molstar
Version:
A comprehensive macromolecular library.
129 lines (128 loc) • 6.37 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __extends } from "tslib";
import { StructureSelection, StructureQuery, Structure, Queries, StructureProperties as SP, StructureElement, Unit } from '../../mol-model/structure';
import { SequenceWrapper } from './wrapper';
import { OrderedSet, Interval, SortedArray } from '../../mol-data/int';
import { ColorNames } from '../../mol-util/color/names';
import { applyMarkerAction, applyMarkerActionAtPosition } from '../../mol-util/marker-action';
var PolymerSequenceWrapper = /** @class */ (function (_super) {
__extends(PolymerSequenceWrapper, _super);
function PolymerSequenceWrapper(data) {
var _this = this;
var l = StructureElement.Location.create(data.structure, data.units[0], data.units[0].elements[0]);
var entitySeq = data.units[0].model.sequence.byEntityKey[SP.entity.key(l)];
var length = entitySeq.sequence.length;
var markerArray = new Uint8Array(length);
_this = _super.call(this, data, markerArray, length) || this;
_this.unitMap = new Map();
for (var _i = 0, _a = data.units; _i < _a.length; _i++) {
var unit = _a[_i];
_this.unitMap.set(unit.id, unit);
}
_this.sequence = entitySeq.sequence;
_this.missing = data.units[0].model.properties.missingResidues;
_this.modelNum = data.units[0].model.modelNum;
_this.asymId = Unit.isAtomic(data.units[0]) ? SP.chain.label_asym_id(l) : SP.coarse.asym_id(l);
var missing = [];
for (var i = 0; i < length; ++i) {
if (_this.missing.has(_this.modelNum, _this.asymId, _this.seqId(i)))
missing.push(i);
}
_this.observed = OrderedSet.subtract(Interval.ofBounds(0, length), SortedArray.ofSortedArray(missing));
return _this;
}
PolymerSequenceWrapper.prototype.seqId = function (seqIdx) {
return this.sequence.seqId.value(seqIdx);
};
PolymerSequenceWrapper.prototype.residueLabel = function (seqIdx) {
return this.sequence.label.value(seqIdx) || this.sequence.code.value(seqIdx);
};
PolymerSequenceWrapper.prototype.residueColor = function (seqIdx) {
return this.missing.has(this.modelNum, this.asymId, this.seqId(seqIdx))
? ColorNames.grey
: ColorNames.black;
};
PolymerSequenceWrapper.prototype.residueClass = function (seqIdx) {
return this.missing.has(this.modelNum, this.asymId, this.seqId(seqIdx))
? 'msp-sequence-missing'
: 'msp-sequence-present';
};
PolymerSequenceWrapper.prototype.mark = function (loci, action) {
var _this = this;
var changed = false;
var structure = this.data.structure;
var index = function (seqId) { return _this.sequence.index(seqId); };
if (StructureElement.Loci.is(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return false;
loci = StructureElement.Loci.remap(loci, structure);
for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
var e = _a[_i];
if (!this.unitMap.has(e.unit.id))
continue;
if (Unit.isAtomic(e.unit)) {
changed = applyMarkerAtomic(e, action, this.markerArray, index) || changed;
}
else {
changed = applyMarkerCoarse(e, action, this.markerArray, index) || changed;
}
}
}
else if (Structure.isLoci(loci)) {
if (!Structure.areRootsEquivalent(loci.structure, structure))
return false;
if (applyMarkerAction(this.markerArray, this.observed, action))
changed = true;
}
return changed;
};
PolymerSequenceWrapper.prototype.getLoci = function (seqIdx) {
var query = createResidueQuery(this.data.units[0].chainGroupId, this.data.units[0].conformation.operator.name, this.seqId(seqIdx));
return StructureSelection.toLociWithSourceUnits(StructureQuery.run(query, this.data.structure));
};
return PolymerSequenceWrapper;
}(SequenceWrapper));
export { PolymerSequenceWrapper };
function createResidueQuery(chainGroupId, operatorName, label_seq_id) {
return Queries.generators.atoms({
unitTest: function (ctx) {
return (SP.unit.chainGroupId(ctx.element) === chainGroupId &&
SP.unit.operator_name(ctx.element) === operatorName);
},
residueTest: function (ctx) {
if (ctx.element.unit.kind === 0 /* Unit.Kind.Atomic */) {
return SP.residue.label_seq_id(ctx.element) === label_seq_id;
}
else {
return (SP.coarse.seq_id_begin(ctx.element) <= label_seq_id &&
SP.coarse.seq_id_end(ctx.element) >= label_seq_id);
}
}
});
}
function applyMarkerAtomic(e, action, markerArray, index) {
var _a = e.unit, model = _a.model, elements = _a.elements;
var residueIndex = model.atomicHierarchy.residueAtomSegments.index;
var label_seq_id = model.atomicHierarchy.residues.label_seq_id;
OrderedSet.forEachSegment(e.indices, function (i) { return residueIndex[elements[i]]; }, function (rI) {
var seqId = label_seq_id.value(rI);
applyMarkerActionAtPosition(markerArray, index(seqId), action);
});
return true;
}
function applyMarkerCoarse(e, action, markerArray, index) {
var _a = e.unit, model = _a.model, elements = _a.elements;
var begin = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_begin : model.coarseHierarchy.gaussians.seq_id_begin;
var end = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_end : model.coarseHierarchy.gaussians.seq_id_end;
OrderedSet.forEach(e.indices, function (i) {
var eI = elements[i];
for (var s = index(begin.value(eI)), e_1 = index(end.value(eI)); s <= e_1; s++) {
applyMarkerActionAtPosition(markerArray, s, action);
}
});
return true;
}