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molstar

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A comprehensive macromolecular library.

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/** * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> * @author David Sehnal <david.sehnal@gmail.com> */ import { SortedArray } from '../../../../mol-data/int'; import { SymmetryOperator } from '../../../../mol-math/geometry'; import { Mat4 } from '../../../../mol-math/linear-algebra'; import { ModelSymmetry } from '../../../../mol-model-formats/structure/property/symmetry'; import { CustomStructureProperty } from '../../../../mol-model-props/common/custom-structure-property'; import { Structure, Unit } from '../../../../mol-model/structure'; import { Symmetry } from '../../../../mol-model/structure/model/properties/symmetry'; import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin-state/objects'; import { StateTransformer } from '../../../../mol-state/transformer'; import { Task } from '../../../../mol-task'; import { deepEqual } from '../../../../mol-util'; import { ParamDefinition as PD } from '../../../../mol-util/param-definition'; import { partitionUnits } from '../util'; function createModelChainMap(model) { const builder = new Structure.StructureBuilder(); const units = new Map(); const { label_asym_id, _rowCount } = model.atomicHierarchy.chains; const { offsets } = model.atomicHierarchy.chainAtomSegments; for (let i = 0; i < _rowCount; i++) { const elements = SortedArray.ofBounds(offsets[i], offsets[i + 1]); const unit = builder.addUnit(0 /* Unit.Kind.Atomic */, model, SymmetryOperator.Default, elements, Unit.Trait.FastBoundary); units.set(label_asym_id.value(i), unit); } return units; } function buildAssembly(model, assembly) { const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { assembly: { id: assembly.id, operId: 0, operList: [] } }); const assembler = Structure.Builder({ coordinateSystem, label: model.label, }); const units = createModelChainMap(model); for (const g of assembly.operatorGroups) { for (const oper of g.operators) { for (const id of g.asymIds) { const u = units.get(id); if (u) { assembler.addWithOperator(u, oper); } else { console.log(`missing asymId '${id}'`); } } } } return assembler.getStructure(); } export { MmcifAssembly }; const MmcifAssembly = PluginStateTransform.BuiltIn({ name: 'mmcif-assembly', display: { name: 'Mmcif Assembly' }, from: PSO.Molecule.Model, to: PSO.Molecule.Structure, params: { id: PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' }), } })({ canAutoUpdate({ newParams }) { return true; }, apply({ a, params }, plugin) { return Task.create('Build Structure', async (ctx) => { const model = a.data; let id = params.id; let asm = void 0; const symmetry = ModelSymmetry.Provider.get(model); // if no id is specified, use the 1st assembly. if (!id && symmetry && symmetry.assemblies.length !== 0) { id = symmetry.assemblies[0].id; } if (!symmetry || symmetry.assemblies.length === 0) { plugin.log.warn(`Model '${model.entryId}' has no assembly, returning model structure.`); } else { asm = Symmetry.findAssembly(model, id || ''); if (!asm) { plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning model structure.`); } } const base = Structure.ofModel(model); if (!asm) { const label = { label: 'Model', description: Structure.elementDescription(base) }; return new PSO.Molecule.Structure(base, label); } const s = buildAssembly(model, asm); const objProps = { label: `Assembly ${id}`, description: Structure.elementDescription(s) }; return new PSO.Molecule.Structure(s, objProps); }); }, update({ newParams, oldParams }) { return deepEqual(newParams, oldParams) ? StateTransformer.UpdateResult.Unchanged : StateTransformer.UpdateResult.Recreate; }, dispose({ b }) { b === null || b === void 0 ? void 0 : b.data.customPropertyDescriptors.dispose(); } }); const UnitsByEntity = CustomStructureProperty.createSimple('units_by_entity', 'root'); function getUnitsByEntity(structure) { if (UnitsByEntity.get(structure).value) { return UnitsByEntity.get(structure).value; } const atomicIndex = structure.model.atomicHierarchy.index; const spheresIndex = structure.model.coarseHierarchy.spheres; const map = new Map(); for (const ug of structure.unitSymmetryGroups) { const u = ug.units[0]; let e; if (Unit.isAtomic(u)) { e = atomicIndex.getEntityFromChain(u.chainIndex[u.elements[0]]); } else if (Unit.isSpheres(u)) { e = spheresIndex.getEntityFromChain(u.coarseElements.chainElementSegments.index[u.elements[0]]); } else { continue; } if (!map.has(e)) map.set(e, []); const entityUnits = map.get(e); for (let i = 0, il = ug.units.length; i < il; ++i) { entityUnits.push(ug.units[i]); } } UnitsByEntity.set(structure, { value: map }, map); return map; } export { MmcifStructure }; const MmcifStructure = PluginStateTransform.BuiltIn({ name: 'mmcif-structure', display: { name: 'Mmcif Structure' }, from: PSO.Root, to: PSO.Molecule.Structure, params: { structureRef: PD.Text(''), entityId: PD.Text(''), cellSize: PD.Numeric(500, { min: 0, max: 10000, step: 100 }), } })({ canAutoUpdate({ newParams }) { return true; }, apply({ a, params, dependencies }) { return Task.create('Build Structure', async (ctx) => { const parent = dependencies[params.structureRef].data; const { entities } = parent.model; const idx = entities.getEntityIndex(params.entityId); const unitsByEntity = getUnitsByEntity(parent); const units = unitsByEntity.get(idx) || []; const unitCount = units.length; let structure; if (unitCount > 1 && units.every(u => u.conformation.operator.isIdentity)) { const mergedUnits = partitionUnits(units, params.cellSize); structure = Structure.create(mergedUnits); } else { structure = Structure.create(units); } // could also use _struct_ref.pdbx_db_accession to point to uniprot with _struct_ref.db_name == UNP const label = entities.data.pdbx_description.value(idx).join(', ') || 'model'; const description = `*Entity id* ${entities.data.id.value(idx)} *src_method* ${entities.data.src_method.value(idx)} *type* ${entities.data.type.value(idx)}`; return new PSO.Molecule.Structure(structure, { label, description: description }); }); }, update({ newParams, oldParams }) { return deepEqual(newParams, oldParams) ? StateTransformer.UpdateResult.Unchanged : StateTransformer.UpdateResult.Recreate; }, dispose({ b }) { b === null || b === void 0 ? void 0 : b.data.customPropertyDescriptors.dispose(); } });