molstar
Version:
A comprehensive macromolecular library.
243 lines • 13.6 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.ClashesRepresentationProvider = exports.ClashesRepresentation = exports.getClashesParams = exports.ClashesParams = exports.InterUnitClashVisual = exports.InterUnitClashParams = exports.IntraUnitClashVisual = exports.IntraUnitClashParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../../mol-util/param-definition");
var structure_1 = require("../../../mol-model/structure");
var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
var loci_1 = require("../../../mol-model/loci");
var representation_1 = require("../../../mol-repr/representation");
var representation_2 = require("../../../mol-repr/structure/representation");
var link_1 = require("../../../mol-repr/structure/visual/util/link");
var units_visual_1 = require("../../../mol-repr/structure/units-visual");
var location_iterator_1 = require("../../../mol-geo/util/location-iterator");
var prop_1 = require("./prop");
var complex_visual_1 = require("../../../mol-repr/structure/complex-visual");
var color_1 = require("../../../mol-util/color");
var marker_action_1 = require("../../../mol-util/marker-action");
var centroid_helper_1 = require("../../../mol-math/geometry/centroid-helper");
var label_1 = require("../../../mol-theme/label");
var params_1 = require("../../../mol-repr/structure/params");
//
function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, mesh) {
if (!structure_1.Unit.isAtomic(unit))
return mesh_1.Mesh.createEmpty(mesh);
var clashes = prop_1.ClashesProvider.get(structure).value.intraUnit.get(unit.id);
var edgeCount = clashes.edgeCount, a = clashes.a, b = clashes.b, edgeProps = clashes.edgeProps;
var magnitude = edgeProps.magnitude;
var sizeFactor = props.sizeFactor;
if (!edgeCount)
return mesh_1.Mesh.createEmpty(mesh);
var elements = unit.elements;
var pos = unit.conformation.invariantPosition;
var builderProps = {
linkCount: edgeCount * 2,
position: function (posA, posB, edgeIndex) {
pos(elements[a[edgeIndex]], posA);
pos(elements[b[edgeIndex]], posB);
},
style: function (edgeIndex) { return 6 /* Disk */; },
radius: function (edgeIndex) { return magnitude[edgeIndex] * sizeFactor; },
};
return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
}
exports.IntraUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
function IntraUnitClashVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitClashParams),
createGeometry: createIntraUnitClashCylinderMesh,
createLocationIterator: createIntraClashIterator,
getLoci: getIntraClashLoci,
eachLocation: eachIntraClash,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.linkCap !== currentProps.linkCap);
}
}, materialId);
}
exports.IntraUnitClashVisual = IntraUnitClashVisual;
function getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere) {
return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, function (i, pA, pB) {
unit.conformation.position(unit.elements[clashes.a[elements[i]]], pA);
unit.conformation.position(unit.elements[clashes.b[elements[i]]], pB);
}, boundingSphere);
}
function getIntraClashLabel(structure, unit, clashes, elements) {
var idx = elements[0];
if (idx === undefined)
return '';
var _a = clashes.edgeProps, id = _a.id, magnitude = _a.magnitude, distance = _a.distance;
var mag = magnitude[idx].toFixed(2);
var dist = distance[idx].toFixed(2);
return [
"Clash id: " + id[idx] + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
(0, label_1.bondLabel)(structure_1.Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
].join('</br>');
}
function IntraClashLoci(structure, unit, clashes, elements) {
return (0, loci_1.DataLoci)('intra-clashes', { unit: unit, clashes: clashes }, elements, function (boundingSphere) { return getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere); }, function () { return getIntraClashLabel(structure, unit, clashes, elements); });
}
function getIntraClashLoci(pickingId, structureGroup, id) {
var objectId = pickingId.objectId, instanceId = pickingId.instanceId, groupId = pickingId.groupId;
if (id === objectId) {
var structure = structureGroup.structure, group = structureGroup.group;
var unit = group.units[instanceId];
if (structure_1.Unit.isAtomic(unit)) {
var clashes = prop_1.ClashesProvider.get(structure).value.intraUnit.get(unit.id);
return IntraClashLoci(structure, unit, clashes, [groupId]);
}
}
return loci_1.EmptyLoci;
}
function eachIntraClash(loci, structureGroup, apply) {
var changed = false;
// TODO
return changed;
}
function createIntraClashIterator(structureGroup) {
var structure = structureGroup.structure, group = structureGroup.group;
var unit = group.units[0];
var clashes = prop_1.ClashesProvider.get(structure).value.intraUnit.get(unit.id);
var a = clashes.a;
var groupCount = clashes.edgeCount * 2;
var instanceCount = group.units.length;
var location = structure_1.StructureElement.Location.create(structure);
var getLocation = function (groupIndex, instanceIndex) {
var unit = group.units[instanceIndex];
location.unit = unit;
location.element = unit.elements[a[groupIndex]];
return location;
};
return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation);
}
//
function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
var clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
var edges = clashes.edges, edgeCount = clashes.edgeCount;
var sizeFactor = props.sizeFactor;
if (!edgeCount)
return mesh_1.Mesh.createEmpty(mesh);
var builderProps = {
linkCount: edgeCount,
position: function (posA, posB, edgeIndex) {
var b = edges[edgeIndex];
var uA = structure.unitMap.get(b.unitA);
var uB = structure.unitMap.get(b.unitB);
uA.conformation.position(uA.elements[b.indexA], posA);
uB.conformation.position(uB.elements[b.indexB], posB);
},
style: function (edgeIndex) { return 6 /* Disk */; },
radius: function (edgeIndex) { return edges[edgeIndex].props.magnitude * sizeFactor; }
};
return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
}
exports.InterUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
function InterUnitClashVisual(materialId) {
return (0, complex_visual_1.ComplexMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitClashParams),
createGeometry: createInterUnitClashCylinderMesh,
createLocationIterator: createInterClashIterator,
getLoci: getInterClashLoci,
eachLocation: eachInterClash,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.linkCap !== currentProps.linkCap);
}
}, materialId);
}
exports.InterUnitClashVisual = InterUnitClashVisual;
function getInterClashBoundingSphere(structure, clashes, elements, boundingSphere) {
return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, function (i, pA, pB) {
var c = clashes.edges[elements[i]];
var uA = structure.unitMap.get(c.unitA);
var uB = structure.unitMap.get(c.unitB);
uA.conformation.position(uA.elements[c.indexA], pA);
uB.conformation.position(uB.elements[c.indexB], pB);
}, boundingSphere);
}
function getInterClashLabel(structure, clashes, elements) {
var idx = elements[0];
if (idx === undefined)
return '';
var c = clashes.edges[idx];
var uA = structure.unitMap.get(c.unitA);
var uB = structure.unitMap.get(c.unitB);
var mag = c.props.magnitude.toFixed(2);
var dist = c.props.distance.toFixed(2);
return [
"Clash id: " + c.props.id + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
(0, label_1.bondLabel)(structure_1.Bond.Location(structure, uA, c.indexA, structure, uB, c.indexB))
].join('</br>');
}
function InterClashLoci(structure, clashes, elements) {
return (0, loci_1.DataLoci)('inter-clashes', clashes, elements, function (boundingSphere) { return getInterClashBoundingSphere(structure, clashes, elements, boundingSphere); }, function () { return getInterClashLabel(structure, clashes, elements); });
}
function getInterClashLoci(pickingId, structure, id) {
var objectId = pickingId.objectId, groupId = pickingId.groupId;
if (id === objectId) {
var clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
return InterClashLoci(structure, clashes, [groupId]);
}
return loci_1.EmptyLoci;
}
function eachInterClash(loci, structure, apply) {
var changed = false;
// TODO
return changed;
}
function createInterClashIterator(structure) {
var clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
var groupCount = clashes.edgeCount;
var instanceCount = 1;
var location = structure_1.StructureElement.Location.create(structure);
var getLocation = function (groupIndex) {
var clash = clashes.edges[groupIndex];
location.unit = structure.unitMap.get(clash.unitA);
location.element = location.unit.elements[clash.indexA];
return location;
};
return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation, true);
}
//
var ClashesVisuals = {
'intra-clash': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit clash cylinder', ctx, getParams, IntraUnitClashVisual); },
'inter-clash': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit clash cylinder', ctx, getParams, InterUnitClashVisual); },
};
exports.ClashesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.IntraUnitClashParams), exports.InterUnitClashParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-clash', 'inter-clash'], param_definition_1.ParamDefinition.objectToOptions(ClashesVisuals)) });
function getClashesParams(ctx, structure) {
return param_definition_1.ParamDefinition.clone(exports.ClashesParams);
}
exports.getClashesParams = getClashesParams;
function ClashesRepresentation(ctx, getParams) {
var repr = representation_1.Representation.createMulti('Clashes', ctx, getParams, representation_2.StructureRepresentationStateBuilder, ClashesVisuals);
repr.setState({ markerActions: marker_action_1.MarkerActions.Highlighting });
return repr;
}
exports.ClashesRepresentation = ClashesRepresentation;
exports.ClashesRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
name: prop_1.ValidationReport.Tag.Clashes,
label: 'Validation Clashes',
description: 'Displays clashes between atoms as disks. Data from wwPDB Validation Report, obtained via RCSB PDB.',
factory: ClashesRepresentation,
getParams: getClashesParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ClashesParams),
defaultColorTheme: { name: 'uniform', props: { value: (0, color_1.Color)(0xFA28FF) } },
defaultSizeTheme: { name: 'physical' },
isApplicable: function (structure) { return structure.elementCount > 0; },
ensureCustomProperties: {
attach: function (ctx, structure) { return prop_1.ClashesProvider.attach(ctx, structure, void 0, true); },
detach: function (data) { return prop_1.ClashesProvider.ref(data, false); }
}
});
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