molstar
Version:
A comprehensive macromolecular library.
159 lines (158 loc) • 8.69 kB
JavaScript
"use strict";
/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getAtomicHierarchyAndConformation = getAtomicHierarchyAndConformation;
const db_1 = require("../../../mol-data/db");
const int_1 = require("../../../mol-data/int");
const schema_1 = require("../../../mol-io/reader/cif/schema");
const geometry_1 = require("../../../mol-math/geometry");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const atom_site_operator_mapping_1 = require("../../../mol-model/structure/export/categories/atom_site_operator_mapping");
const atomic_1 = require("../../../mol-model/structure/model/properties/atomic");
const atomic_derived_1 = require("../../../mol-model/structure/model/properties/utils/atomic-derived");
const atomic_index_1 = require("../../../mol-model/structure/model/properties/utils/atomic-index");
const types_1 = require("../../../mol-model/structure/model/types");
const uuid_1 = require("../../../mol-util/uuid");
const mmcif_1 = require("../mmcif");
function findHierarchyOffsets(atom_site) {
if (atom_site._rowCount === 0)
return { residues: [], chains: [] };
const start = 0, end = atom_site._rowCount;
const residues = [start], chains = [start];
const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = atom_site;
for (let i = start + 1; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !label_seq_id.areValuesEqual(i - 1, i)
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i);
// not checking label_comp_id to allow for MICROHETEROGENEITY
if (newResidue)
residues[residues.length] = i;
if (newChain)
chains[chains.length] = i;
}
return { residues, chains };
}
function createHierarchyData(atom_site, sourceIndex, offsets) {
const atoms = db_1.Table.ofColumns(atomic_1.AtomsSchema, {
type_symbol: db_1.Column.ofArray({ array: db_1.Column.mapToArray(atom_site.type_symbol, types_1.ElementSymbol), schema: db_1.Column.Schema.Aliased(db_1.Column.Schema.str) }),
label_atom_id: atom_site.label_atom_id,
auth_atom_id: atom_site.auth_atom_id,
label_alt_id: atom_site.label_alt_id,
label_comp_id: atom_site.label_comp_id,
auth_comp_id: atom_site.auth_comp_id,
pdbx_formal_charge: atom_site.pdbx_formal_charge
});
const residues = db_1.Table.view(atom_site, atomic_1.ResiduesSchema, offsets.residues);
const chains = db_1.Table.view(atom_site, atomic_1.ChainsSchema, offsets.chains);
if (!residues.label_seq_id.isDefined) {
const seqIds = new Int32Array(residues.label_seq_id.rowCount);
const { residues: residueOffsets, chains: chainOffsets } = offsets;
let cI = 0;
let seqId = 0;
for (let i = 0, il = seqIds.length; i < il; ++i) {
if (residueOffsets[i] >= chainOffsets[cI + 1]) {
cI += 1;
seqId = 0;
}
seqIds[i] = ++seqId; // start id on one
}
residues.label_seq_id = db_1.Column.ofIntArray(seqIds);
}
// Optimize the numeric columns
db_1.Table.columnToArray(residues, 'label_seq_id', Int32Array);
db_1.Table.columnToArray(residues, 'auth_seq_id', Int32Array);
return { atoms, residues, chains, atomSourceIndex: sourceIndex };
}
function getConformation(atom_site) {
return {
id: uuid_1.UUID.create22(),
atomId: atom_site.id,
occupancy: atom_site.occupancy.isDefined ? atom_site.occupancy : db_1.Column.ofConst(1, atom_site._rowCount, db_1.Column.Schema.float),
B_iso_or_equiv: atom_site.B_iso_or_equiv,
xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
x: atom_site.Cartn_x.toArray({ array: Float32Array }),
y: atom_site.Cartn_y.toArray({ array: Float32Array }),
z: atom_site.Cartn_z.toArray({ array: Float32Array }),
};
}
function isHierarchyDataEqual(a, b) {
return db_1.Table.areEqual(a.chains, b.chains)
&& db_1.Table.areEqual(a.residues, b.residues)
&& db_1.Table.areEqual(a.atoms, b.atoms);
}
function createChainOperatorMappingAndSubstituteNames(hierarchy, format) {
const mapping = new Map();
if (!mmcif_1.MmcifFormat.is(format))
return mapping;
const { molstar_atom_site_operator_mapping: entries } = (0, schema_1.toDatabase)(atom_site_operator_mapping_1.AtomSiteOperatorMappingSchema, format.data.frame);
if (entries._rowCount === 0)
return mapping;
const labelMap = new Map();
const authMap = new Map();
for (let i = 0; i < entries._rowCount; i++) {
const assembly = entries.assembly_operator_id.valueKind(i) === db_1.Column.ValueKinds.Present
? { id: entries.assembly_id.value(i), operList: [], operId: entries.assembly_operator_id.value(i) }
: void 0;
const operator = geometry_1.SymmetryOperator.create(entries.operator_name.value(i), linear_algebra_1.Mat4.identity(), {
assembly,
spgrOp: entries.symmetry_operator_index.valueKind(i) === db_1.Column.ValueKinds.Present ? entries.symmetry_operator_index.value(i) : void 0,
hkl: linear_algebra_1.Vec3.ofArray(entries.symmetry_hkl.value(i)),
ncsId: entries.ncs_id.value(i)
});
const suffix = entries.suffix.value(i);
const label = entries.label_asym_id.value(i);
labelMap.set(`${label}${suffix}`, { name: label, operator });
const auth = entries.auth_asym_id.value(i);
authMap.set(`${auth}${suffix}`, auth);
}
const { label_asym_id, auth_asym_id } = hierarchy.chains;
const mappedLabel = new Array(label_asym_id.rowCount);
const mappedAuth = new Array(label_asym_id.rowCount);
for (let i = 0; i < label_asym_id.rowCount; i++) {
const label = label_asym_id.value(i), auth = auth_asym_id.value(i);
if (!labelMap.has(label)) {
mappedLabel[i] = label;
mappedAuth[i] = auth;
continue;
}
const { name, operator } = labelMap.get(label);
mapping.set(i, operator);
mappedLabel[i] = name;
mappedAuth[i] = authMap.get(auth) || auth;
}
hierarchy.chains.label_asym_id = db_1.Column.ofArray({ array: mappedLabel, valueKind: hierarchy.chains.label_asym_id.valueKind, schema: hierarchy.chains.label_asym_id.schema });
hierarchy.chains.auth_asym_id = db_1.Column.ofArray({ array: mappedAuth, valueKind: hierarchy.chains.auth_asym_id.valueKind, schema: hierarchy.chains.auth_asym_id.schema });
return mapping;
}
function getAtomicHierarchy(atom_site, sourceIndex, entities, chemicalComponentMap, format, previous) {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, sourceIndex, hierarchyOffsets);
const chainOperatorMapping = createChainOperatorMappingAndSubstituteNames(hierarchyData, format);
if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
return {
sameAsPrevious: true,
hierarchy: previous.atomicHierarchy,
chainOperatorMapping
};
}
const hierarchySegments = {
residueAtomSegments: int_1.Segmentation.ofOffsets(hierarchyOffsets.residues, int_1.Interval.ofBounds(0, atom_site._rowCount)),
chainAtomSegments: int_1.Segmentation.ofOffsets(hierarchyOffsets.chains, int_1.Interval.ofBounds(0, atom_site._rowCount)),
};
const index = (0, atomic_index_1.getAtomicIndex)(hierarchyData, entities, hierarchySegments);
const derived = (0, atomic_derived_1.getAtomicDerivedData)(hierarchyData, hierarchySegments, index, chemicalComponentMap);
const hierarchy = { ...hierarchyData, ...hierarchySegments, index, derived };
return { sameAsPrevious: false, hierarchy, chainOperatorMapping };
}
function getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, chemicalComponentMap, format, previous) {
const { sameAsPrevious, hierarchy, chainOperatorMapping } = getAtomicHierarchy(atom_site, sourceIndex, entities, chemicalComponentMap, format, previous);
const conformation = getConformation(atom_site);
return { sameAsPrevious, hierarchy, conformation, chainOperatorMapping };
}