molstar
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A comprehensive macromolecular library.
362 lines (361 loc) • 18.1 kB
JavaScript
"use strict";
/**
* Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getAtomRangesForRow = getAtomRangesForRow;
exports.getAtomRangesForRows = getAtomRangesForRows;
exports.atomQualifies = atomQualifies;
exports.rowToExpression = rowToExpression;
exports.rowsToExpression = rowsToExpression;
exports.groupRows = groupRows;
const db_1 = require("../../../mol-data/db");
const structure_1 = require("../../../mol-model/structure");
const array_1 = require("../../../mol-util/array");
const atom_ranges_1 = require("./atom-ranges");
const indexing_1 = require("./indexing");
const utils_1 = require("./utils");
const EmptyArray = [];
/** Return atom ranges in `model` which satisfy criteria given by `row` */
function getAtomRangesForRow(model, row, indices) {
const h = model.atomicHierarchy;
const nAtoms = h.atoms._rowCount;
const hasAtomIds = (0, utils_1.isAnyDefined)(row.atom_id, row.atom_index);
const hasAtomFilter = (0, utils_1.isAnyDefined)(row.label_atom_id, row.auth_atom_id, row.type_symbol)
|| (0, utils_1.isDefined)(row.label_comp_id) && !indices.residuesByLabelCompIdIsPure
|| (0, utils_1.isDefined)(row.auth_comp_id) && !indices.residuesByAuthCompIdIsPure;
const hasResidueFilter = (0, utils_1.isAnyDefined)(row.label_seq_id, row.auth_seq_id, row.pdbx_PDB_ins_code, row.beg_label_seq_id, row.end_label_seq_id, row.beg_auth_seq_id, row.end_auth_seq_id, row.label_comp_id, row.auth_comp_id);
const hasChainFilter = (0, utils_1.isAnyDefined)(row.label_asym_id, row.auth_asym_id, row.label_entity_id);
if (hasAtomIds) {
const theAtom = getTheAtomForRow(model, row, indices);
return theAtom !== undefined ? atom_ranges_1.AtomRanges.single(theAtom, theAtom + 1) : atom_ranges_1.AtomRanges.empty();
}
if (!hasChainFilter && !hasResidueFilter && !hasAtomFilter) {
return atom_ranges_1.AtomRanges.single(0, nAtoms);
}
const qualifyingChains = getQualifyingChains(model, row, indices);
if (!hasResidueFilter && !hasAtomFilter) {
const chainOffsets = h.chainAtomSegments.offsets;
const ranges = atom_ranges_1.AtomRanges.empty();
for (const iChain of qualifyingChains) {
atom_ranges_1.AtomRanges.add(ranges, chainOffsets[iChain], chainOffsets[iChain + 1]);
}
return ranges;
}
const qualifyingResidues = getQualifyingResidues(model, row, indices, qualifyingChains);
if (!hasAtomFilter) {
const residueOffsets = h.residueAtomSegments.offsets;
const ranges = atom_ranges_1.AtomRanges.empty();
for (const iRes of qualifyingResidues) {
atom_ranges_1.AtomRanges.add(ranges, residueOffsets[iRes], residueOffsets[iRes + 1]);
}
return ranges;
}
const qualifyingAtoms = getQualifyingAtoms(model, row, indices, qualifyingResidues);
const ranges = atom_ranges_1.AtomRanges.empty();
for (const iAtom of qualifyingAtoms) {
atom_ranges_1.AtomRanges.add(ranges, iAtom, iAtom + 1);
}
return ranges;
}
/** Return atom ranges in `model` which satisfy criteria given by any of `rows` (atoms that satisfy more rows are still included only once) */
function getAtomRangesForRows(model, rows, indices) {
if (Array.isArray(rows)) {
return atom_ranges_1.AtomRanges.union(rows.map(row => getAtomRangesForRow(model, row, indices)));
}
else {
return getAtomRangesForRow(model, rows, indices);
}
}
/** Return an array of chain indexes which satisfy criteria given by `row` */
function getQualifyingChains(model, row, indices) {
var _a, _b, _c;
const { auth_asym_id, label_entity_id, _rowCount: nChains } = model.atomicHierarchy.chains;
let result = undefined;
if ((0, utils_1.isDefined)(row.label_asym_id)) {
result = (_a = indices.chainsByLabelAsymId.get(row.label_asym_id)) !== null && _a !== void 0 ? _a : EmptyArray;
}
if ((0, utils_1.isDefined)(row.auth_asym_id)) {
if (result) {
result = result.filter(i => auth_asym_id.value(i) === row.auth_asym_id);
}
else {
result = (_b = indices.chainsByAuthAsymId.get(row.auth_asym_id)) !== null && _b !== void 0 ? _b : EmptyArray;
}
}
if ((0, utils_1.isDefined)(row.label_entity_id)) {
if (result) {
result = result.filter(i => label_entity_id.value(i) === row.label_entity_id);
}
else {
result = (_c = indices.chainsByLabelEntityId.get(row.label_entity_id)) !== null && _c !== void 0 ? _c : EmptyArray;
}
}
result !== null && result !== void 0 ? result : (result = (0, array_1.range)(nChains));
return result;
}
/** Return an array of residue indexes which satisfy criteria given by `row` */
function getQualifyingResidues(model, row, indices, fromChains) {
var _a, _b, _c;
const { label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = model.atomicHierarchy.residues;
const { label_comp_id, auth_comp_id } = model.atomicHierarchy.atoms;
const { residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
const { Present } = db_1.Column.ValueKind;
const result = [];
for (const iChain of fromChains) {
let residuesHere = undefined;
if ((0, utils_1.isDefined)(row.label_seq_id)) {
const sorting = indices.residuesSortedByLabelSeqId.get(iChain);
residuesHere = indexing_1.Sorting.getKeysWithValue(sorting, row.label_seq_id);
}
if ((0, utils_1.isDefined)(row.auth_seq_id)) {
if (residuesHere) {
residuesHere = residuesHere.filter(i => auth_seq_id.valueKind(i) === Present && auth_seq_id.value(i) === row.auth_seq_id);
}
else {
const sorting = indices.residuesSortedByAuthSeqId.get(iChain);
residuesHere = indexing_1.Sorting.getKeysWithValue(sorting, row.auth_seq_id);
}
}
if ((0, utils_1.isDefined)(row.pdbx_PDB_ins_code)) {
if (residuesHere) {
residuesHere = residuesHere.filter(i => pdbx_PDB_ins_code.value(i) === row.pdbx_PDB_ins_code);
}
else {
residuesHere = (_a = indices.residuesByInsCode.get(iChain).get(row.pdbx_PDB_ins_code)) !== null && _a !== void 0 ? _a : EmptyArray;
}
}
if ((0, utils_1.isDefined)(row.beg_label_seq_id) || (0, utils_1.isDefined)(row.end_label_seq_id)) {
if (residuesHere) {
if ((0, utils_1.isDefined)(row.beg_label_seq_id)) {
residuesHere = residuesHere.filter(i => label_seq_id.valueKind(i) === Present && label_seq_id.value(i) >= row.beg_label_seq_id);
}
if ((0, utils_1.isDefined)(row.end_label_seq_id)) {
residuesHere = residuesHere.filter(i => label_seq_id.valueKind(i) === Present && label_seq_id.value(i) <= row.end_label_seq_id);
}
}
else {
const sorting = indices.residuesSortedByLabelSeqId.get(iChain);
residuesHere = indexing_1.Sorting.getKeysWithValueInRange(sorting, row.beg_label_seq_id, row.end_label_seq_id);
}
}
if ((0, utils_1.isDefined)(row.beg_auth_seq_id) || (0, utils_1.isDefined)(row.end_auth_seq_id)) {
if (residuesHere) {
if ((0, utils_1.isDefined)(row.beg_auth_seq_id)) {
residuesHere = residuesHere.filter(i => auth_seq_id.valueKind(i) === Present && auth_seq_id.value(i) >= row.beg_auth_seq_id);
}
if ((0, utils_1.isDefined)(row.end_auth_seq_id)) {
residuesHere = residuesHere.filter(i => auth_seq_id.valueKind(i) === Present && auth_seq_id.value(i) <= row.end_auth_seq_id);
}
}
else {
const sorting = indices.residuesSortedByAuthSeqId.get(iChain);
residuesHere = indexing_1.Sorting.getKeysWithValueInRange(sorting, row.beg_auth_seq_id, row.end_auth_seq_id);
}
}
if ((0, utils_1.isDefined)(row.label_comp_id)) {
if (residuesHere) {
if (indices.residuesByLabelCompIdIsPure) {
residuesHere = residuesHere.filter(i => label_comp_id.value(residueAtomSegments.offsets[i]) === row.label_comp_id);
}
else {
residuesHere = residuesHere.filter(i => {
for (let iAtom = residueAtomSegments.offsets[i], stop = residueAtomSegments.offsets[i + 1]; iAtom < stop; iAtom++) {
if (label_comp_id.value(iAtom) === row.label_comp_id)
return true;
}
});
}
}
else {
residuesHere = (_b = indices.residuesByLabelCompId.get(iChain).get(row.label_comp_id)) !== null && _b !== void 0 ? _b : EmptyArray;
}
}
if ((0, utils_1.isDefined)(row.auth_comp_id)) {
if (residuesHere) {
if (indices.residuesByAuthCompIdIsPure) {
residuesHere = residuesHere.filter(i => auth_comp_id.value(residueAtomSegments.offsets[i]) === row.auth_comp_id);
}
else {
residuesHere = residuesHere.filter(i => {
for (let iAtom = residueAtomSegments.offsets[i], stop = residueAtomSegments.offsets[i + 1]; iAtom < stop; iAtom++) {
if (auth_comp_id.value(iAtom) === row.auth_comp_id)
return true;
}
});
}
}
else {
residuesHere = (_c = indices.residuesByAuthCompId.get(iChain).get(row.auth_comp_id)) !== null && _c !== void 0 ? _c : EmptyArray;
}
}
if (!residuesHere) {
const firstResidueForChain = residueAtomSegments.index[chainAtomSegments.offsets[iChain]];
const firstResidueAfterChain = residueAtomSegments.index[chainAtomSegments.offsets[iChain + 1] - 1] + 1;
residuesHere = (0, array_1.range)(firstResidueForChain, firstResidueAfterChain);
}
(0, array_1.arrayExtend)(result, residuesHere);
}
return result;
}
/** Return an array of atom indexes which satisfy criteria given by `row` */
function getQualifyingAtoms(model, row, indices, fromResidues) {
const { label_atom_id, auth_atom_id, type_symbol, label_comp_id, auth_comp_id } = model.atomicHierarchy.atoms;
const residueAtomSegments_offsets = model.atomicHierarchy.residueAtomSegments.offsets;
const result = [];
for (const iRes of fromResidues) {
const atomIdcs = (0, array_1.range)(residueAtomSegments_offsets[iRes], residueAtomSegments_offsets[iRes + 1]);
if ((0, utils_1.isDefined)(row.label_atom_id)) {
(0, array_1.filterInPlace)(atomIdcs, iAtom => label_atom_id.value(iAtom) === row.label_atom_id);
}
if ((0, utils_1.isDefined)(row.auth_atom_id)) {
(0, array_1.filterInPlace)(atomIdcs, iAtom => auth_atom_id.value(iAtom) === row.auth_atom_id);
}
if ((0, utils_1.isDefined)(row.type_symbol)) {
(0, array_1.filterInPlace)(atomIdcs, iAtom => { var _a; return type_symbol.value(iAtom) === ((_a = row.type_symbol) === null || _a === void 0 ? void 0 : _a.toUpperCase()); });
}
if ((0, utils_1.isDefined)(row.label_comp_id) && !indices.residuesByLabelCompIdIsPure) {
(0, array_1.filterInPlace)(atomIdcs, iAtom => label_comp_id.value(iAtom) === row.label_comp_id);
}
if ((0, utils_1.isDefined)(row.auth_comp_id) && !indices.residuesByAuthCompIdIsPure) {
(0, array_1.filterInPlace)(atomIdcs, iAtom => auth_comp_id.value(iAtom) === row.auth_comp_id);
}
(0, array_1.arrayExtend)(result, atomIdcs);
}
return result;
}
/** Return index of atom in `model` which satistfies criteria given by `row`, if any.
* Only works when `row.atom_id` and/or `row.atom_index` is defined (otherwise use `getAtomRangesForRow`). */
function getTheAtomForRow(model, row, indices) {
let iAtom = undefined;
if (!(0, utils_1.isDefined)(row.atom_id) && !(0, utils_1.isDefined)(row.atom_index))
throw new Error('ArgumentError: at least one of row.atom_id, row.atom_index must be defined.');
if ((0, utils_1.isDefined)(row.atom_id) && (0, utils_1.isDefined)(row.atom_index)) {
const a1 = indices.atomsById.get(row.atom_id);
const a2 = indices.atomsByIndex.get(row.atom_index);
if (a1 !== a2)
return undefined;
iAtom = a1;
}
if ((0, utils_1.isDefined)(row.atom_id)) {
iAtom = indices.atomsById.get(row.atom_id);
}
if ((0, utils_1.isDefined)(row.atom_index)) {
iAtom = indices.atomsByIndex.get(row.atom_index);
}
if (iAtom === undefined)
return undefined;
if (!atomQualifies(model, iAtom, row))
return undefined;
return iAtom;
}
/** Return true if `iAtom`-th atom in `model` satisfies all selection criteria given by `row`. */
function atomQualifies(model, iAtom, row) {
var _a;
const h = model.atomicHierarchy;
const iChain = h.chainAtomSegments.index[iAtom];
const label_asym_id = h.chains.label_asym_id.value(iChain);
const auth_asym_id = h.chains.auth_asym_id.value(iChain);
const label_entity_id = h.chains.label_entity_id.value(iChain);
if (!matches(row.label_asym_id, label_asym_id))
return false;
if (!matches(row.auth_asym_id, auth_asym_id))
return false;
if (!matches(row.label_entity_id, label_entity_id))
return false;
const iRes = h.residueAtomSegments.index[iAtom];
const label_seq_id = (h.residues.label_seq_id.valueKind(iRes) === db_1.Column.ValueKind.Present) ? h.residues.label_seq_id.value(iRes) : undefined;
const auth_seq_id = (h.residues.auth_seq_id.valueKind(iRes) === db_1.Column.ValueKind.Present) ? h.residues.auth_seq_id.value(iRes) : undefined;
const pdbx_PDB_ins_code = h.residues.pdbx_PDB_ins_code.value(iRes);
if (!matches(row.label_seq_id, label_seq_id))
return false;
if (!matches(row.auth_seq_id, auth_seq_id))
return false;
if (!matches(row.pdbx_PDB_ins_code, pdbx_PDB_ins_code))
return false;
if (!matchesRange(row.beg_label_seq_id, row.end_label_seq_id, label_seq_id))
return false;
if (!matchesRange(row.beg_auth_seq_id, row.end_auth_seq_id, auth_seq_id))
return false;
const label_comp_id = h.atoms.label_comp_id.value(iAtom);
const auth_comp_id = h.atoms.auth_comp_id.value(iAtom);
const label_atom_id = h.atoms.label_atom_id.value(iAtom);
const auth_atom_id = h.atoms.auth_atom_id.value(iAtom);
const type_symbol = h.atoms.type_symbol.value(iAtom);
const atom_id = model.atomicConformation.atomId.value(iAtom);
const atom_index = h.atomSourceIndex.value(iAtom);
if (!matches(row.label_comp_id, label_comp_id))
return false;
if (!matches(row.auth_comp_id, auth_comp_id))
return false;
if (!matches(row.label_atom_id, label_atom_id))
return false;
if (!matches(row.auth_atom_id, auth_atom_id))
return false;
if (!matches((_a = row.type_symbol) === null || _a === void 0 ? void 0 : _a.toUpperCase(), type_symbol))
return false;
if (!matches(row.atom_id, atom_id))
return false;
if (!matches(row.atom_index, atom_index))
return false;
return true;
}
/** Return true if `value` equals `requiredValue` or if `requiredValue` if not defined. */
function matches(requiredValue, value) {
return !(0, utils_1.isDefined)(requiredValue) || value === requiredValue;
}
/** Return true if `requiredMin <= value <= requiredMax`.
* Undefined `requiredMin` behaves like negative infinity.
* Undefined `requiredMax` behaves like positive infinity. */
function matchesRange(requiredMin, requiredMax, value) {
if ((0, utils_1.isDefined)(requiredMin) && (!(0, utils_1.isDefined)(value) || value < requiredMin))
return false;
if ((0, utils_1.isDefined)(requiredMax) && (!(0, utils_1.isDefined)(value) || value > requiredMax))
return false;
return true;
}
/** Convert an annotation row into a MolScript expression */
function rowToExpression(row) {
return structure_1.StructureElement.Schema.toExpression(row);
}
/** Convert multiple annotation rows into a MolScript expression.
* (with union semantics, i.e. an atom qualifies if it qualifies for at least one of the rows) */
function rowsToExpression(rows) {
return structure_1.StructureElement.Schema.toExpression({
items: rows
});
}
/** Return row indices grouped by `row.group_id`. Rows with `row.group_id===undefined` are treated as separate groups. */
function groupRows(rows) {
let counter = 0;
const groupMap = new Map();
const groups = [];
for (let i = 0; i < rows.length; i++) {
const group_id = rows[i].group_id;
if (group_id === undefined) {
groups.push(counter++);
}
else {
const groupIndex = groupMap.get(group_id);
if (groupIndex === undefined) {
groupMap.set(group_id, counter);
groups.push(counter);
counter++;
}
else {
groups.push(groupIndex);
}
}
}
const rowIndices = (0, array_1.range)(rows.length).sort((i, j) => groups[i] - groups[j]);
const offsets = [];
for (let i = 0; i < rows.length; i++) {
if (i === 0 || groups[rowIndices[i]] !== groups[rowIndices[i - 1]])
offsets.push(i);
}
offsets.push(rowIndices.length);
return { count: offsets.length - 1, offsets, grouped: rowIndices };
}