molstar
Version:
A comprehensive macromolecular library.
83 lines (82 loc) • 3.73 kB
JavaScript
;
/**
* Copyright (c) 2018-2021 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.getAtomicDerivedData = getAtomicDerivedData;
const atomic_1 = require("../atomic");
const types_1 = require("../../types");
const util_1 = require("../../../../../mol-model/structure/util");
const debug_1 = require("../../../../../mol-util/debug");
function getAtomicDerivedData(data, segments, index, chemicalComponentMap) {
const { label_comp_id, type_symbol, _rowCount: atomCount } = data.atoms;
const { _rowCount: residueCount } = data.residues;
const { offsets } = segments.residueAtomSegments;
const atomicNumber = new Uint8Array(atomCount);
for (let i = 0; i < atomCount; ++i) {
atomicNumber[i] = (0, atomic_1.AtomNumber)(type_symbol.value(i));
}
const traceElementIndex = new Int32Array(residueCount);
const directionFromElementIndex = new Int32Array(residueCount);
const directionToElementIndex = new Int32Array(residueCount);
const moleculeType = new Uint8Array(residueCount);
const polymerType = new Uint8Array(residueCount);
const moleculeTypeMap = new Map();
const polymerTypeMap = new Map();
for (let i = 0; i < residueCount; ++i) {
const compId = label_comp_id.value(offsets[i]);
const chemCompMap = chemicalComponentMap;
let molType;
let polyType;
if (moleculeTypeMap.has(compId)) {
molType = moleculeTypeMap.get(compId);
polyType = polymerTypeMap.get(compId);
}
else {
let type;
if (chemCompMap.has(compId)) {
type = chemCompMap.get(compId).type;
}
else {
if (!debug_1.isProductionMode)
console.info('chemComp not found', compId);
type = (0, types_1.getComponentType)(compId);
}
molType = (0, types_1.getMoleculeType)(type, compId);
// TODO if unknown molecule type, use atom names to guess molecule type
polyType = (0, types_1.getPolymerType)(type, molType);
moleculeTypeMap.set(compId, molType);
polymerTypeMap.set(compId, polyType);
}
moleculeType[i] = molType;
polymerType[i] = polyType;
const traceAtomId = (0, util_1.getAtomIdForAtomRole)(polyType, 'trace');
let traceIndex = index.findAtomsOnResidue(i, traceAtomId);
if (traceIndex === -1) {
const coarseAtomId = (0, util_1.getAtomIdForAtomRole)(polyType, 'coarseBackbone');
traceIndex = index.findAtomsOnResidue(i, coarseAtomId);
if (traceIndex === -1 && (0, types_1.isPolymer)(molType)) {
traceIndex = index.findElementOnResidue(i, (0, types_1.ElementSymbol)('C'));
}
}
traceElementIndex[i] = traceIndex;
const directionFromAtomId = (0, util_1.getAtomIdForAtomRole)(polyType, 'directionFrom');
directionFromElementIndex[i] = index.findAtomsOnResidue(i, directionFromAtomId);
const directionToAtomId = (0, util_1.getAtomIdForAtomRole)(polyType, 'directionTo');
directionToElementIndex[i] = index.findAtomsOnResidue(i, directionToAtomId);
}
return {
atom: {
atomicNumber: atomicNumber
},
residue: {
traceElementIndex: traceElementIndex,
directionFromElementIndex: directionFromElementIndex,
directionToElementIndex: directionToElementIndex,
moleculeType: moleculeType,
polymerType: polymerType,
}
};
}