@datagrok/bio 2.12.13 → 2.12.15

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.13",
+  "version": "2.12.15",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",

package/src/utils/helm-to-molfile/converter/converter.ts

@@ -25,7 +25,7 @@ export class HelmToMolfileConverter {
   }
 
   private async getSmilesList(): Promise<string[]> {
-    const molfilesV2K = (await this.convertToMolfileV2KColumn()).toList();
+    const molfilesV2K = (await this.convertToMolfileV3KColumn()).toList();
     const smiles = molfilesV2K.map((mol) => DG.chem.convert(mol, DG.chem.Notation.MolBlock, DG.chem.Notation.Smiles));
     return smiles;
   }
@@ -34,7 +34,7 @@ export class HelmToMolfileConverter {
     const beautifiedMolV2000 = beautifiedMols.map((mol) => {
       if (mol === null)
         return '';
-      const molBlock = mol.get_molblock();
+      const molBlock = mol.get_v3Kmolblock();
       mol!.delete();
       return molBlock;
     });
@@ -52,14 +52,15 @@ export class HelmToMolfileConverter {
   }
 
   async convertToRdKitBeautifiedMolfileColumn(chiralityEngine?: boolean): Promise<DG.Column<string>> {
-    const smiles = await this.getSmilesList();
+    const molfilesV3K = (await this.convertToMolfileV3KColumn()).toList();
     const rdKitModule: RDModule = await grok.functions.call('Chem:getRdKitModule');
-    const beautifiedMols = smiles.map((item) =>{
+    const beautifiedMols = molfilesV3K.map((item) =>{
       if (item === '')
         return null;
       const mol = rdKitModule.get_mol(item);
       if (!mol)
         return null;
+      mol.set_new_coords();
       mol.normalize_depiction(1);
       mol.straighten_depiction(true);
       return mol;
@@ -77,7 +78,7 @@ export class HelmToMolfileConverter {
     }));
   }
 
-  private async convertToMolfileV2KColumn(): Promise<DG.Column<string>> {
+  private async convertToMolfileV3KColumn(): Promise<DG.Column<string>> {
     const polymerGraphColumn: DG.Column<string> = await this.getPolymerGraphColumn();
     const rdKitModule = await grok.functions.call('Chem:getRdKitModule');
     const molfileList = polymerGraphColumn.toList().map(

package/src/utils/helm-to-molfile/converter/mol-atoms-v3k.ts

@@ -1,7 +1,7 @@
 import {MolfileHandlerBase} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler-base';
 import {MolfileAtoms} from './mol-atoms';
 
-const PRECISION = 6;
+const PRECISION = 4;
 
 export class MolfileAtomsV3K extends MolfileAtoms {
   constructor(private molfileHandler: MolfileHandlerBase) {
@@ -21,13 +21,13 @@ export class MolfileAtomsV3K extends MolfileAtoms {
 
   get atomLines(): string[] {
     // todo: optimize, optionally port to molfile-handler
-    const coordinateRegex = /^(M  V30 .*)(-?\d+\.\d+)( )(-?\d+\.\d+)( -?\d+\.\d+.*)$/;
+    const coordinateRegex = /^(M  V30 [^-]*)(-?\d+\.\d+)( )(-?\d+\.\d+)( -?\d+\.\d+.*)$/;
     const rGroupsRegex = /\sRGROUPS=\(\d+(\s+\d+)*\)/;
 
     return this.rawAtomLines.map((line: string, idx: number) => {
       const coordinates = this.coordinates[idx];
-      const x = coordinates.x.toFixed(PRECISION);
-      const y = coordinates.y.toFixed(PRECISION);
+      const x = coordinates.x.toFixed(PRECISION) + '00';
+      const y = coordinates.y.toFixed(PRECISION) + '00';
 
       return line.replace(coordinateRegex, (match, p1, p2, p3, p4, p5) => {
         return p1 + x + p3 + y + p5;

package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts

@@ -1,6 +1,6 @@
 import {Monomer} from '@datagrok-libraries/bio/src/types';
 import {HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';
-import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {MonomerLibManager} from '../../monomer-lib/lib-manager';
 import {Helm} from './helm';
 import {MolfileWrapper} from './mol-wrapper';
@@ -22,7 +22,7 @@ export class MonomerWrapper {
 
     let molfile = libraryMonomerObject.molfile;
     if (MolfileHandler.isMolfileV2K(molfile))
-      molfile = this.convertMolfileToV3KFormat(molfile, rdKitModule);
+      molfile = this.convertMolfileToV3KFormat(molfile, monomerSymbol, rdKitModule);
 
     this.molfileWrapper = MolfileWrapperFactory.getInstance(molfile, monomerSymbol);
     this.capGroupElements = this.getCapGroupElements(libraryMonomerObject);
@@ -34,8 +34,17 @@ export class MonomerWrapper {
     this.shiftCoordinates(shift);
   }
 
-  private convertMolfileToV3KFormat(molfileV2K: string, rdKitModule: RDModule): string {
-    return rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true})).get_v3Kmolblock();
+  private convertMolfileToV3KFormat(molfileV2K: string, monomerSymbol: string, rdKitModule: RDModule): string {
+    let mol: RDMol | null = null;
+    try {
+      mol = rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true}))
+      if (mol)
+        return mol.get_v3Kmolblock();
+      else
+        throw new Error(`Cannot convert ${monomerSymbol} to molV3000`);
+    } finally {
+      mol?.delete();
+    }
   }
 
   private getLibraryMonomerObject(): Monomer {

package/src/utils/helm-to-molfile/converter/polymer.ts

@@ -72,7 +72,7 @@ export class Polymer {
   }
 
   private getV3KHeader(atomCount: number, bondCount: number): string {
-    const countsLine = `${V3K_CONST.COUNTS_LINE_START}${atomCount} ${bondCount}${V3K_CONST.COUNTS_LINE_DUMMY_END}`;
+    const countsLine = `${V3K_CONST.COUNTS_LINE_START}${atomCount} ${bondCount} 0 0 1`;
     return `${V3K_CONST.DUMMY_HEADER}\n${V3K_CONST.BEGIN_CTAB}\n${countsLine}`;
   }