From 199b27a8eb963bd3e2d31afb48a625344bed2cf0 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 8 Jun 2018 15:47:29 +0200
Subject: [PATCH] Support modified residues in Sequence
---
src/mol-app/ui/visualization/sequence-view.tsx | 3 ++-
src/mol-model/sequence/constants.ts | 2 ++
src/mol-model/sequence/sequence.ts | 18 ++++++++++++++----
src/mol-model/structure/model/formats/mmcif.ts | 6 ++++--
.../structure/model/formats/mmcif/sequence.ts | 6 +++---
.../structure/model/properties/sequence.ts | 4 ++--
6 files changed, 27 insertions(+), 12 deletions(-)
diff --git a/src/mol-app/ui/visualization/sequence-view.tsx b/src/mol-app/ui/visualization/sequence-view.tsx
index 4105dea2e..21bef90b8 100644
--- a/src/mol-app/ui/visualization/sequence-view.tsx
+++ b/src/mol-app/ui/visualization/sequence-view.tsx
@@ -42,7 +42,8 @@ class EntitySequence extends React.Component<{ ctx: Context, seq: StructureSeque
const query = createQuery(this.props.seq.entityId, seqId);
const loci = Selection.toLoci(await query(this.props.structure, SyncRuntimeContext));
- InteractivityEvents.HighlightElementLoci.dispatch(this.props.ctx, loci);
+ if (loci.elements.length === 0) InteractivityEvents.HighlightElementLoci.dispatch(this.props.ctx, void 0);
+ else InteractivityEvents.HighlightElementLoci.dispatch(this.props.ctx, loci);
}
diff --git a/src/mol-model/sequence/constants.ts b/src/mol-model/sequence/constants.ts
index 192d137f5..17796f599 100644
--- a/src/mol-model/sequence/constants.ts
+++ b/src/mol-model/sequence/constants.ts
@@ -7,10 +7,12 @@
export type AminoAlphabet =
| 'H' | 'R' | 'K' | 'I' | 'F' | 'L' | 'W' | 'A' | 'M' | 'P' | 'C' | 'N' | 'V' | 'G' | 'S' | 'Q' | 'Y' | 'D' | 'E' | 'T' | 'U' | 'O'
| 'X' /** = Unknown */
+ | '-' /** = Gap */
export type NuclecicAlphabet =
| 'A' | 'C' | 'G' | 'T' | 'U'
| 'X' /** = Unknown */
+ | '-' /** = Gap */
// from NGL
const ProteinOneLetterCodes: { [name: string]: AminoAlphabet } = {
diff --git a/src/mol-model/sequence/sequence.ts b/src/mol-model/sequence/sequence.ts
index 7f99ca54c..9401390e5 100644
--- a/src/mol-model/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -29,7 +29,7 @@ namespace Sequence {
export interface Protein extends Base<Kind.Protein, AminoAlphabet> { }
export interface RNA extends Base<Kind.RNA, NuclecicAlphabet> { }
export interface DNA extends Base<Kind.DNA, NuclecicAlphabet> { }
- export interface Generic extends Base<Kind.Generic, 'X'> { }
+ 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 };
@@ -49,11 +49,21 @@ namespace Sequence {
return { kind: Kind.Generic, code: (v: string) => 'X' };
}
- export function ofResidueNames(residueName: Column<string>, seqId: Column<number>): Sequence {
+ function modCode(code: (name: string) => string, map: Map<string, string>): (name: string) => string {
+ return n => {
+ const ret = code(n);
+ if (ret !== 'X' || !map.has(n)) return ret;
+ return code(map.get(n)!);
+ }
+ }
+
+ export function ofResidueNames(residueName: Column<string>, seqId: Column<number>, modifiedMap?: Map<string, string>): Sequence {
if (seqId.rowCount === 0) throw new Error('cannot be empty');
const { kind, code } = determineKind(residueName);
- 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> {
@@ -83,7 +93,7 @@ namespace Sequence {
const count = maxSeqId - minSeqId + 1;
const sequenceArray = new Array(maxSeqId + 1);
for (let i = 0; i < count; i++) {
- sequenceArray[i] = 'X';
+ sequenceArray[i] = '-';
}
for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 48d8c4754..49bcfc52c 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -159,6 +159,8 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
? format.data.entry.id.value(0)
: format.data._name;
+ const modifiedResidueNameMap = modResMap(format);
+
return {
id: UUID.create(),
label,
@@ -166,13 +168,13 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
entities,
atomicHierarchy,
- sequence: getSequence(format.data, entities, atomicHierarchy),
+ sequence: getSequence(format.data, entities, atomicHierarchy, modifiedResidueNameMap),
atomicConformation: getConformation(format, bounds),
coarseHierarchy: coarse.hierarchy,
coarseConformation: coarse.conformation,
properties: {
secondaryStructure: getSecondaryStructureMmCif(format.data, atomicHierarchy),
- modifiedResidueNameMap: modResMap(format)
+ modifiedResidueNameMap
},
symmetry: getSymmetry(format)
};
diff --git a/src/mol-model/structure/model/formats/mmcif/sequence.ts b/src/mol-model/structure/model/formats/mmcif/sequence.ts
index 67e617ef3..a279b6122 100644
--- a/src/mol-model/structure/model/formats/mmcif/sequence.ts
+++ b/src/mol-model/structure/model/formats/mmcif/sequence.ts
@@ -21,8 +21,8 @@ import { Sequence } from '../../../../sequence';
// corresponding ATOM_SITE entries should reflect this
// heterogeneity.
-export function getSequence(cif: mmCIF, entities: Entities, hierarchy: AtomicHierarchy): StructureSequence {
- if (!cif.entity_poly_seq._rowCount) return StructureSequence.fromAtomicHierarchy(entities, hierarchy);
+export function getSequence(cif: mmCIF, entities: Entities, hierarchy: AtomicHierarchy, modResMap: Map<string, string>): StructureSequence {
+ if (!cif.entity_poly_seq._rowCount) return StructureSequence.fromAtomicHierarchy(entities, hierarchy, modResMap);
const { entity_id, num, mon_id } = cif.entity_poly_seq;
@@ -45,7 +45,7 @@ export function getSequence(cif: mmCIF, entities: Entities, hierarchy: AtomicHie
entityId: id,
compId: _compId,
num: _num,
- sequence: Sequence.ofResidueNames(_compId, _num)
+ sequence: Sequence.ofResidueNames(_compId, _num, modResMap)
};
sequences.push(byEntityKey[entityKey]);
diff --git a/src/mol-model/structure/model/properties/sequence.ts b/src/mol-model/structure/model/properties/sequence.ts
index 3cd6e601a..7725eb561 100644
--- a/src/mol-model/structure/model/properties/sequence.ts
+++ b/src/mol-model/structure/model/properties/sequence.ts
@@ -23,7 +23,7 @@ namespace StructureSequence {
readonly sequence: Sequence
}
- export function fromAtomicHierarchy(entities: Entities, hierarchy: AtomicHierarchy): StructureSequence {
+ export function fromAtomicHierarchy(entities: Entities, hierarchy: AtomicHierarchy, modResMap?: Map<string, string>): StructureSequence {
const { label_comp_id, label_seq_id } = hierarchy.residues
const { chainSegments, residueSegments } = hierarchy
@@ -52,7 +52,7 @@ namespace StructureSequence {
entityId: entities.data.id.value(entityKey),
compId,
num,
- sequence: Sequence.ofResidueNames(compId, num)
+ sequence: Sequence.ofResidueNames(compId, num, modResMap)
};
sequences.push(byEntityKey[entityKey]);
--
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