molstar
Version:
A comprehensive macromolecular library.
128 lines (127 loc) • 6.26 kB
JavaScript
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PluginBehavior } from '../../../behavior';
import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
import { AccessibleSurfaceAreaProvider, AccessibleSurfaceAreaSymbols } from '../../../../../mol-model-props/computed/accessible-surface-area';
import { AccessibleSurfaceAreaColorThemeProvider } from '../../../../../mol-model-props/computed/themes/accessible-surface-area';
import { OrderedSet } from '../../../../../mol-data/int';
import { arraySum } from '../../../../../mol-util/array';
import { DefaultQueryRuntimeTable } from '../../../../../mol-script/runtime/query/compiler';
import { StructureSelectionQuery, StructureSelectionCategory } from '../../../../../mol-plugin-state/helpers/structure-selection-query';
import { MolScriptBuilder as MS } from '../../../../../mol-script/language/builder';
export const AccessibleSurfaceArea = PluginBehavior.create({
name: 'computed-accessible-surface-area-prop',
category: 'custom-props',
display: { name: 'Accessible Surface Area' },
ctor: class extends PluginBehavior.Handler {
constructor() {
super(...arguments);
this.provider = AccessibleSurfaceAreaProvider;
this.labelProvider = {
label: (loci) => {
if (!this.params.showTooltip)
return;
return accessibleSurfaceAreaLabel(loci);
}
};
}
update(p) {
const updated = (this.params.autoAttach !== p.autoAttach ||
this.params.showTooltip !== p.showTooltip);
this.params.autoAttach = p.autoAttach;
this.params.showTooltip = p.showTooltip;
this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
return updated;
}
register() {
DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
this.ctx.representation.structure.themes.colorThemeRegistry.add(AccessibleSurfaceAreaColorThemeProvider);
this.ctx.managers.lociLabels.addProvider(this.labelProvider);
this.ctx.query.structure.registry.add(isBuried);
this.ctx.query.structure.registry.add(isAccessible);
}
unregister() {
DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
this.ctx.representation.structure.themes.colorThemeRegistry.remove(AccessibleSurfaceAreaColorThemeProvider);
this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
this.ctx.query.structure.registry.remove(isBuried);
this.ctx.query.structure.registry.remove(isAccessible);
}
},
params: () => ({
autoAttach: PD.Boolean(false),
showTooltip: PD.Boolean(true)
})
});
//
function accessibleSurfaceAreaLabel(loci) {
if (loci.kind === 'element-loci') {
if (loci.elements.length === 0)
return;
const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
if (!accessibleSurfaceArea || loci.structure.customPropertyDescriptors.hasReference(AccessibleSurfaceAreaProvider.descriptor))
return;
const { getSerialIndex } = loci.structure.root.serialMapping;
const { area, serialResidueIndex } = accessibleSurfaceArea;
const seen = new Set();
let cummulativeArea = 0;
for (const { indices, unit } of loci.elements) {
const { elements } = unit;
OrderedSet.forEach(indices, idx => {
const rSI = serialResidueIndex[getSerialIndex(unit, elements[idx])];
if (rSI !== -1 && !seen.has(rSI)) {
cummulativeArea += area[rSI];
seen.add(rSI);
}
});
}
if (seen.size === 0)
return;
const residueCount = `<small>(${seen.size} ${seen.size > 1 ? 'Residues sum' : 'Residue'})</small>`;
return `Accessible Surface Area ${residueCount}: ${cummulativeArea.toFixed(2)} \u212B<sup>2</sup>`;
}
else if (loci.kind === 'structure-loci') {
const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
if (!accessibleSurfaceArea || loci.structure.customPropertyDescriptors.hasReference(AccessibleSurfaceAreaProvider.descriptor))
return;
return `Accessible Surface Area <small>(Whole Structure)</small>: ${arraySum(accessibleSurfaceArea.area).toFixed(2)} \u212B<sup>2</sup>`;
}
}
//
const isBuried = StructureSelectionQuery('Buried Protein Residues', MS.struct.modifier.union([
MS.struct.modifier.wholeResidues([
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
'residue-test': AccessibleSurfaceAreaSymbols.isBuried.symbol(),
})
])
])
]), {
description: 'Select buried protein residues.',
category: StructureSelectionCategory.Residue,
ensureCustomProperties: (ctx, structure) => {
return AccessibleSurfaceAreaProvider.attach(ctx, structure);
}
});
const isAccessible = StructureSelectionQuery('Accessible Protein Residues', MS.struct.modifier.union([
MS.struct.modifier.wholeResidues([
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
'residue-test': AccessibleSurfaceAreaSymbols.isAccessible.symbol(),
})
])
])
]), {
description: 'Select accessible protein residues.',
category: StructureSelectionCategory.Residue,
ensureCustomProperties: (ctx, structure) => {
return AccessibleSurfaceAreaProvider.attach(ctx, structure);
}
});