molstar
Version:
A comprehensive macromolecular library.
106 lines (105 loc) • 4.25 kB
JavaScript
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { StructureElement, Bond } from '../../mol-model/structure';
import { ColorScale, Color } from '../../mol-util/color';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
var DefaultColor = Color(0xCCCCCC);
var Description = 'Gives every polymer residue a color based on its `seq_id` value.';
export var SequenceIdColorThemeParams = {
list: PD.ColorList('turbo', { presetKind: 'scale' }),
};
export function getSequenceIdColorThemeParams(ctx) {
return SequenceIdColorThemeParams; // TODO return copy
}
function getSeqId(unit, element) {
var model = unit.model;
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
var residueIndex = model.atomicHierarchy.residueAtomSegments.index[element];
return model.atomicHierarchy.residues.label_seq_id.value(residueIndex);
case 1 /* Unit.Kind.Spheres */:
return Math.round((model.coarseHierarchy.spheres.seq_id_begin.value(element) +
model.coarseHierarchy.spheres.seq_id_end.value(element)) / 2);
case 2 /* Unit.Kind.Gaussians */:
return Math.round((model.coarseHierarchy.gaussians.seq_id_begin.value(element) +
model.coarseHierarchy.gaussians.seq_id_end.value(element)) / 2);
}
}
function getSequenceLength(unit, element) {
var model = unit.model;
var entityId = '';
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
var chainIndex = model.atomicHierarchy.chainAtomSegments.index[element];
entityId = model.atomicHierarchy.chains.label_entity_id.value(chainIndex);
break;
case 1 /* Unit.Kind.Spheres */:
entityId = model.coarseHierarchy.spheres.entity_id.value(element);
break;
case 2 /* Unit.Kind.Gaussians */:
entityId = model.coarseHierarchy.gaussians.entity_id.value(element);
break;
}
if (entityId === '')
return 0;
var entityIndex = model.entities.getEntityIndex(entityId);
if (entityIndex === -1)
return 0;
var entity = model.sequence.byEntityKey[entityIndex];
if (entity === undefined)
return 0;
return entity.sequence.length;
}
export function SequenceIdColorTheme(ctx, props) {
var scale = ColorScale.create({
listOrName: props.list.colors,
minLabel: 'Start',
maxLabel: 'End',
});
var color = function (location) {
if (StructureElement.Location.is(location)) {
var unit = location.unit, element = location.element;
var seq_id = getSeqId(unit, element);
if (seq_id > 0) {
var seqLen = getSequenceLength(unit, element);
if (seqLen) {
scale.setDomain(0, seqLen - 1);
return scale.color(seq_id);
}
}
}
else if (Bond.isLocation(location)) {
var aUnit = location.aUnit, aIndex = location.aIndex;
var seq_id = getSeqId(aUnit, aUnit.elements[aIndex]);
if (seq_id > 0) {
var seqLen = getSequenceLength(aUnit, aUnit.elements[aIndex]);
if (seqLen) {
scale.setDomain(0, seqLen - 1);
return scale.color(seq_id);
}
}
}
return DefaultColor;
};
return {
factory: SequenceIdColorTheme,
granularity: 'group',
preferSmoothing: true,
color: color,
props: props,
description: Description,
legend: scale ? scale.legend : undefined
};
}
export var SequenceIdColorThemeProvider = {
name: 'sequence-id',
label: 'Sequence Id',
category: "Residue Property" /* ColorTheme.Category.Residue */,
factory: SequenceIdColorTheme,
getParams: getSequenceIdColorThemeParams,
defaultValues: PD.getDefaultValues(SequenceIdColorThemeParams),
isApplicable: function (ctx) { return !!ctx.structure; }
};