diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index 0a4cca600a8226afda02b5ec155e417adc970c75..fe4ab89136da9c20237902db70943d0299fc0650 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -55,7 +55,7 @@ class BasicWrapper {
const state = this.stateTemplate.build();
state.to('url').update(StateTransforms.Data.Download, p => ({ ...p, url }));
- state.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId }));
+ state.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree: state });
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index 727daf63ccc5d83b0ce9e6b9dbd59d7e661d3f3a..855cecb9bf74387ad68f08325da0bdfa00da2c8c 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -61,10 +61,10 @@ export namespace CifCategory {
export type SomeFields<S> = { [P in keyof S]?: CifField }
export type Fields<S> = { [P in keyof S]: CifField }
- export function ofFields(name: string, fields: { [name: string]: CifField }): CifCategory {
+ export function ofFields(name: string, fields: { [name: string]: CifField | undefined }): CifCategory {
const fieldNames = Object.keys(fields);
return {
- rowCount: fieldNames.length > 0 ? fields[fieldNames[0]].rowCount : 0,
+ rowCount: fieldNames.length > 0 ? fields[fieldNames[0]]!.rowCount : 0,
name,
fieldNames,
getField(name) { return fields[name]; }
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index b18fb3e5cc57036ca1ea9d69a9dba0f5162bf7cb..abf5cfb9660c20a43039510c799baa7e568f88f2 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -119,6 +119,10 @@ namespace Mat4 {
a[4 * j + i] = value;
}
+ export function getValue(a: Mat4, i: number, j: number) {
+ return a[4 * j + i];
+ }
+
export function toArray(a: Mat4, out: NumberArray, offset: number) {
out[offset + 0] = a[0];
out[offset + 1] = a[1];
diff --git a/src/mol-model-formats/structure/pdb/assembly.ts b/src/mol-model-formats/structure/pdb/assembly.ts
index 00827dddc59c96c3661c249a2ac18050a1da1a70..778a343705e60bcb6e3cc2842c5117061c4ee4b3 100644
--- a/src/mol-model-formats/structure/pdb/assembly.ts
+++ b/src/mol-model-formats/structure/pdb/assembly.ts
@@ -6,6 +6,8 @@
import { CifCategory, CifField } from 'mol-io/reader/cif';
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+import { Mat4 } from 'mol-math/linear-algebra';
+import { Tokens } from 'mol-io/reader/common/text/tokenizer';
export function parseCryst1(id: string, record: string): CifCategory[] {
// COLUMNS DATA TYPE CONTENTS
@@ -41,4 +43,130 @@ export function parseCryst1(id: string, record: string): CifCategory[] {
space_group_name_Hall: CifField.ofString('?')
}
return [CifCategory.ofFields('cell', cell), CifCategory.ofFields('symmetry', symmetry)];
+}
+
+interface PdbAssembly {
+ id: string,
+ details: string,
+ groups: { chains: string[], operators: { id: number, matrix: Mat4 }[] }[]
+}
+
+function PdbAssembly(id: string, details: string): PdbAssembly {
+ return { id, details, groups: [] };
+}
+
+export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number): CifCategory[] {
+ const assemblies: PdbAssembly[] = [];
+
+ // Read the assemblies
+ let current: PdbAssembly, group: PdbAssembly['groups'][0], matrix: Mat4, operId = 1;
+ const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
+ for (let i = lineStart; i < lineEnd; i++) {
+ let line = getLine(i);
+ if (line.substr(11, 12) === 'BIOMOLECULE:') {
+ const id = line.substr(23).trim();
+ line = getLine(++i);
+ const details = line.substr(11).trim();
+ current = PdbAssembly(id, details);
+ assemblies.push(current);
+ } else if (line.substr(13, 5) === 'BIOMT') {
+ const biomt = line.split(/\s+/)
+ const row = parseInt(line[18]) - 1
+
+ if (row === 0) {
+ matrix = Mat4.identity();
+ group!.operators.push({ id: operId++, matrix });
+ }
+
+ Mat4.setValue(matrix!, row, 0, parseFloat(biomt[4]));
+ Mat4.setValue(matrix!, row, 1, parseFloat(biomt[5]));
+ Mat4.setValue(matrix!, row, 2, parseFloat(biomt[6]));
+ Mat4.setValue(matrix!, row, 3, parseFloat(biomt[7]));
+ } else if (
+ line.substr(11, 30) === 'APPLY THE FOLLOWING TO CHAINS:' ||
+ line.substr(11, 30) === ' AND CHAINS:') {
+
+ if (line.substr(11, 5) === 'APPLY') {
+ group = { chains: [], operators: [] };
+ current!.groups.push(group);
+ }
+
+ const chainList = line.substr(41, 30).split(',');
+ for (let j = 0, jl = chainList.length; j < jl; ++j) {
+ const c = chainList[j].trim();
+ if (c) group!.chains.push(c);
+ }
+ }
+ }
+
+ if (assemblies.length === 0) return [];
+
+ // Generate CIF
+
+ // pdbx_struct_assembly
+ const pdbx_struct_assembly: CifCategory.SomeFields<mmCIF_Schema['pdbx_struct_assembly']> = {
+ id: CifField.ofStrings(assemblies.map(a => a.id)),
+ details: CifField.ofStrings(assemblies.map(a => a.details))
+ };
+
+
+ // pdbx_struct_assembly_gen
+ const pdbx_struct_assembly_gen_rows: { [P in keyof CifCategory.Fields<mmCIF_Schema['pdbx_struct_assembly_gen']>]: string }[] = [];
+ for (const asm of assemblies) {
+ for (const group of asm.groups) {
+ pdbx_struct_assembly_gen_rows.push({
+ assembly_id: asm.id,
+ oper_expression: group.operators.map(o => o.id).join(','),
+ asym_id_list: group.chains.join(',')
+ });
+ }
+ }
+ const pdbx_struct_assembly_gen: CifCategory.Fields<mmCIF_Schema['pdbx_struct_assembly_gen']> = {
+ assembly_id: CifField.ofStrings(pdbx_struct_assembly_gen_rows.map(r => r.assembly_id)),
+ oper_expression: CifField.ofStrings(pdbx_struct_assembly_gen_rows.map(r => r.oper_expression)),
+ asym_id_list: CifField.ofStrings(pdbx_struct_assembly_gen_rows.map(r => r.asym_id_list))
+ };
+
+ // pdbx_struct_oper_list
+ const pdbx_struct_oper_list_rows: { [P in keyof CifCategory.Fields<mmCIF_Schema['pdbx_struct_oper_list']>]?: string }[] = [];
+ for (const asm of assemblies) {
+ for (const group of asm.groups) {
+ for (const oper of group.operators) {
+ const row = {
+ id: '' + oper.id,
+ type: '?',
+ name: '?',
+ symmetry_operation: '?'
+ } as any;
+ for (let i = 0; i < 3; i++) {
+ for (let j = 0; j < 3; j++) {
+ row[`matrix[${i + 1}][${j + 1}]`] = '' + Mat4.getValue(oper.matrix, i, j);
+ }
+ row[`vector[${i + 1}]`] = '' + Mat4.getValue(oper.matrix, i, 3);
+ }
+ pdbx_struct_oper_list_rows.push(row);
+ }
+ }
+ }
+
+ const pdbx_struct_oper_list: CifCategory.SomeFields<mmCIF_Schema['pdbx_struct_oper_list']> = {
+ id: CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => r.id!)),
+ type: CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => r.type!)),
+ name: CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => r.name!)),
+ symmetry_operation: CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => r.symmetry_operation!))
+ };
+ for (let i = 0; i < 3; i++) {
+ for (let j = 0; j < 3; j++) {
+ const k = `matrix[${i + 1}][${j + 1}]`;
+ (pdbx_struct_oper_list as any)[k] = CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => (r as any)[k]!));
+ }
+ const k = `vector[${i + 1}]`;
+ (pdbx_struct_oper_list as any)[k] = CifField.ofStrings(pdbx_struct_oper_list_rows.map(r => (r as any)[k]!));
+ }
+
+ return [
+ CifCategory.ofFields('pdbx_struct_assembly', pdbx_struct_assembly),
+ CifCategory.ofFields('pdbx_struct_assembly_gen', pdbx_struct_assembly_gen),
+ CifCategory.ofFields('pdbx_struct_oper_list', pdbx_struct_oper_list)
+ ];
}
\ 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 2f5da2c27103eb8074c3e56f3f4d3b641c2f9c37..369d3d37d6efc8b7a56b22d1ee461632ce8bb099 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -9,17 +9,7 @@ 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 { PdbFile } from 'mol-io/reader/pdb/schema';
-
-function toCategory(name: string, fields: { [name: string]: CifField | undefined }, rowCount: number): CifCategory {
- return {
- name,
- fieldNames: Object.keys(fields),
- rowCount,
- getField(f: string) {
- return fields[f];
- }
- }
-}
+import { parseCryst1, parseRemark350 } from './assembly';
function _entity(): { [K in keyof mmCIF_Schema['entity']]?: CifField } {
return {
@@ -88,7 +78,7 @@ function _atom_site(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_s
};
}
-const WaterNames = new Set([ 'SOL', 'WAT', 'HOH', 'H2O', 'W', 'DOD', 'D3O', 'TIP3', 'TIP4', 'SPC' ]);
+const WaterNames = new Set(['SOL', 'WAT', 'HOH', 'H2O', 'W', 'DOD', 'D3O', 'TIP3', 'TIP4', 'SPC']);
function getEntityId(residueName: string, isHet: boolean) {
if (isHet) {
@@ -205,16 +195,23 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
const atom_site = atom_site_template(data, atomCount);
+ const helperCategories: CifCategory[] = [];
+
let modelNum = 0, modelStr = '';
for (let i = 0, _i = lines.count; i < _i; i++) {
- const s = indices[2 * i], e = indices[2 * i + 1];
+ 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(atom_site, modelStr, tokenizer, s, e, false);
break;
+ case 'C':
+ if (substringStartsWith(data, s, e, 'CRYST1')) {
+ helperCategories.push(...parseCryst1(pdb.id || '?', data.substring(s, e)));
+ }
+ break;
case 'H':
if (!substringStartsWith(data, s, e, 'HETATM')) continue;
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
@@ -226,13 +223,30 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
modelStr = '' + modelNum;
}
break;
+ case 'R': {
+ if (substringStartsWith(data, s, e, 'REMARK 350')) {
+ let j = i + 1;
+ while (true) {
+ s = indices[2 * j]; e = indices[2 * j + 1];
+ if (!substringStartsWith(data, s, e, 'REMARK 350')) break;
+ j++;
+ }
+ helperCategories.push(...parseRemark350(lines, i, j));
+ i = j - 1;
+ }
+ break;
+ }
}
}
const categories = {
- entity: toCategory('entity', _entity(), 3),
- atom_site: toCategory('atom_site', _atom_site(atom_site), atomCount)
+ entity: CifCategory.ofFields('entity', _entity()),
+ atom_site: CifCategory.ofFields('atom_site', _atom_site(atom_site))
+ } as any;
+
+ for (const c of helperCategories) {
+ categories[c.name] = c;
}
return {
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 10a92df5b64ef9ebbc6016ea6e9be91b1bcfaeb2..c97a78899e8c428a050ca83e95f28e409ebcf1a9 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -129,11 +129,11 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
to: SO.Molecule.Structure,
params(a) {
if (!a) {
- return { id: PD.makeOptional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.' })) };
+ return { id: PD.makeOptional(PD.Text('', { label: 'Assembly Id', description: 'Assembly Id. Value \'deposited\' can be used to specify deposited asymmetric unit.' })) };
}
const model = a.data;
const ids = model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]);
- if (!ids.length) ids.push(['deposited', 'Deposited'])
+ ids.push(['deposited', 'Deposited']);
return { id: PD.makeOptional(PD.Select(ids[0][0], ids, { label: 'Asm Id', description: 'Assembly Id' })) };
}
})({
@@ -146,7 +146,7 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
const base = Structure.ofModel(model);
if (!asm) {
- plugin.log.warn(`Model '${a.label}' has no assembly, returning deposited structure.`);
+ if (!!id && id !== 'deposited') plugin.log.warn(`Model '${a.label}' has no assembly, returning deposited structure.`);
const label = { label: a.data.label, description: structureDesc(base) };
return new SO.Molecule.Structure(base, label);
}
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index 657d2767601f2685228e5499e5f9c1551dfdd5fc..d92ceaf2ebc2cd787262fc52fca8420cb5693b47 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -248,8 +248,9 @@ export class SelectControl extends SimpleParam<PD.Select<string | number>> {
}
}
renderControl() {
- return <select value={this.props.value || ''} onChange={this.onChange} disabled={this.props.isDisabled}>
- {!this.props.param.options.some(e => e[0] === this.props.value) && <option key={this.props.value} value={this.props.value}>{`[Invalid] ${this.props.value}`}</option>}
+ const isInvalid = this.props.value !== void 0 && !this.props.param.options.some(e => e[0] === this.props.value);
+ return <select value={this.props.value || this.props.param.defaultValue} onChange={this.onChange} disabled={this.props.isDisabled}>
+ {isInvalid && <option key={this.props.value} value={this.props.value}>{`[Invalid] ${this.props.value}`}</option>}
{this.props.param.options.map(([value, label]) => <option key={value} value={value}>{label}</option>)}
</select>;
}