Merge branch 'master' into #1899-add-right-click-menu-for-atoms

packages/ketcher-core/src/application/actions/action.types.ts

@@ -14,6 +14,13 @@
  * limitations under the License.
  ***************************************************************************/
 
+// import { Operation } from "application/operations"
+// import { ReStruct } from "application/render"
+
 export interface Action {
   perform: () => void
+  // operations: Array<Operation>
+  // mergeWith(action: Action): Action
+  // addOp(operation: Operation, restruct?: ReStruct): Operation
+  // isDummy(restruct?: ReStruct): boolean
 }

packages/ketcher-core/src/application/editor/editor.types.ts

@@ -52,4 +52,5 @@ export interface Editor {
   setOptions: (opts: string) => any
   zoom: (value?: any) => any
   structSelected: () => Struct
+  // update: (action: Action | true, ignoreHistory?: boolean) => void
 }

packages/ketcher-core/src/application/formatters/formatProperties.ts

@@ -100,6 +100,12 @@ const formatProperties: FormatPropertiesMap = {
     ChemicalMimeType.CDX,
     ['.cdx'],
     true
+  ),
+  unknown: new SupportedFormatProperties(
+    'Unknown',
+    ChemicalMimeType.UNKNOWN,
+    ['.'],
+    true
   )
 }
 

packages/ketcher-core/src/application/formatters/formatterFactory.ts

@@ -92,6 +92,7 @@ export class FormatterFactory {
       case SupportedFormat.smarts:
       case SupportedFormat.cdxml:
       case SupportedFormat.cdx:
+      case SupportedFormat.unknown:
       default:
         formatter = new ServerFormatter(
           this.#structService,

packages/ketcher-core/src/application/formatters/identifyStructFormat.ts

@@ -32,6 +32,10 @@ export function identifyStructFormat(
     return SupportedFormat.rxn
   }
 
+  if (sanitizedString.indexOf('V2000') !== -1) {
+    return SupportedFormat.mol
+  }
+
   if (sanitizedString.indexOf('V3000') !== -1) {
     return SupportedFormat.molV3000
   }
@@ -55,12 +59,16 @@ export function identifyStructFormat(
     return SupportedFormat.cml
   }
 
-  const clearStr = sanitizedString.replace(/\s/g, '')
-  const anyLetterAnyDigitContainsSlashesEndsWithEqualSign =
-    /^[a-zA-Z0-9+/]*={0,2}$/
+  const clearStr = sanitizedString
+    .replace(/\s/g, '')
+    .replace(/(\\r)|(\\n)/g, '')
+  const isBase64String =
+    /^([0-9a-zA-Z+/]{4})*(([0-9a-zA-Z+/]{2}==)|([0-9a-zA-Z+/]{3}=))?$/
+  const cdxHeader = 'VjCD0100'
   if (
-    anyLetterAnyDigitContainsSlashesEndsWithEqualSign.test(clearStr) &&
-    clearStr.length % 4 === 0
+    clearStr.length % 4 === 0 &&
+    isBase64String.test(clearStr) &&
+    window.atob(clearStr).startsWith(cdxHeader)
   ) {
     return SupportedFormat.cdx
   }
@@ -69,17 +77,14 @@ export function identifyStructFormat(
     return SupportedFormat.inChI
   }
 
-  if (
-    sanitizedString.indexOf('\n') === -1 &&
-    sanitizedString === sanitizedString.toUpperCase()
-  ) {
+  if (sanitizedString.indexOf('\n') === -1) {
     // TODO: smiles regexp
     return SupportedFormat.smiles
   }
 
   if (sanitizedString.indexOf('<CDXML') !== -1) {
     return SupportedFormat.cdxml
   }
-  // Molfile by default as Indigo does
-  return SupportedFormat.mol
+
+  return SupportedFormat.unknown
 }

packages/ketcher-core/src/application/formatters/structFormatter.types.ts

@@ -37,7 +37,8 @@ export enum SupportedFormat {
   cml = 'cml',
   ket = 'ket',
   cdxml = 'cdxml',
-  cdx = 'cdx'
+  cdx = 'cdx',
+  unknown = 'unknown'
 }
 
 export type FormatterFactoryOptions = Partial<

packages/ketcher-core/src/application/operations/index.ts

@@ -25,3 +25,4 @@ export * from './rxnPlus'
 export * from './sgroup'
 export * from './simpleObject'
 export * from './text'
+export * from './baseOperation'

packages/ketcher-core/src/application/operations/operations.types.ts

@@ -14,6 +14,7 @@
  * limitations under the License.
  ***************************************************************************/
 
+import { ReStruct } from 'application/render'
 import { Struct } from 'domain/entities'
 
 export type OperationType =
@@ -70,8 +71,13 @@ export type OperationType =
 export interface Operation {
   readonly type: OperationType
   readonly priority: number
+  readonly _inverted: OperationType | undefined
+  data: any
   // eslint-disable-next-line no-use-before-define
   perform: (struct: Struct) => PerformOperationResult
+  invert(): Operation
+  isDummy(_restruct: ReStruct): boolean
+  execute(_restruct: ReStruct): void
 }
 
 export type PerformOperationResult = {

packages/ketcher-core/src/application/render/restruct/restruct.ts

@@ -605,10 +605,14 @@ class ReStruct {
             item.selected = sGroupAtoms.length > 0 && sGroupAtoms[0].selected
           }
 
-          const selected = selection?.[map]
+          let selected = selection?.[map]
             ? selection[map].indexOf(id) > -1
             : item.selected
 
+          if (selection === null) {
+            selected = false
+          }
+
           this.showItemSelection(item, selected)
         })
       }

packages/ketcher-core/src/domain/entities/functionalGroup.ts

@@ -60,9 +60,14 @@ export class FunctionalGroup {
   static getFunctionalGroupByName(searchName: string): Struct | null {
     const provider = FunctionalGroupsProvider.getInstance()
     const functionalGroups = provider.getFunctionalGroupsList()
-    const foundGroup = functionalGroups.find(({ name, abbreviation }) => {
-      return name === searchName || abbreviation === searchName
-    })
+
+    let foundGroup
+    if (searchName) {
+      foundGroup = functionalGroups.find(({ name, abbreviation }) => {
+        return name === searchName || abbreviation === searchName
+      })
+    }
+
     return foundGroup || null
   }
 

packages/ketcher-core/src/domain/services/struct/structService.types.ts

@@ -25,7 +25,8 @@ export enum ChemicalMimeType {
   CDX = 'chemical/x-cdx',
   CDXML = 'chemical/x-cdxml',
   CML = 'chemical/x-cml',
-  KET = 'chemical/x-indigo-ket'
+  KET = 'chemical/x-indigo-ket',
+  UNKNOWN = 'chemical/x-unknown'
 }
 
 export interface WithStruct {

packages/ketcher-react/package.json

@@ -126,6 +126,7 @@
     "rollup-plugin-delete": "^2.0.0",
     "rollup-plugin-peer-deps-external": "^2.2.4",
     "rollup-plugin-postcss": "^4.0.2",
+    "rollup-plugin-string": "^3.0.0",
     "rollup-plugin-typescript2": "^0.31.1",
     "rollup-plugin-visualizer": "^5.5.2",
     "stylelint": "13.13.1",

packages/ketcher-react/rollup.config.js

@@ -16,6 +16,7 @@ import strip from '@rollup/plugin-strip'
 import svgr from '@svgr/rollup'
 import typescript from 'rollup-plugin-typescript2'
 import { license } from '../../license.ts'
+import { string } from 'rollup-plugin-string'
 
 const mode = {
   PRODUCTION: 'production',
@@ -98,7 +99,10 @@ const config = {
       comments: 'none',
       include: includePattern
     }),
-    ...(isProduction ? [strip({ include: includePattern })] : [])
+    ...(isProduction ? [strip({ include: includePattern })] : []),
+    string({
+      include: '**/*.sdf'
+    })
   ]
 }
 

packages/ketcher-react/src/script/editor/Editor.ts

@@ -387,7 +387,7 @@ class Editor implements KetcherEditor {
     }
   }
 
-  update(action: Action | true, ignoreHistory?) {
+  update(action: Action | true, ignoreHistory?: boolean) {
     if (action === true) {
       this.render.update(true) // force
     } else {
@@ -606,6 +606,10 @@ function domEventSetup(editor: Editor, clientArea) {
       editor.lastEvent = event
       if (EditorTool && eventName in EditorTool) {
         EditorTool[eventName](event)
+        return true
+      }
+      if (eventName === 'mouseup') {
+        editor.selection(null)
       }
       return true
     }, -1)

packages/ketcher-react/src/script/editor/tool/bond.ts

@@ -284,7 +284,7 @@ class BondTool {
 
         this.editor.update(bondAddition[0])
       } else if (dragCtx.item.map === 'atoms') {
-        // when does it hapend?
+        // click on atom
         this.editor.update(
           fromBondAddition(
             rnd.ctab,

packages/ketcher-react/src/script/editor/tool/select.ts

@@ -34,7 +34,7 @@ import {
 
 import LassoHelper from './helper/lasso'
 import { atomLongtapEvent } from './atom'
-import { sgroupDialog } from './sgroup'
+import SGroupTool from './sgroup'
 import utils from '../shared/utils'
 import { xor } from 'lodash/fp'
 import { Editor } from '../Editor'
@@ -193,6 +193,7 @@ class SelectTool {
     if (event.shiftKey) {
       this.editor.selection(selMerge(sel, selection, true))
     } else {
+      this.editor.selection(null)
       this.editor.selection(isSelected(selection, ci) ? selection : sel)
     }
     return true
@@ -535,7 +536,7 @@ class SelectTool {
       ci.map === 'sgroupData'
     ) {
       editor.selection(closestToSel(ci))
-      sgroupDialog(editor, ci.id, null)
+      SGroupTool.sgroupDialog(editor, ci.id, null)
     } else if (ci.map === 'texts') {
       editor.selection(closestToSel(ci))
       const text = molecule.texts.get(ci.id)