offset = 0;
- private _seq: string | undefined = void 0;
+ private _seq: ArrayLike<Alphabet> | undefined = void 0;
+ private _labels: ArrayLike<string> | undefined = void 0;
+ private _microHet: ReadonlyMap<number, string[]> | undefined = void 0;
get offset() {
if (this._seq !== void 0) return this._offset;
@@ -76,10 +84,22 @@ namespace Sequence {
return this._offset;
}
- get sequence(): any {
+ get sequence(): ArrayLike<Alphabet> {
if (this._seq !== void 0) return this._seq;
this.create();
- return this._seq;
+ return this._seq!;
+ }
+
+ get labels(): ArrayLike<string> {
+ if (this._labels !== void 0) return this._labels;
+ this.create();
+ return this._labels!;
+ }
+
+ get microHet(): ReadonlyMap<number, string[]> {
+ if (this._microHet !== void 0) return this._microHet;
+ this.create();
+ return this._microHet!;
}
private create() {
@@ -91,20 +111,43 @@ namespace Sequence {
}
const count = maxSeqId - minSeqId + 1;
- const sequenceArray = new Array(maxSeqId + 1);
+ const sequenceArray = new Array<string>(maxSeqId + 1);
+ const labels = new Array<string[]>(maxSeqId + 1);
for (let i = 0; i < count; i++) {
sequenceArray[i] = '-';
+ labels[i] = [];
+ }
+
+ const compIds = new Array<string[]>(maxSeqId + 1);
+ for (let i = minSeqId; i <= maxSeqId; ++i) {
+ compIds[i] = [];
}
for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
- sequenceArray[this.seqId.value(i) - minSeqId] = this.code(this.residueName.value(i) || '');
+ const seqId = this.seqId.value(i)
+ const idx = seqId - minSeqId;
+ const name = this.residueName.value(i);
+ const code = this.code(name);
+ // in case of MICROHETEROGENEITY `sequenceArray[idx]` may already be set
+ if (!sequenceArray[idx] || sequenceArray[idx] === '-') {
+ sequenceArray[idx] = code;
+ }
+ labels[idx].push(code === 'X' ? name : code);
+ compIds[seqId].push(name);
+ }
+
+ const microHet = new Map()
+ for (let i = minSeqId; i <= maxSeqId; ++i) {
+ if (compIds[i].length > 1) microHet.set(i, compIds[i])
}
- this._seq = sequenceArray.join('');
+ this._seq = sequenceArray.join('') as unknown as ArrayLike<Alphabet>;
+ this._labels = labels.map(l => l.length > 1 ? `(${l.join('|')})` : l.join(''));
+ this._microHet = microHet
this._offset = minSeqId - 1;
}
- constructor(public kind: Kind, private residueName: Column<string>, private seqId: Column<number>, private code: (name: string) => string) {
+ constructor(public kind: K, private residueName: Column<string>, private seqId: Column<number>, private code: (name: string) => string) {
}
}
diff --git a/src/mol-model/structure/model/properties/sequence.ts b/src/mol-model/structure/model/properties/sequence.ts
index 368ea2293f004126e7ec491dd783a522098771c1..a9cd6715eb3fb1718821fabca0e7e9da6fcef96f 100644
--- a/src/mol-model/structure/model/properties/sequence.ts
+++ b/src/mol-model/structure/model/properties/sequence.ts
@@ -19,7 +19,7 @@ namespace StructureSequence {
export interface Entity {
readonly entityId: string,
readonly num: Column<number>,
- // Corresponds to _entity_poly_seq.mon_id
+ /** Corresponds to _entity_poly_seq.mon_id */
readonly compId: Column<string>,
readonly sequence: Sequence
}
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 5ca9b5caa1bf81fd1592e5cf601683ce53429626..2e02f6a7680dbb943906e4a4b0b791418c77d3a5 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -57,13 +57,33 @@ function compId(l: StructureElement.Location) {
return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])
}
+function seqId(l: StructureElement.Location) {
+ return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.value(l.unit.residueIndex[l.element])
+}
+
+function hasMicroheterogeneity(l: StructureElement.Location) {
+ if (!Unit.isAtomic(l.unit)) notAtomic()
+ const entitySeq = l.unit.model.sequence.byEntityKey[eK(l)]
+ return entitySeq && entitySeq.sequence.microHet.has(seqId(l))
+}
+
+function microheterogeneityCompIds(l: StructureElement.Location) {
+ if (!Unit.isAtomic(l.unit)) notAtomic()
+ const entitySeq = l.unit.model.sequence.byEntityKey[eK(l)]
+ if (entitySeq) {
+ return entitySeq.sequence.microHet.get(seqId(l)) || [compId(l)]
+ } else {
+ return [compId(l)]
+ }
+}
+
const residue = {
key: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.residueIndex[l.element]),
group_PDB: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.group_PDB.value(l.unit.residueIndex[l.element])),
label_comp_id: p(compId),
auth_comp_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_comp_id.value(l.unit.residueIndex[l.element])),
- label_seq_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.value(l.unit.residueIndex[l.element])),
+ label_seq_id: p(seqId),
auth_seq_id: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.element])),
pdbx_PDB_ins_code: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.pdbx_PDB_ins_code.value(l.unit.residueIndex[l.element])),
@@ -74,6 +94,8 @@ const residue = {
const id = compId(l)
return l.unit.model.properties.modifiedResidues.parentId.get(id) || id
}),
+ hasMicroheterogeneity: p(hasMicroheterogeneity),
+ microheterogeneityCompIds: p(microheterogeneityCompIds),
secondary_structure_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
secondary_structure_key: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.key[l.unit.residueIndex[l.element]]),
chem_comp_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.type),
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index 641e8288b0f5bc9f9c8872e9db762be710394bfc..63fcd6e6f3cf1d99453953872a9924bdddcf3839 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -25,7 +25,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
}
residueLabel(seqIdx: number) {
- return this.sequence.sequence[seqIdx]
+ return this.sequence.labels[seqIdx]
}
residueColor(seqIdx: number) {
return this.missing.has(this.modelNum, this.asymId, this.seqId(seqIdx))
diff --git a/src/mol-plugin/ui/sequence/residue.tsx b/src/mol-plugin/ui/sequence/residue.tsx
index 6e9d19a262f3032c3aae454a61dcbc510c55b48f..35a97ea2609cb516fe10f911e2d11755969c4d91 100644
--- a/src/mol-plugin/ui/sequence/residue.tsx
+++ b/src/mol-plugin/ui/sequence/residue.tsx
@@ -38,8 +38,8 @@ export class Residue extends PurePluginUIComponent<{ seqIdx: number, label: stri
}
get margin() {
- return this.props.label.length > 1 && this.props.seqIdx
- ? `0px 0px 0px 4px`
+ return this.props.label.length > 1
+ ? (this.props.seqIdx === 0 ? `0px 2px 0px 0px` : `0px 2px 0px 2px`)
: undefined
}
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 338eb8e6b25899d6540aa30e22bb5d59daee2305..4abe73ffa93575b94b6a16ea35dbfb2bf76fa782 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -108,13 +108,18 @@ export function atomicElementLabel(location: StructureElement.Location<Unit.Atom
const atom_id = Props.atom.label_atom_id(location)
const alt_id = Props.atom.label_alt_id(location)
+ const microHetCompIds = Props.residue.microheterogeneityCompIds(location)
+ const compId = granularity === 'residue' && microHetCompIds.length > 1 ?
+ `(${microHetCompIds.join('|')})` : comp_id
+
+
const label: string[] = []
switch (granularity) {
case 'element':
label.push(`${atom_id}${alt_id ? `%${alt_id}` : ''}`)
case 'residue':
- label.push(`${comp_id} ${seq_id}`)
+ label.push(`${compId} ${seq_id}`)
case 'chain':
label.push(`Chain ${label_asym_id}:${auth_asym_id}`)
}