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atom-site.ts
atom-site.ts 8.55 KiB
/**
* Copyright (c) 2019-2022 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>
*/
import { CifField } from '../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { guessElementSymbolTokens } from '../util';
import { Column } from '../../../mol-data/db';
import { areTokensEmpty } from '../../../mol-io/reader/common/text/column/token';
type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
export function getAtomSiteTemplate(data: string, count: number) {
const str = () => [] as string[];
const ts = () => TokenBuilder.create(data, 2 * count);
return {
index: 0,
group_PDB: ts(),
id: str(),
auth_atom_id: ts(),
label_alt_id: ts(),
auth_comp_id: ts(),
auth_asym_id: ts(),
auth_seq_id: ts(),
pdbx_PDB_ins_code: ts(),
Cartn_x: ts(),
Cartn_y: ts(),
Cartn_z: ts(),
occupancy: ts(),
B_iso_or_equiv: ts(),
type_symbol: ts(),
pdbx_PDB_model_num: str(),
label_entity_id: str(),
partial_charge: ts(),
};
}
export function getAtomSite(sites: AtomSiteTemplate, terIndices: Set<number>, options: { hasAssemblies: boolean }): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
const pdbx_PDB_model_num = CifField.ofStrings(sites.pdbx_PDB_model_num);
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
const auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
const auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
const id = CifField.ofStrings(sites.id);
//
let currModelNum = pdbx_PDB_model_num.str(0);
let currAsymId = auth_asym_id.str(0);
let currSeqId = auth_seq_id.int(0);
let currLabelAsymId = currAsymId;
const asymIdCounts = new Map<string, number>();
const atomIdCounts = new Map<string, number>();
const labelAsymIds: string[] = [];
const labelAtomIds: string[] = [];
// ensure unique asym ids per model and unique atom ids per seq id
for (let i = 0, il = id.rowCount; i < il; ++i) {
const modelNum = pdbx_PDB_model_num.str(i);
const asymId = auth_asym_id.str(i);
const seqId = auth_seq_id.int(i);
let atomId = auth_atom_id.str(i);
if (modelNum !== currModelNum) { asymIdCounts.clear();
atomIdCounts.clear();
currModelNum = modelNum;
currAsymId = asymId;
currSeqId = seqId;
currLabelAsymId = asymId;
} else if (currAsymId !== asymId) {
atomIdCounts.clear();
currAsymId = asymId;
currSeqId = seqId;
currLabelAsymId = asymId;
} else if (currSeqId !== seqId) {
atomIdCounts.clear();
currSeqId = seqId;
}
if (asymIdCounts.has(asymId)) {
// only change the chains name if there are TER records
// otherwise assume repeated chain name use is from interleaved chains
if (terIndices.has(i) && !options.hasAssemblies) {
const asymIdCount = asymIdCounts.get(asymId)! + 1;
asymIdCounts.set(asymId, asymIdCount);
currLabelAsymId = `${asymId}_${asymIdCount}`;
}
} else {
asymIdCounts.set(asymId, 0);
}
labelAsymIds[i] = currLabelAsymId;
if (atomIdCounts.has(atomId)) {
const atomIdCount = atomIdCounts.get(atomId)! + 1;
atomIdCounts.set(atomId, atomIdCount);
atomId = `${atomId}_${atomIdCount}`;
} else {
atomIdCounts.set(atomId, 0);
}
labelAtomIds[i] = atomId;
}
const labelAsymId = Column.ofStringArray(labelAsymIds);
const labelAtomId = Column.ofStringArray(labelAtomIds);
//
return {
auth_asym_id,
auth_atom_id,
auth_comp_id,
auth_seq_id,
B_iso_or_equiv: CifField.ofTokens(sites.B_iso_or_equiv),
Cartn_x: CifField.ofTokens(sites.Cartn_x),
Cartn_y: CifField.ofTokens(sites.Cartn_y),
Cartn_z: CifField.ofTokens(sites.Cartn_z),
group_PDB: CifField.ofTokens(sites.group_PDB),
id,
label_alt_id: CifField.ofTokens(sites.label_alt_id),
label_asym_id: CifField.ofColumn(labelAsymId),
label_atom_id: CifField.ofColumn(labelAtomId),
label_comp_id: auth_comp_id,
label_seq_id: CifField.ofUndefined(sites.index, Column.Schema.int),
label_entity_id: CifField.ofStrings(sites.label_entity_id),
occupancy: areTokensEmpty(sites.occupancy) ? CifField.ofUndefined(sites.index, Column.Schema.float) : CifField.ofTokens(sites.occupancy),
type_symbol: CifField.ofTokens(sites.type_symbol),
pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),
pdbx_PDB_model_num,
partial_charge: CifField.ofTokens(sites.partial_charge)
};
}
export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number, isPdbqt: boolean) {
const { data: str } = data;
const length = e - s;
// TODO: filter invalid atoms
// COLUMNS DATA TYPE CONTENTS
// --------------------------------------------------------------------------------
// 1 - 6 Record name "ATOM "
TokenBuilder.addToken(sites.group_PDB, Tokenizer.trim(data, s, s + 6));
// 7 - 11 Integer Atom serial number.
// TODO: support HEX
Tokenizer.trim(data, s + 6, s + 11);
sites.id[sites.index] = data.data.substring(data.tokenStart, data.tokenEnd);
// 13 - 16 Atom Atom name.
TokenBuilder.addToken(sites.auth_atom_id, Tokenizer.trim(data, s + 12, s + 16));
// 17 Character Alternate location indicator.
if (str.charCodeAt(s + 16) === 32) { // ' '
TokenBuilder.add(sites.label_alt_id, 0, 0);
} else {
TokenBuilder.add(sites.label_alt_id, s + 16, s + 17);
}
// 18 - 20 Residue name Residue name.
TokenBuilder.addToken(sites.auth_comp_id, Tokenizer.trim(data, s + 17, s + 20));
// 22 Character Chain identifier.
TokenBuilder.add(sites.auth_asym_id, s + 21, s + 22);
// 23 - 26 Integer Residue sequence number.
// TODO: support HEX
TokenBuilder.addToken(sites.auth_seq_id, Tokenizer.trim(data, s + 22, s + 26));
// 27 AChar Code for insertion of residues.
if (str.charCodeAt(s + 26) === 32) { // ' '
TokenBuilder.add(sites.pdbx_PDB_ins_code, 0, 0);
} else {
TokenBuilder.add(sites.pdbx_PDB_ins_code, s + 26, s + 27);
}
// 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
TokenBuilder.addToken(sites.Cartn_x, Tokenizer.trim(data, s + 30, s + 38));
// 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
TokenBuilder.addToken(sites.Cartn_y, Tokenizer.trim(data, s + 38, s + 46));
// 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
TokenBuilder.addToken(sites.Cartn_z, Tokenizer.trim(data, s + 46, s + 54));
// 55 - 60 Real(6.2) Occupancy.
TokenBuilder.addToken(sites.occupancy, Tokenizer.trim(data, s + 54, s + 60));
// 61 - 66 Real(6.2) Temperature factor (Default = 0.0).
if (length >= 66) {
TokenBuilder.addToken(sites.B_iso_or_equiv, Tokenizer.trim(data, s + 60, s + 66));
} else {
TokenBuilder.add(sites.B_iso_or_equiv, 0, 0);
}
// 73 - 76 LString(4) Segment identifier, left-justified.
if (isPdbqt) {
TokenBuilder.addToken(sites.partial_charge, Tokenizer.trim(data, s + 70, s + 76));
} else { // ignored
}
// 77 - 78 LString(2) Element symbol, right-justified.
if (length >= 78 && !isPdbqt) {
Tokenizer.trim(data, s + 76, s + 78);
if (data.tokenStart < data.tokenEnd) {
TokenBuilder.addToken(sites.type_symbol, data);
} else {
guessElementSymbolTokens(sites.type_symbol, str, s + 12, s + 16);
}
} else {
guessElementSymbolTokens(sites.type_symbol, str, s + 12, s + 16);
}
// 79 - 80 LString(2) charge Charge on the atom.
// TODO
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
}