From f4beba52156f0cc9d5bf7bd2200419ac335b8eaf Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 10 Sep 2019 16:49:10 -0700
Subject: [PATCH] pdb-parser, aniso records
---
.../structure/pdb/anisotropic.ts | 146 ++++++++++++++++++
src/mol-model-formats/structure/pdb/to-cif.ts | 16 +-
2 files changed, 158 insertions(+), 4 deletions(-)
create mode 100644 src/mol-model-formats/structure/pdb/anisotropic.ts
diff --git a/src/mol-model-formats/structure/pdb/anisotropic.ts b/src/mol-model-formats/structure/pdb/anisotropic.ts
new file mode 100644
index 000000000..869d59209
--- /dev/null
+++ b/src/mol-model-formats/structure/pdb/anisotropic.ts
@@ -0,0 +1,146 @@
+/**
+ * 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
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index 9ef1223cd..cf967d435 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -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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