molstar
Version:
A comprehensive macromolecular library.
136 lines (135 loc) • 7.03 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 { __extends } from "tslib";
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 var AccessibleSurfaceArea = PluginBehavior.create({
name: 'computed-accessible-surface-area-prop',
category: 'custom-props',
display: { name: 'Accessible Surface Area' },
ctor: /** @class */ (function (_super) {
__extends(class_1, _super);
function class_1() {
var _this = _super !== null && _super.apply(this, arguments) || this;
_this.provider = AccessibleSurfaceAreaProvider;
_this.labelProvider = {
label: function (loci) {
if (!_this.params.showTooltip)
return;
return accessibleSurfaceAreaLabel(loci);
}
};
return _this;
}
class_1.prototype.update = function (p) {
var 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;
};
class_1.prototype.register = function () {
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);
};
class_1.prototype.unregister = function () {
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);
};
return class_1;
}(PluginBehavior.Handler)),
params: function () { return ({
autoAttach: PD.Boolean(false),
showTooltip: PD.Boolean(true)
}); }
});
//
function accessibleSurfaceAreaLabel(loci) {
if (loci.kind === 'element-loci') {
if (loci.elements.length === 0)
return;
var accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
if (!accessibleSurfaceArea || loci.structure.customPropertyDescriptors.hasReference(AccessibleSurfaceAreaProvider.descriptor))
return;
var getSerialIndex_1 = loci.structure.root.serialMapping.getSerialIndex;
var area_1 = accessibleSurfaceArea.area, serialResidueIndex_1 = accessibleSurfaceArea.serialResidueIndex;
var seen_1 = new Set();
var cummulativeArea_1 = 0;
var _loop_1 = function (indices, unit) {
var elements = unit.elements;
OrderedSet.forEach(indices, function (idx) {
var rSI = serialResidueIndex_1[getSerialIndex_1(unit, elements[idx])];
if (rSI !== -1 && !seen_1.has(rSI)) {
cummulativeArea_1 += area_1[rSI];
seen_1.add(rSI);
}
});
};
for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
var _b = _a[_i], indices = _b.indices, unit = _b.unit;
_loop_1(indices, unit);
}
if (seen_1.size === 0)
return;
var residueCount = "<small>(".concat(seen_1.size, " ").concat(seen_1.size > 1 ? 'Residues sum' : 'Residue', ")</small>");
return "Accessible Surface Area ".concat(residueCount, ": ").concat(cummulativeArea_1.toFixed(2), " \u212B<sup>2</sup>");
}
else if (loci.kind === 'structure-loci') {
var accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
if (!accessibleSurfaceArea || loci.structure.customPropertyDescriptors.hasReference(AccessibleSurfaceAreaProvider.descriptor))
return;
return "Accessible Surface Area <small>(Whole Structure)</small>: ".concat(arraySum(accessibleSurfaceArea.area).toFixed(2), " \u212B<sup>2</sup>");
}
}
//
var 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: function (ctx, structure) {
return AccessibleSurfaceAreaProvider.attach(ctx, structure);
}
});
var 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: function (ctx, structure) {
return AccessibleSurfaceAreaProvider.attach(ctx, structure);
}
});