diff --git a/README.md b/README.md
index 043668a218ce34cd7fafd11f0da749b2172919f2..bea25cde6c5ecf65b2286159027280754b09413c 100644
--- a/README.md
+++ b/README.md
@@ -95,7 +95,7 @@ Install CIFTools `npm install ciftools -g`
### Other scripts
**Create chem comp bond table**
- export NODE_PATH="lib"; node --max-old-space-size=8192 build/src/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+ export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
**Test model server**
diff --git a/src/apps/chem-comp-bond/create-table.ts b/src/apps/chem-comp-bond/create-table.ts
index cc29af24a60f6490751d22ec1b4101d68cb3665e..ba541008609cb3c9c61c6dd09ff192f8e3535ad9 100644
--- a/src/apps/chem-comp-bond/create-table.ts
+++ b/src/apps/chem-comp-bond/create-table.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -15,12 +15,13 @@ const readFile = util.promisify(fs.readFile)
const writeFile = util.promisify(fs.writeFile)
import { Progress } from '../../mol-task'
-import { Database, Table, DatabaseCollection, Column } from '../../mol-data/db'
+import { Database, Table, DatabaseCollection } from '../../mol-data/db'
import { CIF } from '../../mol-io/reader/cif'
import { CifWriter } from '../../mol-io/writer/cif'
import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd'
import { SetUtils } from '../../mol-util/set'
import { DefaultMap } from '../../mol-util/map'
+import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
export async function ensureAvailable(path: string, url: string) {
if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
@@ -74,16 +75,6 @@ export function getEncodedCif(name: string, database: Database<Database.Schema>,
type CCB = Table<CCD_Schema['chem_comp_bond']>
type CCA = Table<CCD_Schema['chem_comp_atom']>
-const ChemCompBond_Schema = {
- comp_id: CCD_Schema['chem_comp_bond'].comp_id,
- atom_id_1: CCD_Schema['chem_comp_bond'].atom_id_1,
- atom_id_2: CCD_Schema['chem_comp_bond'].atom_id_2,
- value_order: CCD_Schema['chem_comp_bond'].value_order,
- pdbx_aromatic_flag: CCD_Schema['chem_comp_bond'].pdbx_aromatic_flag,
- pdbx_stereo_config: CCD_Schema['chem_comp_bond'].pdbx_stereo_config,
- molstar_protonation_variant: Column.Schema.Str()
-}
-
function ccbKey(compId: string, atomId1: string, atomId2: string) {
return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`
}
@@ -202,14 +193,14 @@ async function createBonds() {
}
}
- const bondTable = Table.ofArrays(ChemCompBond_Schema, {
+ const bondTable = Table.ofArrays(mmCIF_chemCompBond_schema, {
comp_id, atom_id_1, atom_id_2, value_order,
pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
})
const bondDatabase = Database.ofTables(
TABLE_NAME,
- { chem_comp_bond: ChemCompBond_Schema },
+ { chem_comp_bond: mmCIF_chemCompBond_schema },
{ chem_comp_bond: bondTable }
)
@@ -220,12 +211,15 @@ async function run(out: string, binary = false) {
const bonds = await createBonds()
const cif = getEncodedCif(TABLE_NAME, bonds, binary)
+ if (!fs.existsSync(path.dirname(out))) {
+ fs.mkdirSync(path.dirname(out));
+ }
writeFile(out, cif)
}
const TABLE_NAME = 'CHEM_COMP_BONDS'
-const DATA_DIR = path.join(__dirname, '..', '..', '..', 'data')
+const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data')
const CCD_PATH = path.join(DATA_DIR, 'components.cif')
const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif')
const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif'
diff --git a/src/mol-io/reader/cif/schema/mmcif-extras.ts b/src/mol-io/reader/cif/schema/mmcif-extras.ts
index 10b5e32f74df25b17eaf76414e89f7cd9d98b74b..cb35f4879008bbffd1cc4fbd6c4f577aae29a53a 100644
--- a/src/mol-io/reader/cif/schema/mmcif-extras.ts
+++ b/src/mol-io/reader/cif/schema/mmcif-extras.ts
@@ -1,10 +1,12 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 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 { mmCIF_Schema } from './mmcif';
+import { mmCIF_Schema } from './mmcif';
+import { Column } from '../../../../mol-data/db';
export const mmCIF_residueId_schema = {
label_comp_id: mmCIF_Schema.atom_site.label_comp_id,
@@ -15,4 +17,10 @@ export const mmCIF_residueId_schema = {
auth_comp_id: mmCIF_Schema.atom_site.auth_atom_id,
auth_seq_id: mmCIF_Schema.atom_site.auth_seq_id,
auth_asym_id: mmCIF_Schema.atom_site.auth_asym_id
+}
+
+export const mmCIF_chemCompBond_schema = {
+ ...mmCIF_Schema.chem_comp_bond,
+ /** Indicates if the bond entry was taken from the protonation variant dictionary */
+ molstar_protonation_variant: Column.Schema.Str()
}
\ No newline at end of file
diff --git a/src/mol-model-props/wwpdb/chem-comp-bond.ts b/src/mol-model-props/wwpdb/chem-comp-bond.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2395d4832d341d32eb8aa32d44dfbbaab79aafc5
--- /dev/null
+++ b/src/mol-model-props/wwpdb/chem-comp-bond.ts
@@ -0,0 +1,84 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { toTable } from '../../mol-io/reader/cif/schema';
+import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
+import { CifWriter } from '../../mol-io/writer/cif';
+
+export namespace ChemCompBond {
+ export type Property = Table<Schema['chem_comp_bond']>
+
+ export function getFromModel(model: Model): Property {
+ if (model.sourceData.kind !== 'mmCIF') return Table.ofUndefinedColumns(Schema.chem_comp_bond, 0);
+ const { chem_comp_bond } = model.sourceData.data
+ return Table.ofColumns(Schema.chem_comp_bond, {
+ ...chem_comp_bond,
+ molstar_protonation_variant: Column.Undefined(chem_comp_bond._rowCount, Column.Schema.Str())
+ });
+ }
+
+ export function get(model: Model): Property {
+ return model._staticPropertyData.__ChemCompBond__ || getFromModel(model);
+ }
+ function set(model: Model, prop: Property) {
+ (model._staticPropertyData.__ChemCompBond__ as Property) = prop;
+ }
+
+ export const Schema = { chem_comp_bond: mmCIF_chemCompBond_schema };
+ export type Schema = typeof Schema
+
+ export const Descriptor = CustomPropertyDescriptor({
+ isStatic: true,
+ name: 'chem_comp_bond',
+ cifExport: {
+ prefix: '',
+ context(ctx): Property { return get(ctx.firstModel); },
+ categories: [{
+ name: 'chem_comp_bond',
+ instance(ctx: Property) {
+ return CifWriter.Category.ofTable(ctx);
+ }
+ }]
+ }
+ });
+
+ function fromCifData(model: Model): Table<Schema['chem_comp_bond']> | undefined {
+ if (model.sourceData.kind !== 'mmCIF') return void 0;
+ const cat = model.sourceData.frame.categories.chem_comp_bond;
+ if (!cat) return void 0;
+ return toTable(Schema.chem_comp_bond, cat);
+ }
+
+ export async function attachFromCifOrTable(model: Model, params: {
+ // optional Table source
+ wwPDB_apiSourceTable?: (model: Model) => Promise<Table<Schema['chem_comp_bond']>>
+ }) {
+ if (model.customProperties.has(Descriptor)) return true;
+
+ let chemCompBond: Table<Schema['chem_comp_bond']> | undefined = fromCifData(model);
+ if (chemCompBond === void 0 && params.wwPDB_apiSourceTable) {
+ const data = await params.wwPDB_apiSourceTable(model);
+ if (!data) return false;
+ chemCompBond = chemCompBondFromTable(model, data);
+ } else {
+ return false;
+ }
+
+ if (!chemCompBond) return false;
+
+ model.customProperties.add(Descriptor);
+ set(model, chemCompBond);
+ return true;
+ }
+}
+
+function chemCompBondFromTable(model: Model, table: Table<ChemCompBond.Schema['chem_comp_bond']>): Table<ChemCompBond.Schema['chem_comp_bond']> {
+ return Table.pick(table, ChemCompBond.Schema.chem_comp_bond, (i: number) => {
+ return model.properties.chemicalComponentMap.has(table.comp_id.value(i))
+ })
+}
\ No newline at end of file