molstar
Version:
A comprehensive macromolecular library.
127 lines (126 loc) • 5.56 kB
JavaScript
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/**
* Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.createAssemblies = createAssemblies;
exports.operatorGroupsProvider = operatorGroupsProvider;
exports.getMatrices = getMatrices;
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const symmetry_operator_1 = require("../../../mol-math/geometry/symmetry-operator");
const symmetry_1 = require("../../../mol-model/structure/model/properties/symmetry");
const structure_1 = require("../../../mol-model/structure");
const structure_2 = require("../../../mol-model/structure");
function createAssemblies(pdbx_struct_assembly, pdbx_struct_assembly_gen, pdbx_struct_oper_list) {
if (!pdbx_struct_assembly._rowCount)
return [];
const matrices = getMatrices(pdbx_struct_oper_list);
const assemblies = [];
for (let i = 0; i < pdbx_struct_assembly._rowCount; i++) {
assemblies[assemblies.length] = createAssembly(pdbx_struct_assembly, pdbx_struct_assembly_gen, i, matrices);
}
return assemblies;
}
function createAssembly(pdbx_struct_assembly, pdbx_struct_assembly_gen, index, matrices) {
const id = pdbx_struct_assembly.id.value(index);
const details = pdbx_struct_assembly.details.value(index);
const generators = [];
const { assembly_id, oper_expression, asym_id_list } = pdbx_struct_assembly_gen;
for (let i = 0, _i = pdbx_struct_assembly_gen._rowCount; i < _i; i++) {
if (assembly_id.value(i) !== id)
continue;
generators[generators.length] = {
assemblyId: id,
expression: oper_expression.value(i),
asymIds: asym_id_list.value(i)
};
}
return symmetry_1.Assembly.create(id, details, operatorGroupsProvider(generators, matrices));
}
function operatorGroupsProvider(generators, matrices) {
return () => {
const groups = [];
let operatorOffset = 0;
for (let i = 0; i < generators.length; i++) {
const gen = generators[i];
const operatorList = parseOperatorList(gen.expression);
const operatorNames = expandOperators(operatorList);
const operators = getAssemblyOperators(matrices, operatorNames, operatorOffset, gen.assemblyId);
const selector = structure_1.Queries.generators.atoms({ chainTest: structure_1.Queries.pred.and(structure_1.Queries.pred.eq(ctx => structure_2.StructureProperties.unit.operator_name(ctx.element), symmetry_operator_1.SymmetryOperator.DefaultName), structure_1.Queries.pred.inSet(ctx => structure_2.StructureProperties.chain.label_asym_id(ctx.element), gen.asymIds)) });
groups[groups.length] = { selector, operators, asymIds: gen.asymIds };
operatorOffset += operators.length;
}
return groups;
};
}
function getMatrices(pdbx_struct_oper_list) {
const { id, matrix, vector, _schema } = pdbx_struct_oper_list;
const matrices = new Map();
const t = (0, linear_algebra_1.Vec3)();
for (let i = 0, _i = pdbx_struct_oper_list._rowCount; i < _i; i++) {
const m = linear_algebra_1.Tensor.toMat4((0, linear_algebra_1.Mat4)(), _schema.matrix.space, matrix.value(i));
linear_algebra_1.Tensor.toVec3(t, _schema.vector.space, vector.value(i));
linear_algebra_1.Mat4.setTranslation(m, t);
linear_algebra_1.Mat4.setValue(m, 3, 3, 1);
matrices.set(id.value(i), m);
}
return matrices;
}
function expandOperators(operatorList) {
const ops = [];
const currentOp = [];
for (let i = 0; i < operatorList.length; i++)
currentOp[i] = '';
expandOperators1(operatorList, ops, operatorList.length - 1, currentOp);
return ops;
}
function expandOperators1(operatorNames, list, i, current) {
if (i < 0) {
list[list.length] = current.slice(0);
return;
}
const ops = operatorNames[i], len = ops.length;
for (let j = 0; j < len; j++) {
current[i] = ops[j];
expandOperators1(operatorNames, list, i - 1, current);
}
}
function getAssemblyOperators(matrices, operatorNames, startIndex, assemblyId) {
const operators = [];
let index = startIndex;
for (const op of operatorNames) {
const m = linear_algebra_1.Mat4.identity();
for (let i = 0; i < op.length; i++) {
linear_algebra_1.Mat4.mul(m, m, matrices.get(op[i]));
}
index++;
operators[operators.length] = symmetry_operator_1.SymmetryOperator.create(`ASM_${index}`, m, { assembly: { id: assemblyId, operId: index, operList: op } });
}
return operators;
}
function parseOperatorList(value) {
// '(X0)(1-5)' becomes [['X0'], ['1', '2', '3', '4', '5']]
// kudos to Glen van Ginkel.
const oeRegex = /\(?([^\(\)]+)\)?]*/g, groups = [], ret = [];
let g;
while (g = oeRegex.exec(value))
groups[groups.length] = g[1];
groups.forEach(g => {
const group = [];
g.split(',').forEach(e => {
const dashIndex = e.indexOf('-');
if (dashIndex > 0) {
const from = parseInt(e.substring(0, dashIndex)), to = parseInt(e.substr(dashIndex + 1));
for (let i = from; i <= to; i++)
group[group.length] = i.toString();
}
else {
group[group.length] = e.trim();
}
});
ret[ret.length] = group;
});
return ret;
}