molstar
Version:
A comprehensive macromolecular library.
273 lines (272 loc) • 13.3 kB
JavaScript
;
/**
* Copyright (c) 2020-2023 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.ClashesParams = exports.InterUnitClashParams = exports.IntraUnitClashParams = void 0;
exports.IntraUnitClashVisual = IntraUnitClashVisual;
exports.InterUnitClashVisual = InterUnitClashVisual;
exports.getClashesParams = getClashesParams;
exports.ClashesRepresentation = ClashesRepresentation;
const param_definition_1 = require("../../../mol-util/param-definition");
const structure_1 = require("../../../mol-model/structure");
const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
const loci_1 = require("../../../mol-model/loci");
const representation_1 = require("../../../mol-repr/representation");
const representation_2 = require("../../../mol-repr/structure/representation");
const link_1 = require("../../../mol-repr/structure/visual/util/link");
const units_visual_1 = require("../../../mol-repr/structure/units-visual");
const location_iterator_1 = require("../../../mol-geo/util/location-iterator");
const prop_1 = require("./prop");
const complex_visual_1 = require("../../../mol-repr/structure/complex-visual");
const color_1 = require("../../../mol-util/color");
const marker_action_1 = require("../../../mol-util/marker-action");
const centroid_helper_1 = require("../../../mol-math/geometry/centroid-helper");
const geometry_1 = require("../../../mol-math/geometry");
const label_1 = require("../../../mol-theme/label");
const 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);
const clashes = prop_1.ClashesProvider.get(structure).value.intraUnit.get(unit.id);
const { edgeCount, a, b, edgeProps } = clashes;
const { magnitude } = edgeProps;
const { sizeFactor } = props;
if (!edgeCount)
return mesh_1.Mesh.createEmpty(mesh);
const { elements, conformation: c } = unit;
const builderProps = {
linkCount: edgeCount * 2,
position: (posA, posB, edgeIndex) => {
c.invariantPosition(elements[a[edgeIndex]], posA);
c.invariantPosition(elements[b[edgeIndex]], posB);
},
style: (edgeIndex) => link_1.LinkStyle.Disk,
radius: (edgeIndex) => magnitude[edgeIndex] * sizeFactor,
};
const { mesh: m, boundingSphere } = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
if (boundingSphere) {
m.setBoundingSphere(boundingSphere);
}
else if (m.triangleCount > 0) {
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
m.setBoundingSphere(sphere);
}
return m;
}
exports.IntraUnitClashParams = {
...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: (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);
}
function getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere) {
return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, (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) {
const idx = elements[0];
if (idx === undefined)
return '';
const { edgeProps: { id, magnitude, distance } } = clashes;
const mag = magnitude[idx].toFixed(2);
const 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, clashes }, elements, (boundingSphere) => getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere), () => getIntraClashLabel(structure, unit, clashes, elements));
}
function getIntraClashLoci(pickingId, structureGroup, id) {
const { objectId, instanceId, groupId } = pickingId;
if (id === objectId) {
const { structure, group } = structureGroup;
const unit = group.units[instanceId];
if (structure_1.Unit.isAtomic(unit)) {
const 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) {
const changed = false;
// TODO
return changed;
}
function createIntraClashIterator(structureGroup) {
const { structure, group } = structureGroup;
const unit = group.units[0];
const clashes = prop_1.ClashesProvider.get(structure).value.intraUnit.get(unit.id);
const { a } = clashes;
const groupCount = clashes.edgeCount * 2;
const instanceCount = group.units.length;
const location = structure_1.StructureElement.Location.create(structure);
const getLocation = (groupIndex, instanceIndex) => {
const 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) {
const clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
const { edges, edgeCount } = clashes;
const { sizeFactor } = props;
if (!edgeCount)
return mesh_1.Mesh.createEmpty(mesh);
const builderProps = {
linkCount: edgeCount,
position: (posA, posB, edgeIndex) => {
const b = edges[edgeIndex];
const uA = structure.unitMap.get(b.unitA);
const uB = structure.unitMap.get(b.unitB);
uA.conformation.position(uA.elements[b.indexA], posA);
uB.conformation.position(uB.elements[b.indexB], posB);
},
style: (edgeIndex) => link_1.LinkStyle.Disk,
radius: (edgeIndex) => edges[edgeIndex].props.magnitude * sizeFactor
};
const { mesh: m, boundingSphere } = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
if (boundingSphere) {
m.setBoundingSphere(boundingSphere);
}
else {
const sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
m.setBoundingSphere(sphere);
}
return m;
}
exports.InterUnitClashParams = {
...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: (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);
}
function getInterClashBoundingSphere(structure, clashes, elements, boundingSphere) {
return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
const c = clashes.edges[elements[i]];
const uA = structure.unitMap.get(c.unitA);
const 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) {
const idx = elements[0];
if (idx === undefined)
return '';
const c = clashes.edges[idx];
const uA = structure.unitMap.get(c.unitA);
const uB = structure.unitMap.get(c.unitB);
const mag = c.props.magnitude.toFixed(2);
const 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, (boundingSphere) => getInterClashBoundingSphere(structure, clashes, elements, boundingSphere), () => getInterClashLabel(structure, clashes, elements));
}
function getInterClashLoci(pickingId, structure, id) {
const { objectId, groupId } = pickingId;
if (id === objectId) {
const clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
return InterClashLoci(structure, clashes, [groupId]);
}
return loci_1.EmptyLoci;
}
function eachInterClash(loci, structure, apply) {
const changed = false;
// TODO
return changed;
}
function createInterClashIterator(structure) {
const clashes = prop_1.ClashesProvider.get(structure).value.interUnit;
const groupCount = clashes.edgeCount;
const instanceCount = 1;
const location = structure_1.StructureElement.Location.create(structure);
const getLocation = (groupIndex) => {
const 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);
}
//
const ClashesVisuals = {
'intra-clash': (ctx, getParams) => (0, representation_2.UnitsRepresentation)('Intra-unit clash cylinder', ctx, getParams, IntraUnitClashVisual),
'inter-clash': (ctx, getParams) => (0, representation_2.ComplexRepresentation)('Inter-unit clash cylinder', ctx, getParams, InterUnitClashVisual),
};
exports.ClashesParams = {
...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);
}
function ClashesRepresentation(ctx, getParams) {
const repr = representation_1.Representation.createMulti('Clashes', ctx, getParams, representation_2.StructureRepresentationStateBuilder, ClashesVisuals);
repr.setState({ markerActions: marker_action_1.MarkerActions.Highlighting });
return repr;
}
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: (structure) => structure.elementCount > 0,
ensureCustomProperties: {
attach: (ctx, structure) => prop_1.ClashesProvider.attach(ctx, structure, void 0, true),
detach: (data) => prop_1.ClashesProvider.ref(data, false)
}
});