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Commit 5d186433 authored by Alexander Rose's avatar Alexander Rose
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pdb-parser, move atom-site methods to separate file

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src/mol-model-formats/structure/pdb/atom-site.ts 0 → 100644
+ 154
− 0
View file @ 5d186433
/**
* Copyright (c) 2019 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';
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,
count,
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()
};
}
export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_site']]?: CifField } {
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
const auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
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: CifField.ofStrings(sites.id),
label_alt_id: CifField.ofTokens(sites.label_alt_id),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
label_seq_id: auth_seq_id,
label_entity_id: CifField.ofStrings(sites.label_entity_id),
occupancy: 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: CifField.ofStrings(sites.pdbx_PDB_model_num)
};
}
export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number) {
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.label_alt_id, 0, 0);
} else {
TokenBuilder.add(sites.label_alt_id, 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.label_alt_id, 0, 0);
}
// 73 - 76 LString(4) Segment identifier, left-justified.
// ignored
// 77 - 78 LString(2) Element symbol, right-justified.
if (length >= 78) {
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)
}
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
}
\ No newline at end of file
src/mol-model-formats/structure/pdb/to-cif.ts
+ 4
− 148
View file @ 5d186433
......@@ -6,161 +6,17 @@
*/
import { substringStartsWith } from '../../../mol-util/string';
import { CifField, CifCategory, CifFrame } 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 { CifCategory, CifFrame } from '../../../mol-io/reader/cif';
import { Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { PdbFile } from '../../../mol-io/reader/pdb/schema';
import { parseCryst1, parseRemark350, parseMtrix } from './assembly';
import { parseHelix, parseSheet } from './secondary-structure';
import { guessElementSymbolTokens } from '../util';
import { parseCmpnd, parseHetnam } from './entity';
import { ComponentBuilder } from '../common/component';
import { EntityBuilder } from '../common/entity';
import { Column } from '../../../mol-data/db';
import { getMoleculeType } from '../../../mol-model/structure/model/types';
type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
function getAtomSiteTemplate(data: string, count: number) {
const str = () => [] as string[];
const ts = () => TokenBuilder.create(data, 2 * count);
return {
index: 0,
count,
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()
};
}
function getAomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_site']]?: CifField } {
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
const auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
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: CifField.ofStrings(sites.id),
label_alt_id: CifField.ofTokens(sites.label_alt_id),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
label_seq_id: auth_seq_id,
label_entity_id: CifField.ofStrings(sites.label_entity_id),
occupancy: 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: CifField.ofStrings(sites.pdbx_PDB_model_num)
};
}
function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number) {
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.label_alt_id, 0, 0);
} else {
TokenBuilder.add(sites.label_alt_id, 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.label_alt_id, 0, 0);
}
// 73 - 76 LString(4) Segment identifier, left-justified.
// ignored
// 77 - 78 LString(2) Element symbol, right-justified.
if (length >= 78) {
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)
}
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
}
import { getAtomSiteTemplate, addAtom, getAtomSite } from './atom-site';
export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const { lines } = pdb;
......@@ -301,7 +157,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const categories = {
entity: entityBuilder.getEntityCategory(),
chem_comp: componentBuilder.getChemCompCategory(),
atom_site: CifCategory.ofFields('atom_site', getAomSite(atomSite))
atom_site: CifCategory.ofFields('atom_site', getAtomSite(atomSite))
} as any;
for (const c of helperCategories) {
......
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