@datagrok/bio 2.11.2 → 2.11.5

package/src/utils/poly-tool/ui.ts

@@ -0,0 +1,125 @@
+/* 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 {HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
+import {MonomerLibHelper} from '../../utils/monomer-lib';
+import {ALL_MONOMERS, CYCLIZATION_TYPE, TRANSFORMATION_TYPE} from './const';
+import {addTransformedColumn} from './transformation';
+import * as rxjs from 'rxjs';
+import {MetaData} from './types';
+
+export function getPolyToolDialog(): DG.Dialog {
+  function getMonomerList(cyclizationType: CYCLIZATION_TYPE): string[] {
+    if (cyclizationType === cyclizationTypes[0]) {
+      return [ALL_MONOMERS].concat(
+        monomerLib.getMonomerSymbolsByType(HELM_POLYMER_TYPE.PEPTIDE)
+      );
+    }
+    if (cyclizationType === cyclizationTypes[1]) {
+      return [ALL_MONOMERS].concat(
+        monomerLib.getMonomerSymbolsByRGroup(3, HELM_POLYMER_TYPE.PEPTIDE)
+      );
+    }
+    return ['C'];
+  }
+
+  function updateMonomerList(): void {
+    if (cyclizationTypeChoice.value === CYCLIZATION_TYPE.NCys) {
+      monomerList1 = getMonomerList(CYCLIZATION_TYPE.NO);
+      monomerList2 = getMonomerList(CYCLIZATION_TYPE.NCys);
+    } else {
+      monomerList1 = getMonomerList(cyclizationTypeChoice.value as CYCLIZATION_TYPE);
+      monomerList2 = [...monomerList1];
+    }
+
+    leftTerminalChoice = ui.choiceInput(
+      'R1:', monomerList1[0], monomerList1, () => { onRGroupValueChange.next(); }
+    );
+    rightTerminalChoice = ui.choiceInput('R2:', monomerList2[0], monomerList2, () => { onRGroupValueChange.next(); });
+    onRGroupValueChange.next();
+    ui.empty(terminalControls);
+    [leftTerminalChoice, rightTerminalChoice].forEach((el) => { terminalControls.appendChild(el.root); });
+  }
+
+  function updateMeta() {
+    meta.cyclizationType = cyclizationTypeChoice.value!;
+    meta.leftTerminal = leftTerminalChoice.value!;
+    meta.rightTerminal = rightTerminalChoice.value!;
+    meta.transformationType = transformationChoice.value!;
+  }
+
+
+  const onCyclizationChoice = new rxjs.Subject<string>();
+  const onRGroupValueChange = new rxjs.Subject<string>();
+  onCyclizationChoice.subscribe(() => {
+    meta.cyclizationType = cyclizationTypeChoice.value!;
+    updateMonomerList();
+  });
+  onRGroupValueChange.subscribe(() => {
+    meta.rightTerminal = rightTerminalChoice.value!;
+    meta.leftTerminal = leftTerminalChoice.value!;
+  });
+
+  const meta = {} as MetaData;
+  const transformations = [TRANSFORMATION_TYPE.CYCLIZATION];
+  const transformationChoice = ui.choiceInput(
+    'Modification', transformations[0], transformations, () => meta.transformationType = transformationChoice.value!
+  );
+
+  const cyclizationTypes = [CYCLIZATION_TYPE.NO, CYCLIZATION_TYPE.R3, CYCLIZATION_TYPE.NCys];
+  const cyclizationTypeChoice = ui.choiceInput(
+    'Type', cyclizationTypes[2], cyclizationTypes, () => { onCyclizationChoice.next(); }
+  );
+
+  const monomerLib = MonomerLibHelper.instance.getBioLib();
+  let monomerList1: string[] = [];
+  let monomerList2: string[] = [];
+  let leftTerminalChoice = ui.choiceInput(
+    'R1:', monomerList1[0], monomerList1, () => {
+      meta.leftTerminal = leftTerminalChoice.value!;
+    }
+  );
+  let rightTerminalChoice = ui.choiceInput('R2:', monomerList2[0], monomerList2, () => {
+    meta.rightTerminal = rightTerminalChoice.value!;
+  });
+  const terminalControls = ui.divV([leftTerminalChoice.root, rightTerminalChoice.root]);
+  updateMonomerList();
+
+  updateMeta();
+
+  const targetColumns = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
+  if (!targetColumns)
+    throw new Error('No dataframe with maceomolecule columns open');
+
+  const targetColumnInput = ui.columnInput(
+    'Column', grok.shell.t, targetColumns[0], null,
+    {filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE}
+  );
+
+  const generateHelmChoiceInput = ui.boolInput('Get HELM', true);
+  ui.tooltip.bind(generateHelmChoiceInput.root, 'Add HELM column');
+
+  const div = ui.div([
+    targetColumnInput,
+    transformationChoice,
+    cyclizationTypeChoice,
+    terminalControls,
+    generateHelmChoiceInput,
+  ]);
+
+  const dialog = ui.dialog('Poly Tool')
+    .add(div)
+    .onOK(async () => {
+      const molCol = targetColumnInput.value;
+      if (!molCol) {
+        grok.shell.warning('No marcomolecule column chosen!');
+        return;
+      }
+      addTransformedColumn(molCol!, meta, generateHelmChoiceInput.value!);
+    }
+    );
+
+  return dialog;
+}