diff --git a/src/mol-model-formats/structure/pdb/entity.ts b/src/mol-model-formats/structure/pdb/entity.ts
new file mode 100644
index 0000000000000000000000000000000000000000..99cd0a1e54a9532d2774256e536a048707c27080
--- /dev/null
+++ b/src/mol-model-formats/structure/pdb/entity.ts
@@ -0,0 +1,135 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Tokens } from '../../../mol-io/reader/common/text/tokenizer';
+import { CifCategory, CifField } from '../../../mol-io/reader/cif';
+import { WaterNames } from '../../../mol-model/structure/model/types';
+
+const Spec = {
+ 'MOL_ID': '',
+ 'MOLECULE': '',
+ 'CHAIN': '',
+ 'FRAGMENT': '',
+ 'SYNONYM': '',
+ 'EC': '',
+ 'ENGINEERED': '',
+ 'MUTATION': '',
+ 'OTHER_DETAILS': ''
+}
+type Spec = keyof typeof Spec
+
+type Compound = { chains: string[], name: string }
+
+export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
+ const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1])
+
+ let currentSpec: Spec | undefined
+ let currentCompound: Compound = { chains: [], name: '' }
+ const Compounds: Compound[] = []
+
+ for (let i = lineStart; i < lineEnd; i++) {
+ let line = getLine(i)
+ // COLUMNS DATA TYPE FIELD DEFINITION
+ // ----------------------------------------------------------------------------------
+ // 1 - 6 Record name "COMPND"
+ // 8 - 10 Continuation continuation Allows concatenation of multiple records.
+ // 11 - 80 Specification compound Description of the molecular components.
+ // list
+
+ const cmpnd = line.substr(10, 70).trim()
+ const cmpndSpecEnd = cmpnd.indexOf(':')
+ const cmpndSpec = cmpnd.substring(0, cmpndSpecEnd)
+
+ let value: string
+
+ if (cmpndSpec in Spec) {
+ currentSpec = cmpndSpec as Spec
+ value = cmpnd.substring(cmpndSpecEnd + 2)
+ } else {
+ value = cmpnd
+ }
+ value = value.replace(/;$/, '')
+
+ if (currentSpec === 'MOL_ID') {
+ currentCompound = {
+ chains: [],
+ name: ''
+ }
+ Compounds.push(currentCompound)
+ } else if (currentSpec === 'MOLECULE') {
+ if (currentCompound.name) currentCompound.name += ' '
+ currentCompound.name += value
+ } else if (currentSpec === 'CHAIN') {
+ Array.prototype.push.apply(currentCompound.chains, value.split(/\s*,\s*/))
+ }
+ }
+
+ return Compounds
+}
+
+export class EntityBuilder {
+ private count = 0
+ private ids: string[] = []
+ private types: string[] = []
+ private descriptions: string[] = []
+
+ private compoundsMap = new Map<string, string>()
+ private heteroMap = new Map<string, string>()
+ private chainMap = new Map<string, string>()
+ private waterId?: string
+
+ private add(type: string, description: string) {
+ this.count += 1
+ this.ids.push(`${this.count}`)
+ this.types.push(type)
+ this.descriptions.push(description)
+ }
+
+ getEntityId(residueName: string, chainId: string, isHet: boolean): string {
+ if (isHet) {
+ if (WaterNames.has(residueName)) {
+ if (this.waterId === undefined) {
+ this.add('water', 'Water')
+ this.waterId = `${this.count}`
+ }
+ return this.waterId;
+ } else {
+ if (!this.heteroMap.has(residueName)) {
+ this.add('non-polymer', residueName)
+ this.heteroMap.set(residueName, `${this.count}`)
+ }
+ return this.heteroMap.get(residueName)!
+ }
+ } else if (this.compoundsMap.has(chainId)) {
+ return this.compoundsMap.get(chainId)!
+ } else {
+ if (!this.chainMap.has(chainId)) {
+ this.add('polymer', chainId)
+ this.chainMap.set(chainId, `${this.count}`)
+ }
+ return this.chainMap.get(chainId)!
+ }
+ }
+
+ getEntityCategory() {
+ const entity = {
+ id: CifField.ofStrings(this.ids),
+ type: CifField.ofStrings(this.types),
+ pdbx_description: CifField.ofStrings(this.descriptions)
+ }
+ return CifCategory.ofFields('entity', entity)
+ }
+
+ setCompounds(compounds: Compound[]) {
+ for (let i = 0, il = compounds.length; i < il; ++i) {
+ const { chains, name } = compounds[i]
+ this.add('polymer', name)
+ for (let j = 0, jl = chains.length; j < jl; ++j) {
+ this.compoundsMap.set(chains[j], `${this.count}`)
+ }
+ }
+ }
+}
\ 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 362f8c26b2529edbbc8daa281f6a9a4065559314..a7e1aaf826c1508c51685674205e8b4fdd2604f4 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -11,16 +11,9 @@ import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { PdbFile } from '../../../mol-io/reader/pdb/schema';
import { parseCryst1, parseRemark350, parseMtrix } from './assembly';
-import { WaterNames } from '../../../mol-model/structure/model/types';
import { parseHelix, parseSheet } from './secondary-structure';
import { guessElementSymbolTokens } from '../util';
-
-function _entity(): { [K in keyof mmCIF_Schema['entity']]?: CifField } {
- return {
- id: CifField.ofStrings(['1', '2', '3']),
- type: CifField.ofStrings(['polymer', 'non-polymer', 'water'])
- }
-}
+import { parseCmpnd, EntityBuilder } from './entity';
type AtomSiteTemplate = typeof atom_site_template extends (...args: any) => infer T ? T : never
function atom_site_template(data: string, count: number) {
@@ -82,15 +75,7 @@ function _atom_site(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_s
};
}
-function getEntityId(residueName: string, isHet: boolean) {
- if (isHet) {
- if (WaterNames.has(residueName)) return '3';
- return '2';
- }
- return '1';
-}
-
-function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number, isHet: boolean) {
+function addAtom(sites: AtomSiteTemplate, entityBuilder: EntityBuilder, model: string, data: Tokenizer, s: number, e: number, isHet: boolean) {
const { data: str } = data;
const length = e - s;
@@ -122,6 +107,7 @@ function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: num
// 22 Character Chain identifier.
TokenBuilder.add(sites.auth_asym_id, s + 21, s + 22);
+ const chainId = str.substring(s + 21, s + 22);
// 23 - 26 Integer Residue sequence number.
// TODO: support HEX
@@ -169,7 +155,7 @@ function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: num
guessElementSymbolTokens(sites.type_symbol, str, s + 12, s + 16)
}
- sites.label_entity_id[sites.index] = getEntityId(residueName, isHet);
+ sites.label_entity_id[sites.index] = entityBuilder.getEntityId(residueName, chainId, isHet);
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
@@ -195,7 +181,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
const atom_site = atom_site_template(data, atomCount);
-
+ const entityBuilder = new EntityBuilder();
const helperCategories: CifCategory[] = [];
let modelNum = 0, modelStr = '';
@@ -206,19 +192,28 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
case 'A':
if (!substringStartsWith(data, s, e, 'ATOM ')) continue;
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
- addAtom(atom_site, modelStr, tokenizer, s, e, false);
+ addAtom(atom_site, entityBuilder, modelStr, tokenizer, s, e, false);
break;
case 'C':
if (substringStartsWith(data, s, e, 'CRYST1')) {
helperCategories.push(...parseCryst1(pdb.id || '?', data.substring(s, e)));
+ } else if (substringStartsWith(data, s, e, 'CONNECT')) {
+ // TODO: CONNECT records => struct_conn
+ } else if (substringStartsWith(data, s, e, 'COMPND')) {
+ let j = i + 1;
+ while (true) {
+ s = indices[2 * j]; e = indices[2 * j + 1];
+ if (!substringStartsWith(data, s, e, 'COMPND')) break;
+ j++;
+ }
+ entityBuilder.setCompounds(parseCmpnd(lines, i, j))
+ i = j - 1;
}
- // TODO CONNECT records => struct_conn
- // TODO COMPND records => entity
break;
case 'H':
if (substringStartsWith(data, s, e, 'HETATM')) {
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
- addAtom(atom_site, modelStr, tokenizer, s, e, true);
+ addAtom(atom_site, entityBuilder, modelStr, tokenizer, s, e, true);
} else if (substringStartsWith(data, s, e, 'HELIX')) {
let j = i + 1;
while (true) {
@@ -229,7 +224,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(parseHelix(lines, i, j));
i = j - 1;
}
- // TODO HETNAM records => chem_comp (at least partially, needs to be completed with common bases and amino acids)
+ // TODO: HETNAM records => chem_comp (at least partially, needs to be completed with common bases and amino acids)
break;
case 'M':
if (substringStartsWith(data, s, e, 'MODEL ')) {
@@ -246,10 +241,10 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(...parseMtrix(lines, i, j));
i = j - 1;
}
- // TODO MODRES records => pdbx_struct_mod_residue
+ // TODO: MODRES records => pdbx_struct_mod_residue
break;
case 'O':
- // TODO ORIGX record => cif.database_PDB_matrix.origx, cif.database_PDB_matrix.origx_vector
+ // TODO: ORIGX record => cif.database_PDB_matrix.origx, cif.database_PDB_matrix.origx_vector
break;
case 'R':
if (substringStartsWith(data, s, e, 'REMARK 350')) {
@@ -274,13 +269,13 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(parseSheet(lines, i, j));
i = j - 1;
}
- // TODO SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
+ // TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
break;
}
}
const categories = {
- entity: CifCategory.ofFields('entity', _entity()),
+ entity: entityBuilder.getEntityCategory(),
atom_site: CifCategory.ofFields('atom_site', _atom_site(atom_site))
} as any;
diff --git a/src/mol-plugin/ui/sequence/polymer.ts b/src/mol-plugin/ui/sequence/polymer.ts
index b86f783defd3b14cbc4d22314d297a667cd93db5..14e8bf64d921a55fe673ebb3e2188ea01587388d 100644
--- a/src/mol-plugin/ui/sequence/polymer.ts
+++ b/src/mol-plugin/ui/sequence/polymer.ts
@@ -39,10 +39,11 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
if (StructureElement.isLoci(loci)) {
if (!Structure.areParentsEqual(loci.structure, structure)) return false
+ const { offset } = this.sequence
for (const e of loci.elements) {
if (e.unit.id === unit.id) {
OrderedSet.forEach(e.indices, v => {
- if (apply(getSeqIndices(e.unit, e.unit.elements[v]))) changed = true
+ if (apply(getSeqIndices(e.unit, e.unit.elements[v], offset))) changed = true
})
}
}
@@ -99,22 +100,22 @@ function createResidueQuery(unitId: number, label_seq_id: number) {
});
}
-function getSeqIndices(unit: Unit, element: ElementIndex): Interval {
+function getSeqIndices(unit: Unit, element: ElementIndex, offset: number): Interval {
const { model } = unit
switch (unit.kind) {
case Unit.Kind.Atomic:
const residueIndex = model.atomicHierarchy.residueAtomSegments.index[element]
const seqId = model.atomicHierarchy.residues.label_seq_id.value(residueIndex)
- return Interval.ofSingleton(seqId - 1)
+ return Interval.ofSingleton(seqId - 1 - offset)
case Unit.Kind.Spheres:
return Interval.ofRange(
- model.coarseHierarchy.spheres.seq_id_begin.value(element) - 1,
- model.coarseHierarchy.spheres.seq_id_end.value(element) - 1
+ model.coarseHierarchy.spheres.seq_id_begin.value(element) - 1 - offset,
+ model.coarseHierarchy.spheres.seq_id_end.value(element) - 1 - offset
)
case Unit.Kind.Gaussians:
return Interval.ofRange(
- model.coarseHierarchy.gaussians.seq_id_begin.value(element) - 1,
- model.coarseHierarchy.gaussians.seq_id_end.value(element) - 1
+ model.coarseHierarchy.gaussians.seq_id_begin.value(element) - 1 - offset,
+ model.coarseHierarchy.gaussians.seq_id_end.value(element) - 1 - offset
)
}
}
\ No newline at end of file