From fe8530771699c2d4f56230df46cbc79cef735cc2 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 20 Mar 2018 20:23:45 -0700
Subject: [PATCH] added more helper methods
---
src/mol-data/db/database.ts | 8 ++++++++
src/mol-io/reader/cif.ts | 7 +++++--
src/mol-io/reader/cif/schema.ts | 10 +++++++++-
3 files changed, 22 insertions(+), 3 deletions(-)
diff --git a/src/mol-data/db/database.ts b/src/mol-data/db/database.ts
index e25041fc0..5aa2f2700 100644
--- a/src/mol-data/db/database.ts
+++ b/src/mol-data/db/database.ts
@@ -31,6 +31,14 @@ namespace Database {
}
return ret;
}
+
+ export function getTablesAsRows<S extends Schema>(database: Database<S>) {
+ const ret: { [k: string]: Table.Row<any>[] } = {};
+ for (const k of database._tableNames) {
+ ret[k] = Table.getRows(database[k]);
+ }
+ return ret;
+ }
}
export default Database
\ No newline at end of file
diff --git a/src/mol-io/reader/cif.ts b/src/mol-io/reader/cif.ts
index a8e899269..168cceadb 100644
--- a/src/mol-io/reader/cif.ts
+++ b/src/mol-io/reader/cif.ts
@@ -8,18 +8,21 @@
import parseText from './cif/text/parser'
import parseBinary from './cif/binary/parser'
import { Frame } from './cif/data-model'
-import { toDatabase } from './cif/schema'
+import { toDatabaseCollection, toDatabase } from './cif/schema'
import { mmCIF_Schema, mmCIF_Database } from './cif/schema/mmcif'
import { CCD_Schema, CCD_Database } from './cif/schema/ccd'
+import { BIRD_Schema, BIRD_Database } from './cif/schema/bird'
export default {
parse: (data: string|Uint8Array) => typeof data === 'string' ? parseText(data) : parseBinary(data),
parseText,
parseBinary,
+ toDatabaseCollection,
toDatabase,
schema: {
mmCIF: (frame: Frame) => toDatabase<mmCIF_Schema, mmCIF_Database>(mmCIF_Schema, frame),
- CCD: (frame: Frame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame)
+ CCD: (frame: Frame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame),
+ BIRD: (frame: Frame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame)
}
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 973c16d27..d71b6cc89 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -5,11 +5,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Database, Table, Column, ColumnHelpers } from 'mol-data/db'
+import { DatabaseCollection, Database, Table, Column, ColumnHelpers } from 'mol-data/db'
import { Tensor } from 'mol-math/linear-algebra'
import { arrayEqual } from 'mol-util'
import * as Data from './data-model'
+export function toDatabaseCollection<Schema extends Database.Schema>(schema: Schema, file: Data.File): DatabaseCollection<Schema> {
+ const dbc: DatabaseCollection<Schema> = {}
+ for (const data of file.blocks) {
+ dbc[data.header] = toDatabase(schema, data)
+ }
+ return dbc;
+}
+
export function toDatabase<Schema extends Database.Schema, Frame extends Database<Schema> = Database<Schema>>(schema: Schema, frame: Data.Frame): Frame {
return createDatabase(schema, frame) as Frame;
}
--
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