#1852 Implements automatic selection of mol encoding (#1870)

* #1852 Implements automatic selection of mol encoding * #1852 Refactor types * #1852 Fix errors in identifyStructFormat * #1852 Fix build * #1852 Fix react build errors * #1852 Run prettier to fix build * #1852 Small fix on comments * #1852 Fix build (prettier-write)
epam · Nov 29, 2022 · 1296bd7 · 1296bd7
1 parent 4bc788f
commit 1296bd7
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Showing 8 changed files with 85 additions and 52 deletions.
diff --git a/packages/ketcher-core/src/application/formatters/formatProperties.ts b/packages/ketcher-core/src/application/formatters/formatProperties.ts
@@ -23,6 +23,14 @@ type FormatPropertiesMap = {
 }
 
 const formatProperties: FormatPropertiesMap = {
+  molAuto: new SupportedFormatProperties(
+    // TODO: is it a valid name?
+    'MDL Molfile Auto Format detect',
+    ChemicalMimeType.Mol,
+    ['.mol'],
+    true,
+    { 'molfile-saving-mode': 'auto' }
+  ),
   mol: new SupportedFormatProperties(
     'MDL Molfile V2000',
     ChemicalMimeType.Mol,

diff --git a/packages/ketcher-core/src/application/formatters/formatterFactory.ts b/packages/ketcher-core/src/application/formatters/formatterFactory.ts
@@ -68,29 +68,29 @@ export class FormatterFactory {
 
     let formatter: StructFormatter
     switch (format) {
-      case 'ket':
+      case SupportedFormat.ket:
         formatter = new KetFormatter(new KetSerializer())
         break
 
-      case 'rxn':
+      case SupportedFormat.rxn:
         formatter = new RxnFormatter(new MolSerializer(molSerializerOptions))
         break
 
-      case 'mol':
+      case SupportedFormat.mol:
         formatter = new MolfileV2000Formatter(
           new MolSerializer(molSerializerOptions)
         )
         break
 
-      case 'cml':
-      case 'inChIAuxInfo':
-      case 'inChI':
-      case 'molV3000':
-      case 'smiles':
-      case 'rxnV3000':
-      case 'smilesExt':
-      case 'smarts':
-      case 'cdxml':
+      case SupportedFormat.cml:
+      case SupportedFormat.inChIAuxInfo:
+      case SupportedFormat.inChI:
+      case SupportedFormat.molV3000:
+      case SupportedFormat.smiles:
+      case SupportedFormat.rxnV3000:
+      case SupportedFormat.smilesExt:
+      case SupportedFormat.smarts:
+      case SupportedFormat.cdxml:
       default:
         formatter = new ServerFormatter(
           this.#structService,

diff --git a/packages/ketcher-core/src/application/formatters/identifyStructFormat.ts b/packages/ketcher-core/src/application/formatters/identifyStructFormat.ts
@@ -24,16 +24,16 @@ export function identifyStructFormat(
 
   try {
     if (JSON.parse(sanitizedString)) {
-      return 'ket'
+      return SupportedFormat.ket
     }
   } catch (er) {} // eslint-disable-line
 
   if (sanitizedString.indexOf('$RXN') !== -1) {
-    return 'rxn'
+    return SupportedFormat.rxn
   }
 
   if (sanitizedString.indexOf('V3000') !== -1) {
-    return 'molV3000'
+    return SupportedFormat.molV3000
   }
 
   const match = sanitizedString.match(/^(M {2}END|\$END MOL)$/m)
@@ -44,28 +44,28 @@ export function identifyStructFormat(
       end === sanitizedString.length ||
       sanitizedString.slice(end, end + 20).search(/^\$(MOL|END CTAB)$/m) !== -1
     ) {
-      return 'mol'
+      return SupportedFormat.mol
     }
   }
   if (
     sanitizedString[0] === '<' &&
     sanitizedString.indexOf('<molecule') !== -1
   ) {
-    return 'cml'
+    return SupportedFormat.cml
   }
 
   if (sanitizedString.slice(0, 5) === 'InChI') {
-    return 'inChI'
+    return SupportedFormat.inChI
   }
 
   if (sanitizedString.indexOf('\n') === -1) {
     // TODO: smiles regexp
-    return 'smiles'
+    return SupportedFormat.smiles
   }
 
   if (sanitizedString.indexOf('<CDXML') !== -1) {
-    return 'cdxml'
+    return SupportedFormat.cdxml
   }
   // Molfile by default as Indigo does
-  return 'mol'
+  return SupportedFormat.mol
 }
diff --git a/packages/ketcher-core/src/application/formatters/serverFormatter.ts b/packages/ketcher-core/src/application/formatters/serverFormatter.ts
@@ -89,7 +89,7 @@ export class ServerFormatter implements StructFormatter {
 
     const data: ConvertData | LayoutData = {
       struct: undefined as any,
-      output_format: getPropertiesByFormat('ket').mime
+      output_format: getPropertiesByFormat(SupportedFormat.ket).mime
     }
 
     const withCoords = getPropertiesByFormat(this.#format).supportsCoords
@@ -115,8 +115,10 @@ export class ServerFormatter implements StructFormatter {
 
       const formatError =
         this.#format === 'smiles'
-          ? `${getPropertiesByFormat('smilesExt').name} and opening of ${
-              getPropertiesByFormat('smiles').name
+          ? `${
+              getPropertiesByFormat(SupportedFormat.smilesExt).name
+            } and opening of ${
+              getPropertiesByFormat(SupportedFormat.smiles).name
             }`
           : getPropertiesByFormat(this.#format).name
 

diff --git a/packages/ketcher-core/src/application/formatters/structFormatter.types.ts b/packages/ketcher-core/src/application/formatters/structFormatter.types.ts
@@ -23,19 +23,21 @@ export interface StructFormatter {
   getStructureFromStringAsync: (stringifiedStruct: string) => Promise<Struct>
 }
 
-export type SupportedFormat =
-  | 'rxn'
-  | 'rxnV3000'
-  | 'mol'
-  | 'molV3000'
-  | 'smiles'
-  | 'smilesExt'
-  | 'smarts'
-  | 'inChI'
-  | 'inChIAuxInfo'
-  | 'cml'
-  | 'ket'
-  | 'cdxml'
+export enum SupportedFormat {
+  mol = 'mol',
+  molV3000 = 'molV3000',
+  molAuto = 'molAuto',
+  rxn = 'rxn',
+  rxnV3000 = 'rxnV3000',
+  smiles = 'smiles',
+  smilesExt = 'smilesExt',
+  smarts = 'smarts',
+  inChI = 'inChI',
+  inChIAuxInfo = 'inChIAuxInfo',
+  cml = 'cml',
+  ket = 'ket',
+  cdxml = 'cdxml'
+}
 
 export type FormatterFactoryOptions = Partial<
   MolSerializerOptions & StructServiceOptions

diff --git a/packages/ketcher-core/src/application/ketcher.ts b/packages/ketcher-core/src/application/ketcher.ts
@@ -63,7 +63,7 @@ function parseStruct(
 }
 
 function getStructure(
-  structureFormat: SupportedFormat = 'rxn',
+  structureFormat = SupportedFormat.rxn,
   formatterFactory: FormatterFactory,
   struct: Struct
 ): Promise<string> {
@@ -133,19 +133,23 @@ export class Ketcher {
   }
 
   getSmiles(isExtended = false): Promise<string> {
-    const format: SupportedFormat = isExtended ? 'smilesExt' : 'smiles'
+    const format = isExtended
+      ? SupportedFormat.smilesExt
+      : SupportedFormat.smiles
     return getStructure(format, this.#formatterFactory, this.editor.struct())
   }
 
-  async getMolfile(molfileFormat: MolfileFormat = 'v2000'): Promise<string> {
+  async getMolfile(molfileFormat?: MolfileFormat): Promise<string> {
     if (this.containsReaction()) {
       throw Error(
         'The structure cannot be saved as *.MOL due to reaction arrrows.'
       )
     }
 
-    const format: SupportedFormat =
-      molfileFormat === 'v3000' ? 'molV3000' : 'mol'
+    const formatPassed =
+      molfileFormat === 'v3000' ? SupportedFormat.molV3000 : SupportedFormat.mol
+    const format = molfileFormat ? formatPassed : SupportedFormat.molAuto
+
     const molfile = await getStructure(
       format,
       this.#formatterFactory,
@@ -161,8 +165,8 @@ export class Ketcher {
         'The structure cannot be saved as *.RXN: there is no reaction arrows.'
       )
     }
-    const format: SupportedFormat =
-      molfileFormat === 'v3000' ? 'rxnV3000' : 'rxn'
+    const format =
+      molfileFormat === 'v3000' ? SupportedFormat.rxnV3000 : SupportedFormat.rxn
     const rxnfile = await getStructure(
       format,
       this.#formatterFactory,
@@ -173,28 +177,40 @@ export class Ketcher {
   }
 
   getKet(): Promise<string> {
-    return getStructure('ket', this.#formatterFactory, this.#editor.struct())
+    return getStructure(
+      SupportedFormat.ket,
+      this.#formatterFactory,
+      this.#editor.struct()
+    )
   }
 
   getSmarts(): Promise<string> {
-    return getStructure('smarts', this.#formatterFactory, this.#editor.struct())
+    return getStructure(
+      SupportedFormat.smarts,
+      this.#formatterFactory,
+      this.#editor.struct()
+    )
   }
 
   getCml(): Promise<string> {
-    return getStructure('cml', this.#formatterFactory, this.#editor.struct())
+    return getStructure(
+      SupportedFormat.cml,
+      this.#formatterFactory,
+      this.#editor.struct()
+    )
   }
 
   getInchi(withAuxInfo = false): Promise<string> {
     return getStructure(
-      withAuxInfo ? 'inChIAuxInfo' : 'inChI',
+      withAuxInfo ? SupportedFormat.inChIAuxInfo : SupportedFormat.inChI,
       this.#formatterFactory,
       this.#editor.struct()
     )
   }
 
   async generateInchIKey(): Promise<string> {
     const struct: string = await getStructure(
-      'ket',
+      SupportedFormat.ket,
       this.#formatterFactory,
       this.#editor.struct()
     )

diff --git a/packages/ketcher-react/src/script/ui/action/copyAs.js b/packages/ketcher-react/src/script/ui/action/copyAs.js
@@ -14,7 +14,7 @@
  * limitations under the License.
  ***************************************************************************/
 
-import { KetSerializer, MolSerializer } from 'ketcher-core'
+import { KetSerializer, MolSerializer, SupportedFormat } from 'ketcher-core'
 
 export default function copyAs(type) {
   const state = global.currentState

diff --git a/packages/ketcher-react/src/script/ui/views/modal/components/process/Miew/Miew.tsx b/packages/ketcher-react/src/script/ui/views/modal/components/process/Miew/Miew.tsx
@@ -15,7 +15,12 @@
  ***************************************************************************/
 
 import { Dialog } from '../../../../components'
-import { FormatterFactory, Struct, StructService } from 'ketcher-core'
+import {
+  FormatterFactory,
+  Struct,
+  StructService,
+  SupportedFormat
+} from 'ketcher-core'
 import { MIEW_OPTIONS } from '../../../../../data/schema/options-schema'
 import classes from './Miew.module.less'
 import { connect } from 'react-redux'
@@ -117,7 +122,7 @@ const MiewDialog = ({
     (miew: MiewAsType) => {
       miewRef.current = miew
       const factory = new FormatterFactory(server)
-      const service = factory.create('cml')
+      const service = factory.create(SupportedFormat.cml)
 
       service
         .getStructureFromStructAsync(struct)