@datagrok/bio 2.10.23 → 2.10.24

package/src/utils/sequence-to-mol.ts

@@ -0,0 +1,37 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
+import {helm2mol} from './helm-to-molfile';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {checkInputColumnUI} from './check-input-column';
+import {getMonomerLibHelper} from '../package';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+
+export async function sequenceToMolfile(df: DG.DataFrame, macroMolecule: DG.Column, nonlinear: boolean): Promise<void> {
+  if (DG.Func.find({package: 'Chem', name: 'getRdKitModule'}).length === 0) {
+    grok.shell.warning('Transformation to atomic level requires package "Chem" installed.');
+    return;
+  }
+  if (nonlinear) {
+    const seqUh = UnitsHandler.getOrCreate(macroMolecule);
+    if (!seqUh.isHelm())
+      macroMolecule = seqUh.convert(NOTATION.HELM);
+    helm2mol(df, macroMolecule);
+    return;
+  }
+  if (!checkInputColumnUI(macroMolecule, 'To Atomic Level'))
+    return;
+  const monomerLib: IMonomerLib = getMonomerLibHelper().getBioLib();
+  const atomicLevelRes = await _toAtomicLevel(df, macroMolecule, monomerLib);
+  if (atomicLevelRes.col !== null) {
+    df.columns.add(atomicLevelRes.col, true);
+    await grok.data.detectSemanticTypes(df);
+  }
+
+  if (atomicLevelRes.warnings && atomicLevelRes.warnings.length > 0)
+    grok.shell.warning(ui.list(atomicLevelRes.warnings));
+}