molstar
Version:
A comprehensive macromolecular library.
144 lines (143 loc) • 7.89 kB
JavaScript
;
/**
* Copyright (c) 2024 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.ExternalStructureColorThemeProvider = exports.ExternalStructureColorThemeParams = void 0;
exports.ExternalStructureColorTheme = ExternalStructureColorTheme;
const color_1 = require("../../mol-util/color");
const param_definition_1 = require("../../mol-util/param-definition");
const location_iterator_1 = require("../../mol-geo/util/location-iterator");
const categories_1 = require("./categories");
const selection_1 = require("../../mol-state/state/selection");
const objects_1 = require("../../mol-plugin-state/objects");
const structure_1 = require("../../mol-model/structure");
const chain_id_1 = require("./chain-id");
const entity_id_1 = require("./entity-id");
const entity_source_1 = require("./entity-source");
const molecule_type_1 = require("./molecule-type");
const model_index_1 = require("./model-index");
const structure_index_1 = require("./structure-index");
const type_helpers_1 = require("../../mol-util/type-helpers");
const lookup3d_1 = require("../../mol-model/structure/structure/util/lookup3d");
const structure_selection_query_1 = require("../../mol-plugin-state/helpers/structure-selection-query");
const vec3_1 = require("../../mol-math/linear-algebra/3d/vec3");
const Description = `Assigns a color based on structure property at a given vertex.`;
exports.ExternalStructureColorThemeParams = {
structure: param_definition_1.ParamDefinition.ValueRef((ctx) => {
const structures = ctx.state.data.select(selection_1.StateSelection.Generators.rootsOfType(objects_1.PluginStateObject.Molecule.Structure)).filter(c => { var _a; return (_a = c.obj) === null || _a === void 0 ? void 0 : _a.data; });
return structures.map(v => { var _a, _b; return [v.transform.ref, (_b = (_a = v.obj) === null || _a === void 0 ? void 0 : _a.label) !== null && _b !== void 0 ? _b : '<unknown>']; });
}, (ref, getData) => getData(ref)),
style: param_definition_1.ParamDefinition.MappedStatic('chain-id', {
'chain-id': param_definition_1.ParamDefinition.Group(chain_id_1.ChainIdColorThemeParams),
'entity-id': param_definition_1.ParamDefinition.Group(entity_id_1.EntityIdColorThemeParams),
'entity-source': param_definition_1.ParamDefinition.Group(entity_source_1.EntitySourceColorThemeParams),
'molecule-type': param_definition_1.ParamDefinition.Group(molecule_type_1.MoleculeTypeColorThemeParams),
'model-index': param_definition_1.ParamDefinition.Group(model_index_1.ModelIndexColorThemeParams),
'structure-index': param_definition_1.ParamDefinition.Group(structure_index_1.StructureIndexColorThemeParams),
}),
defaultColor: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xcccccc)),
maxDistance: param_definition_1.ParamDefinition.Numeric(8, { min: 0.1, max: 24, step: 0.1 }, { description: 'Maximum distance to search for the nearest structure element. This is done only if the approximate search fails.' }),
approxMaxDistance: param_definition_1.ParamDefinition.Numeric(4, { min: 0, max: 12, step: 0.1 }, { description: 'Maximum distance to search for an approximately nearest structure element. This is done before the extact search.' }),
normalOffset: param_definition_1.ParamDefinition.Numeric(0, { min: -10, max: 20, step: 0.1 }, { description: 'Offset vertex position along its normal by given amount.' }),
backboneOnly: param_definition_1.ParamDefinition.Boolean(false),
};
function getStyleTheme(ctx, props) {
switch (props.name) {
case 'chain-id': return (0, chain_id_1.ChainIdColorTheme)(ctx, props.params);
case 'entity-id': return (0, entity_id_1.EntityIdColorTheme)(ctx, props.params);
case 'entity-source': return (0, entity_source_1.EntitySourceColorTheme)(ctx, props.params);
case 'molecule-type': return (0, molecule_type_1.MoleculeTypeColorTheme)(ctx, props.params);
case 'model-index': return (0, model_index_1.ModelIndexColorTheme)(ctx, props.params);
case 'structure-index': return (0, structure_index_1.StructureIndexColorTheme)(ctx, props.params);
default: (0, type_helpers_1.assertUnreachable)(props);
}
}
function ExternalStructureColorTheme(ctx, props) {
let structure;
try {
structure = props.structure.getValue();
}
catch (_a) {
// .getValue() is resolved during state reconciliation => would throw from UI
}
// NOTE: this will currently be slow for with GPU/texture meshes due to slow iteration
// TODO: create texture to be able to do the sampling on the GPU
let color;
let contextHash = undefined;
let legend = undefined;
const { maxDistance, approxMaxDistance: approxDistance, normalOffset, defaultColor, backboneOnly } = props;
if (structure) {
const styleTheme = getStyleTheme({ ...ctx, structure }, props.style);
const lookupFirstCtx = (0, lookup3d_1.StructureLookup3DResultContext)();
const lookupNearestCtx = (0, lookup3d_1.StructureLookup3DResultContext)();
let s = structure;
if (backboneOnly) {
s = structure_1.StructureSelection.unionStructure(structure_selection_query_1.StructureSelectionQueries.backbone.query(new structure_1.QueryContext(structure)));
}
const position = (0, vec3_1.Vec3)();
const l = structure_1.StructureElement.Location.create(s);
color = (location, isSecondary) => {
if (!(0, location_iterator_1.isPositionLocation)(location)) {
return defaultColor;
}
// Offset the vertex position along its normal
if (normalOffset !== 0) {
vec3_1.Vec3.scaleAndAdd(position, location.position, location.normal, normalOffset);
}
else {
vec3_1.Vec3.copy(position, location.position);
}
const [x, y, z] = position;
if (approxDistance > 0) {
const rf = s.lookup3d.approxNearest(x, y, z, approxDistance, lookupFirstCtx);
if (rf.count > 0) {
l.unit = rf.units[0];
l.element = l.unit.elements[rf.indices[0]];
return styleTheme.color(l, isSecondary);
}
}
const rn = s.lookup3d.find(x, y, z, maxDistance, lookupNearestCtx);
if (rn.count > 0) {
let idx = 0;
let minD = rn.squaredDistances[0];
for (let i = 1; i < rn.count; ++i) {
if (rn.squaredDistances[i] < minD) {
minD = rn.squaredDistances[i];
idx = i;
}
}
l.unit = rn.units[idx];
l.element = l.unit.elements[rn.indices[idx]];
return styleTheme.color(l, isSecondary);
}
return defaultColor;
};
contextHash = styleTheme.contextHash;
legend = styleTheme.legend;
}
else {
color = () => defaultColor;
}
return {
factory: ExternalStructureColorTheme,
granularity: 'vertex',
preferSmoothing: true,
color,
props,
contextHash,
description: Description,
legend,
};
}
exports.ExternalStructureColorThemeProvider = {
name: 'external-structure',
label: 'External Structure',
category: categories_1.ColorThemeCategory.Misc,
factory: ExternalStructureColorTheme,
getParams: () => exports.ExternalStructureColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ExternalStructureColorThemeParams),
isApplicable: (ctx) => true,
};