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Commit f4beba52 authored by Alexander Rose's avatar Alexander Rose
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pdb-parser, aniso records

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src/mol-model-formats/structure/pdb/anisotropic.ts 0 → 100644
+ 146
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View file @ f4beba52
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @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 { parseIntSkipLeadingWhitespace as fastParseInt } from '../../../mol-io/reader/common/text/number-parser';
type AnisotropicTemplate = typeof getAnisotropicTemplate extends (...args: any) => infer T ? T : never
export function getAnisotropicTemplate(data: string, count: number) {
const str = () => [] as string[];
const float = () => new Float32Array(count);
const ts = () => TokenBuilder.create(data, 2 * count);
return {
index: 0,
count,
id: str(),
type_symbol: ts(),
pdbx_label_atom_id: ts(),
pdbx_label_alt_id: ts(),
pdbx_label_comp_id: ts(),
pdbx_label_asym_id: ts(),
pdbx_label_seq_id: ts(),
pdbx_PDB_ins_code: ts(),
'U[1][1]': float(),
'U[2][2]': float(),
'U[3][3]': float(),
'U[1][2]': float(),
'U[1][3]': float(),
'U[2][3]': float(),
pdbx_auth_seq_id: ts(),
pdbx_auth_comp_id: ts(),
pdbx_auth_asym_id: ts(),
pdbx_auth_atom_id: ts(),
};
}
export function getAnisotropic(sites: AnisotropicTemplate): { [K in keyof mmCIF_Schema['atom_site_anisotrop']]?: CifField } {
const pdbx_auth_seq_id = CifField.ofTokens(sites.pdbx_auth_seq_id);
const pdbx_auth_comp_id = CifField.ofTokens(sites.pdbx_auth_comp_id);
const pdbx_auth_asym_id = CifField.ofTokens(sites.pdbx_auth_asym_id);
const pdbx_auth_atom_id = CifField.ofTokens(sites.pdbx_auth_atom_id);
const fields: { [K in keyof mmCIF_Schema['atom_site_anisotrop']]?: CifField } = {
id: CifField.ofStrings(sites.id),
type_symbol: CifField.ofTokens(sites.type_symbol),
pdbx_label_atom_id: pdbx_auth_atom_id,
pdbx_label_alt_id: CifField.ofTokens(sites.pdbx_label_alt_id),
pdbx_label_comp_id: pdbx_auth_comp_id,
pdbx_label_asym_id: pdbx_auth_asym_id,
pdbx_label_seq_id: pdbx_auth_seq_id,
pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),
pdbx_auth_seq_id,
pdbx_auth_comp_id,
pdbx_auth_asym_id,
pdbx_auth_atom_id,
};
(fields as any)['U[1][1]'] = CifField.ofNumbers(sites['U[1][1]']);
(fields as any)['U[2][2]'] = CifField.ofNumbers(sites['U[2][2]']);
(fields as any)['U[3][3]'] = CifField.ofNumbers(sites['U[3][3]']);
(fields as any)['U[1][2]'] = CifField.ofNumbers(sites['U[1][2]']);
(fields as any)['U[1][3]'] = CifField.ofNumbers(sites['U[1][3]']);
(fields as any)['U[2][3]'] = CifField.ofNumbers(sites['U[2][3]']);
return fields
}
export function addAnisotropic(sites: AnisotropicTemplate, model: string, data: Tokenizer, s: number, e: number) {
const { data: str } = data;
const length = e - s;
// COLUMNS DATA TYPE FIELD DEFINITION
// -----------------------------------------------------------------
// 1 - 6 Record name "ANISOU"
// 7 - 11 Integer serial Atom serial number.
Tokenizer.trim(data, s + 6, s + 11);
sites.id[sites.index] = str.substring(data.tokenStart, data.tokenEnd);
// 13 - 16 Atom name Atom name.
TokenBuilder.addToken(sites.pdbx_auth_atom_id, Tokenizer.trim(data, s + 12, s + 16));
// 17 Character altLoc Alternate location indicator
if (str.charCodeAt(s + 16) === 32) { // ' '
TokenBuilder.add(sites.pdbx_label_alt_id, 0, 0);
} else {
TokenBuilder.add(sites.pdbx_label_alt_id, s + 16, s + 17);
}
// 18 - 20 Residue name resName Residue name.
TokenBuilder.addToken(sites.pdbx_auth_comp_id, Tokenizer.trim(data, s + 17, s + 20));
// 22 Character chainID Chain identifier.
TokenBuilder.add(sites.pdbx_auth_asym_id, s + 21, s + 22);
// 23 - 26 Integer resSeq Residue sequence number.
TokenBuilder.addToken(sites.pdbx_auth_seq_id, Tokenizer.trim(data, s + 22, s + 26));
// 27 AChar iCode Insertion code.
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);
}
// 29 - 35 Integer u[0][0] U(1,1)
sites['U[1][1]'][sites.index] = fastParseInt(str, s + 28, s + 35) / 10000
// 36 - 42 Integer u[1][1] U(2,2)
sites['U[2][2]'][sites.index] = fastParseInt(str, s + 35, s + 42) / 10000
// 43 - 49 Integer u[2][2] U(3,3)
sites['U[3][3]'][sites.index] = fastParseInt(str, s + 42, s + 49) / 10000
// 50 - 56 Integer u[0][1] U(1,2)
sites['U[1][2]'][sites.index] = fastParseInt(str, s + 49, s + 56) / 10000
// 57 - 63 Integer u[0][2] U(1,3)
sites['U[1][3]'][sites.index] = fastParseInt(str, s + 56, s + 63) / 10000
// 64 - 70 Integer u[1][2] U(2,3)
sites['U[2][3]'][sites.index] = fastParseInt(str, s + 63, s + 70) / 10000
// 77 - 78 LString(2) element 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)
}
// 79 - 80 LString(2) charge Charge on the atom.
// TODO
sites.index++;
}
\ No newline at end of file
src/mol-model-formats/structure/pdb/to-cif.ts
+ 12
− 4
View file @ f4beba52
......@@ -17,6 +17,7 @@ import { EntityBuilder } from '../common/entity';
import { Column } from '../../../mol-data/db';
import { getMoleculeType } from '../../../mol-model/structure/model/types';
import { getAtomSiteTemplate, addAtom, getAtomSite } from './atom-site';
import { addAnisotropic, getAnisotropicTemplate, getAnisotropic } from './anisotropic';
export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const { lines } = pdb;
......@@ -25,11 +26,13 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
// Count the atoms
let atomCount = 0;
let anisotropicCount = 0;
for (let i = 0, _i = lines.count; i < _i; i++) {
const s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if (substringStartsWith(data, s, e, 'ATOM ')) atomCount++;
else if (substringStartsWith(data, s, e, 'ANISOU')) anisotropicCount++;
break;
case 'H':
if (substringStartsWith(data, s, e, 'HETATM')) atomCount++;
......@@ -38,6 +41,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
const atomSite = getAtomSiteTemplate(data, atomCount);
const anisotropic = getAnisotropicTemplate(data, anisotropicCount);
const entityBuilder = new EntityBuilder();
const helperCategories: CifCategory[] = [];
const heteroNames: [string, string][] = [];
......@@ -48,9 +52,12 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
let s = indices[2 * i], e = indices[2 * i + 1];
switch (data[s]) {
case 'A':
if (!substringStartsWith(data, s, e, 'ATOM ')) continue;
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
addAtom(atomSite, modelStr, tokenizer, s, e);
if (substringStartsWith(data, s, e, 'ATOM ')) {
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
addAtom(atomSite, modelStr, tokenizer, s, e);
} else if (substringStartsWith(data, s, e, 'ANISOU')) {
addAnisotropic(anisotropic, modelStr, tokenizer, s, e)
}
break;
case 'C':
if (substringStartsWith(data, s, e, 'CRYST1')) {
......@@ -157,7 +164,8 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const categories = {
entity: entityBuilder.getEntityCategory(),
chem_comp: componentBuilder.getChemCompCategory(),
atom_site: CifCategory.ofFields('atom_site', getAtomSite(atomSite))
atom_site: CifCategory.ofFields('atom_site', getAtomSite(atomSite)),
atom_site_anisotrop: CifCategory.ofFields('atom_site_anisotrop', getAnisotropic(anisotropic))
} as any;
for (const c of helperCategories) {
......
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