#3371 - Merge ring bond count, degree and atomic mass atom properties

ketcher-autotests/tests/utils/canvas/types.ts

@@ -9,13 +9,10 @@ export type Chirality = 'clockwise' | 'anticlockwise';
 
 export interface AtomQueryProperties {
   aromaticity?: Aromaticity | null;
-  degree?: number | null;
   ringMembership?: number | null;
   ringSize?: number | null;
   connectivity?: number | null;
-  ringConnectivity?: number | null;
   chirality?: Chirality | null;
-  atomicMass?: number | null;
   customQuery?: string | null;
 }
 

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

@@ -1134,13 +1134,10 @@ export function getAtomCustomQuery(atom) {
     hCount: (value) =>
       Number(value) > 0 ? 'H' + (Number(value) - 1).toString() : '',
     implicitHCount: (value) => `h${value}`,
-    degree: (value) => `D${value}`,
     ringMembership: (value) => `R${value}`,
     ringSize: (value) => `r${value}`,
     connectivity: (value) => `X${value}`,
-    ringConnectivity: (value) => `x${value}`,
     chirality: (value) => (value === 'clockwise' ? '@@' : '@'),
-    atomicMass: (value) => value.toString(),
   };
 
   for (const propertyName in atom) {
@@ -1172,13 +1169,10 @@ function getQueryAttrsText(atom, isAromatized: boolean) {
     implicitHCount,
     queryProperties: {
       aromaticity,
-      degree,
       ringMembership,
       ringSize,
       connectivity,
-      ringConnectivity,
       chirality,
-      atomicMass,
       customQuery,
     },
   } = atom.a;
@@ -1209,10 +1203,6 @@ function getQueryAttrsText(atom, isAromatized: boolean) {
     addSemicolon();
     queryAttrsText += aromaticity === 'aromatic' ? 'a' : 'A';
   }
-  if (Number.isFinite(degree)) {
-    addSemicolon();
-    queryAttrsText += `D${degree}`;
-  }
   if (Number.isFinite(ringMembership)) {
     addSemicolon();
     queryAttrsText += `R${ringMembership}`;
@@ -1225,18 +1215,10 @@ function getQueryAttrsText(atom, isAromatized: boolean) {
     addSemicolon();
     queryAttrsText += `X${connectivity}`;
   }
-  if (Number.isFinite(ringConnectivity)) {
-    addSemicolon();
-    queryAttrsText += `x${ringConnectivity}`;
-  }
   if (chirality !== null) {
     addSemicolon();
     queryAttrsText += chirality === 'clockwise' ? '@@' : '@';
   }
-  if (Number.isFinite(atomicMass)) {
-    addSemicolon();
-    queryAttrsText += `${atomicMass}`;
-  }
   return queryAttrsText;
 }
 

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

@@ -61,13 +61,10 @@ export type Chirality = 'clockwise' | 'anticlockwise';
 
 export interface AtomQueryProperties {
   aromaticity?: Aromaticity | null;
-  degree?: number | null;
   ringMembership?: number | null;
   ringSize?: number | null;
   connectivity?: number | null;
-  ringConnectivity?: number | null;
   chirality?: Chirality | null;
-  atomicMass?: number | null;
   customQuery?: string | null;
 }
 
@@ -147,13 +144,10 @@ export class Atom {
     hCount: 0,
     queryProperties: {
       aromaticity: null,
-      degree: null,
       ringMembership: null,
       ringSize: null,
       connectivity: null,
-      ringConnectivity: null,
       chirality: null,
-      atomicMass: null,
       customQuery: null,
     },
     atomList: null,

packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts

@@ -86,13 +86,10 @@ export function atomToStruct(source) {
 
   const queryAttribute: Array<keyof AtomQueryProperties> = [
     'aromaticity',
-    'degree',
     'ringMembership',
     'connectivity',
     'ringSize',
-    'ringConnectivity',
     'chirality',
-    'atomicMass',
     'customQuery',
   ];
   ifDef(params, 'label', source.label);

packages/ketcher-core/src/domain/serializers/ket/schema.json

@@ -180,11 +180,6 @@
               "type": "string",
               "enum": ["aromatic", "aliphatic"]
             },
-            "degree": {
-              "type": "integer",
-              "minimum": 0,
-              "maximum": 6
-            },
             "ringMembership": {
               "type": "integer",
               "minimum": 0,
@@ -200,16 +195,6 @@
               "minimum": 0,
               "maximum": 5
             },
-            "ringConnectivity": {
-              "type": "integer",
-              "minimum": 0,
-              "maximum": 5
-            },
-            "atomicMass": {
-              "type": "integer",
-              "minimum": 0,
-              "maximum": 1000
-            },
             "chirality": {
               "type": "string",
               "enum": ["clockwise", "anticlockwise"]

packages/ketcher-react/src/script/ui/data/convert/structconv.js

@@ -93,20 +93,14 @@ export function fromAtom(satom) {
     stereoParity: satom.stereoParity,
     implicitHCount: satom.implicitHCount,
     aromaticity: satom.queryProperties.aromaticity,
-    degree: satom.queryProperties.degree,
     ringMembership: satom.queryProperties.ringMembership,
     ringSize: satom.queryProperties.ringSize,
     connectivity: satom.queryProperties.connectivity,
-    ringConnectivity: satom.queryProperties.ringConnectivity,
     chirality: satom.queryProperties.chirality,
     customQuery:
       satom.queryProperties.customQuery === null
         ? ''
         : satom.queryProperties.customQuery.toString(),
-    atomicMass:
-      satom.queryProperties.atomicMass === null
-        ? ''
-        : satom.queryProperties.atomicMass.toString(),
   };
 }
 
@@ -115,13 +109,10 @@ export function toAtom(atom) {
   //      see ratomtool
   const {
     aromaticity,
-    degree,
     ringMembership,
     ringSize,
     connectivity,
-    ringConnectivity,
     chirality,
-    atomicMass,
     customQuery,
     ...restAtom
   } = atom;
@@ -140,14 +131,11 @@ export function toAtom(atom) {
       implicitHCount: null,
       queryProperties: {
         aromaticity: null,
-        degree: null,
         implicitHCount: null,
         ringMembership: null,
         ringSize: null,
         connectivity: null,
-        ringConnectivity: null,
         chirality: null,
-        atomicMass: null,
         customQuery,
       },
       invRet: 0,
@@ -165,14 +153,11 @@ export function toAtom(atom) {
     unsaturatedAtom: +(restAtom.unsaturatedAtom ?? false),
     queryProperties: {
       aromaticity,
-      degree,
       implicitHCount: restAtom.implicitHCount,
       ringMembership,
       ringSize,
       connectivity,
-      ringConnectivity,
       chirality,
-      atomicMass: atomicMass === '' ? null : Number(atomicMass),
       customQuery: customQuery === '' ? null : customQuery,
     },
   });

packages/ketcher-react/src/script/ui/data/schema/struct-schema.js

@@ -49,7 +49,7 @@ export const atom = {
       default: -1,
     },
     isotope: {
-      title: 'Isotope',
+      title: 'Isotope (atomic mass)',
       type: 'integer',
       minimum: 0,
       default: 0,
@@ -73,20 +73,33 @@ export const atom = {
     },
     ringBondCount: {
       title: 'Ring bond count',
-      enum: [0, -2, -1, 2, 3, 4],
-      enumNames: ['', 'As drawn', '0', '2', '3', '4'],
+      enum: [0, -2, -1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', 'As drawn', '0', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
     hCount: {
       title: 'H count',
-      enum: [0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4'],
+      enum: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
     substitutionCount: {
       title: 'Substitution count',
-      enum: [0, -2, -1, 1, 2, 3, 4, 5, 6],
-      enumNames: ['', 'As drawn', '0', '1', '2', '3', '4', '5', '6'],
+      enum: [0, -2, -1, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: [
+        '',
+        'As drawn',
+        '0',
+        '1',
+        '2',
+        '3',
+        '4',
+        '5',
+        '6',
+        '7',
+        '8',
+        '9',
+      ],
       default: 0,
     },
     unsaturatedAtom: {
@@ -100,62 +113,36 @@ export const atom = {
       enumNames: ['', 'aromatic', 'aliphatic'],
       default: 0,
     },
-    degree: {
-      title: 'Degree',
-      enum: [null, 0, 1, 2, 3, 4, 5, 6],
-      enumNames: ['', '0', '1', '2', '3', '4', '5', '6'],
-      default: 0,
-    },
     implicitHCount: {
       title: 'Implicit H count',
-      enum: [null, 0, 1, 2, 3, 4],
-      enumNames: ['', '0', '1', '2', '3', '4'],
+      enum: [null, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
     ringMembership: {
       title: 'Ring membership',
-      enum: [null, 0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4', '5'],
+      enum: [null, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
     ringSize: {
       title: 'Ring size',
-      enum: [null, 0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4', '5'],
+      enum: [null, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
     connectivity: {
       title: 'Connectivity',
-      enum: [null, 0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4', '5'],
-      default: 0,
-    },
-    ringConnectivity1: {
-      title: 'Ring connectivity',
-      enum: [null, 0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4', '5'],
+      enum: [null, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+      enumNames: ['', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9'],
       default: 0,
     },
-    ringConnectivity: {
-      title: 'Ring connectivity',
-      enum: [null, 0, 1, 2, 3, 4, 5],
-      enumNames: ['', '0', '1', '2', '3', '4', '5'],
-      default: null,
-    },
     chirality: {
       title: 'Chirality',
       enum: [null, 'clockwise', 'anticlockwise'],
       enumNames: ['', 'anticlockwise', 'clockwise'],
       default: 0,
     },
-    atomicMass: {
-      title: 'Atomic mass',
-      type: 'string',
-      pattern: '^([+]?)([0-9]{1,3}|1000)([+-]?)$|(^$)',
-      default: '',
-      maxLength: 5,
-      invalidMessage: 'Invalid atomic mass',
-    },
     customQuery: {
       title: 'Custom Query',
       pattern: '[^ ]',

packages/ketcher-react/src/script/ui/state/modal/form.js

@@ -36,14 +36,11 @@ export const formsState = {
       ringBondCount: 0,
       substitutionCount: 0,
       aromaticity: null,
-      degree: null,
       implicitHCount: null,
       ringMembership: null,
       ringSize: null,
       connectivity: null,
-      ringConnectivity: null,
       chirality: null,
-      atomicMass: null,
       customQuery: null,
     },
   },

packages/ketcher-react/src/script/ui/views/components/ContextMenu/menuItems/AtomMenuItems.tsx

@@ -27,11 +27,9 @@ const {
 } = atom.properties;
 const properties: Array<AtomQueryPropertiesName> = [
   'aromaticity',
-  'degree',
   'ringMembership',
   'ringSize',
   'connectivity',
-  'ringConnectivity',
 ];
 
 const atomPropertiesForSubMenu: {

packages/ketcher-react/src/script/ui/views/modal/components/toolbox/Atom/Atom.tsx

@@ -70,14 +70,11 @@ const querySpecificFields: Array<{
   { name: 'substitutionCount', component: 'dropdown' },
   { name: 'unsaturatedAtom', labelPos: 'before', className: classes.checkbox },
   { name: 'aromaticity', component: 'dropdown' },
-  { name: 'degree', component: 'dropdown' },
   { name: 'implicitHCount', component: 'dropdown' },
   { name: 'ringMembership', component: 'dropdown' },
   { name: 'ringSize', component: 'dropdown' },
   { name: 'connectivity', component: 'dropdown' },
-  { name: 'ringConnectivity', component: 'dropdown' },
   { name: 'chirality', component: 'dropdown' },
-  { name: 'atomicMass' },
 ];
 const Atom: FC<Props> = (props: Props) => {
   const {