molstar
Version:
A comprehensive macromolecular library.
131 lines (130 loc) • 5.73 kB
JavaScript
"use strict";
/**
* Copyright (c) 2022-2024 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.createPetworldHierarchy = createPetworldHierarchy;
const mol_state_1 = require("../../../../mol-state");
const model_1 = require("./model");
const spacefill_1 = require("../../../../mol-repr/structure/representation/spacefill");
const representation_1 = require("../../../../mol-plugin-state/transforms/representation");
const state_1 = require("../state");
const names_1 = require("../../../../mol-util/color/names");
const mmcif_1 = require("../../../../mol-model-formats/structure/mmcif");
const mol_task_1 = require("../../../../mol-task");
function getSpacefillParams(color, graphics) {
const gmp = (0, state_1.getGraphicsModeProps)(graphics === 'custom' ? 'quality' : graphics);
return {
type: {
name: 'spacefill',
params: {
...spacefill_1.SpacefillRepresentationProvider.defaultValues,
ignoreHydrogens: true,
instanceGranularity: true,
ignoreLight: true,
lodLevels: gmp.lodLevels,
quality: 'lowest', // avoid 'auto', triggers boundary calc
clip: {
variant: 'instance',
objects: [],
},
clipPrimitive: true,
approximate: gmp.approximate,
alphaThickness: gmp.alphaThickness,
},
},
colorTheme: {
name: 'uniform',
params: {
value: color,
saturation: 0,
lightness: 0,
}
},
sizeTheme: {
name: 'physical',
params: {
scale: 1,
}
},
};
}
async function createPetworldHierarchy(plugin, trajectory) {
var _a;
const cell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, trajectory);
const tr = (_a = cell === null || cell === void 0 ? void 0 : cell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!cell || !tr)
return;
if (!mmcif_1.MmcifFormat.is(tr.representative.sourceData))
return;
const membrane = [];
const other = [];
for (let i = 0; i < tr.frameCount; ++i) {
const m = await mol_task_1.Task.resolveInContext(tr.getFrameAtIndex(i));
// cannot use m.properties.structAsymMap because petworld models
// may assign the same asymId to multiple entities
const { label_asym_id, label_entity_id, _rowCount } = m.atomicHierarchy.chains;
const membraneIds = [];
const otherIds = [];
const seen = new Set();
for (let i = 0; i < _rowCount; i++) {
const entityId = label_entity_id.value(i);
if (seen.has(entityId))
continue;
const asymId = label_asym_id.value(i);
if (asymId.startsWith('MEM')) {
membraneIds.push(entityId);
}
else {
otherIds.push(entityId);
}
seen.add(entityId);
}
if (membraneIds.length) {
membrane.push({ modelIndex: i, entityIds: membraneIds });
}
if (otherIds.length) {
other.push({ modelIndex: i, entityIds: otherIds });
}
}
const state = plugin.state.data;
const graphicsMode = state_1.MesoscaleState.get(plugin).graphics;
const groupParams = (0, state_1.getMesoscaleGroupParams)(graphicsMode);
const group = await state.build()
.toRoot()
.apply(state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', illustrative: false, value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:'], state: { isCollapsed: false, isHidden: groupParams.hidden } })
.commit({ revertOnError: true });
await state.build()
.to(group)
.apply(state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', illustrative: false, value: names_1.ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:mem', 'ent:', '__no_group_color__'], state: { isCollapsed: true, isHidden: groupParams.hidden } })
.commit();
const colors = (0, state_1.getDistinctBaseColors)(other.length, 0);
await state.transaction(async () => {
try {
plugin.animationLoop.stop({ noDraw: true });
let build = state.build();
for (let i = 0, il = membrane.length; i < il; ++i) {
build = build
.to(cell)
.apply(model_1.StructureFromPetworld, membrane[i])
.apply(representation_1.StructureRepresentation3D, getSpacefillParams(names_1.ColorNames.lightgrey, graphicsMode), { tags: ['ent:mem', '__no_group_color__'] });
}
for (let i = 0, il = other.length; i < il; ++i) {
build = build
.to(cell)
.apply(model_1.StructureFromPetworld, other[i])
.apply(representation_1.StructureRepresentation3D, getSpacefillParams(colors[i], graphicsMode), { tags: ['ent:'] });
}
await build.commit();
}
catch (e) {
console.error(e);
plugin.log.error(e);
}
finally {
plugin.animationLoop.start();
}
}).run();
}