diff --git a/src/mol-model-formats/structure/pdb/atom-site.ts b/src/mol-model-formats/structure/pdb/atom-site.ts
new file mode 100644
index 0000000000000000000000000000000000000000..320d88595426ac0d5cd31c017ca5335832ad03c9
--- /dev/null
+++ b/src/mol-model-formats/structure/pdb/atom-site.ts
@@ -0,0 +1,154 @@
+/**
+ * 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
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index 573be9a13229ea981d7c296c2194e23733c5a62f..9ef1223cd7753927fc519ca41ad9e6fbf809a06e 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -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) {