#3298 - Add simple atom query primitives to the query specific proper…

…ties

ketcher-autotests/tests/User-Interface/Right-Click-Menu/right-click.spec.ts

@@ -126,9 +126,9 @@ test.describe('Right-click menu', () => {
     await page.getByText('Ring bond count').click();
     await takeEditorScreenshot(page);
     await page.getByRole('button', { name: 'As drawn' }).first().click();
-    await page.getByText('Substitution count').click();
+    await page.getByText('Aromaticity').click();
     await takeEditorScreenshot(page);
-    await page.getByRole('button', { name: '6' }).last().click();
+    await page.getByRole('button', { name: 'aliphatic' }).click();
     await page.getByText('Unsaturated').first().click();
     await takeEditorScreenshot(page);
     await page.getByRole('button', { name: 'Saturated' }).last().click();

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

@@ -4,7 +4,8 @@ export enum SORT_TYPE {
   ASC_X = 'ASC_X',
   ASC_Y = 'ASC_Y',
 }
-
+export type Aromaticity = 'aromatic' | 'aliphatic';
+export type Chirality = '@' | '@@' | '@?' | '@@?';
 export type AtomAttributes = {
   label?: string;
   charge?: number;
@@ -15,6 +16,15 @@ export type AtomAttributes = {
   explicitValence?: number;
   implicitH?: number;
   ringBondCount?: number;
+  aromaticity?: Aromaticity | null;
+  degree?: number | null;
+  implicitHCount?: number | null;
+  ringMembership?: number | null;
+  ringSize?: number | null;
+  connectivity?: number | null;
+  ringConnectivity?: number | null;
+  chirality?: Chirality | null;
+  atomicMass?: number | null;
   substitutionCount?: number;
   unsaturatedAtom?: number;
   hCount?: number;

packages/ketcher-core/src/application/editor/actions/utils.ts

@@ -23,6 +23,7 @@ import { selectionKeys } from '../shared/constants';
 import { EditorSelection } from '../editor.types';
 
 export type AtomAttributeName = keyof AtomAttributes;
+export type AtomAttributeValue = AtomAttributes[AtomAttributeName];
 
 export function atomGetAttr(
   restruct: ReStruct,

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

@@ -1071,29 +1071,83 @@ function getAamText(atom) {
 
 function getQueryAttrsText(atom) {
   let queryAttrsText = '';
-  if (atom.a.ringBondCount !== 0) {
-    if (atom.a.ringBondCount > 0) {
-      queryAttrsText += 'rb' + atom.a.ringBondCount.toString();
-    } else if (atom.a.ringBondCount === -1) queryAttrsText += 'rb0';
-    else if (atom.a.ringBondCount === -2) queryAttrsText += 'rb*';
+  const addComma = () => {
+    if (queryAttrsText.length > 0) queryAttrsText += ',';
+  };
+  const {
+    ringBondCount,
+    substitutionCount,
+    unsaturatedAtom,
+    hCount,
+    aromaticity,
+    degree,
+    implicitHCount,
+    ringMembership,
+    ringSize,
+    connectivity,
+    ringConnectivity,
+    chirality,
+    atomicMass,
+  } = atom.a;
+  if (ringBondCount !== 0) {
+    if (ringBondCount > 0) {
+      queryAttrsText += 'rb' + ringBondCount.toString();
+    } else if (ringBondCount === -1) queryAttrsText += 'rb0';
+    else if (ringBondCount === -2) queryAttrsText += 'rb*';
     else throw new Error('Ring bond count invalid');
   }
-  if (atom.a.substitutionCount !== 0) {
-    if (queryAttrsText.length > 0) queryAttrsText += ',';
-    if (atom.a.substitutionCount > 0) {
-      queryAttrsText += 's' + atom.a.substitutionCount.toString();
-    } else if (atom.a.substitutionCount === -1) queryAttrsText += 's0';
-    else if (atom.a.substitutionCount === -2) queryAttrsText += 's*';
+  if (substitutionCount !== 0) {
+    addComma();
+    if (substitutionCount > 0) {
+      queryAttrsText += 's' + substitutionCount.toString();
+    } else if (substitutionCount === -1) queryAttrsText += 's0';
+    else if (substitutionCount === -2) queryAttrsText += 's*';
     else throw new Error('Substitution count invalid');
   }
-  if (atom.a.unsaturatedAtom > 0) {
-    if (queryAttrsText.length > 0) queryAttrsText += ',';
-    if (atom.a.unsaturatedAtom === 1) queryAttrsText += 'u';
+  if (unsaturatedAtom > 0) {
+    addComma();
+    if (unsaturatedAtom === 1) queryAttrsText += 'u';
     else throw new Error('Unsaturated atom invalid value');
   }
-  if (atom.a.hCount > 0) {
-    if (queryAttrsText.length > 0) queryAttrsText += ',';
-    queryAttrsText += 'H' + (atom.a.hCount - 1).toString();
+  if (hCount > 0) {
+    addComma();
+    queryAttrsText += 'H' + (hCount - 1).toString();
+  }
+  if (aromaticity !== null) {
+    addComma();
+    queryAttrsText += aromaticity === 'aromatic' ? 'a' : 'A';
+  }
+  if (degree !== null) {
+    addComma();
+    queryAttrsText += `D<${degree}>`;
+  }
+  if (implicitHCount !== null) {
+    addComma();
+    queryAttrsText += `h<${implicitHCount}>`;
+  }
+  if (ringMembership !== null) {
+    addComma();
+    queryAttrsText += `R<${ringMembership}>`;
+  }
+  if (ringSize !== null) {
+    addComma();
+    queryAttrsText += `r<${ringSize}>`;
+  }
+  if (connectivity !== null) {
+    addComma();
+    queryAttrsText += `X<${connectivity}>`;
+  }
+  if (ringConnectivity !== null) {
+    addComma();
+    queryAttrsText += `x<${ringConnectivity}>`;
+  }
+  if (chirality !== null) {
+    addComma();
+    queryAttrsText += chirality;
+  }
+  if (atomicMass !== null) {
+    addComma();
+    queryAttrsText += `<${atomicMass}>`;
   }
   return queryAttrsText;
 }

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

@@ -56,6 +56,8 @@ enum CIP {
   r = 'r',
 }
 
+export type Aromaticity = 'aromatic' | 'aliphatic';
+export type Chirality = '@' | '@@' | '@?' | '@@?';
 export interface AtomAttributes {
   stereoParity?: number;
   stereoLabel?: string | null;
@@ -68,6 +70,14 @@ export interface AtomAttributes {
   unsaturatedAtom?: number;
   substitutionCount?: number;
   ringBondCount?: number;
+  aromaticity?: Aromaticity | null;
+  degree?: number | null;
+  ringMembership?: number | null;
+  ringSize?: number | null;
+  connectivity?: number | null;
+  ringConnectivity?: number | null;
+  chirality?: Chirality | null;
+  atomicMass?: number | null;
   explicitValence?: number;
   /**
    * Rgroup member attachment points
@@ -125,6 +135,14 @@ export class Atom {
     substitutionCount: 0,
     unsaturatedAtom: 0,
     hCount: 0,
+    aromaticity: null,
+    degree: null,
+    ringMembership: null,
+    ringSize: null,
+    connectivity: null,
+    ringConnectivity: null,
+    chirality: null,
+    atomicMass: null,
     atomList: null,
     invRet: 0,
     exactChangeFlag: 0,
@@ -150,6 +168,14 @@ export class Atom {
   charge: number;
   explicitValence: number;
   ringBondCount: number;
+  aromaticity: Aromaticity | null;
+  degree: number | null;
+  ringMembership: number | null;
+  ringSize: number | null;
+  connectivity: number | null;
+  ringConnectivity: number | null;
+  chirality: Chirality | null;
+  atomicMass: number | null;
   unsaturatedAtom: number;
   substitutionCount: number;
   valence: number;
@@ -212,6 +238,35 @@ export class Atom {
       attributes.ringBondCount,
       Atom.attrlist.ringBondCount,
     );
+    this.aromaticity = getValueOrDefault(
+      attributes.aromaticity,
+      Atom.attrlist.aromaticity,
+    );
+    this.degree = getValueOrDefault(attributes.degree, Atom.attrlist.degree);
+    this.ringMembership = getValueOrDefault(
+      attributes.ringMembership,
+      Atom.attrlist.ringMembership,
+    );
+    this.ringSize = getValueOrDefault(
+      attributes.ringSize,
+      Atom.attrlist.ringSize,
+    );
+    this.connectivity = getValueOrDefault(
+      attributes.connectivity,
+      Atom.attrlist.connectivity,
+    );
+    this.ringConnectivity = getValueOrDefault(
+      attributes.ringConnectivity,
+      Atom.attrlist.ringConnectivity,
+    );
+    this.chirality = getValueOrDefault(
+      attributes.chirality,
+      Atom.attrlist.chirality,
+    );
+    this.atomicMass = getValueOrDefault(
+      attributes.atomicMass,
+      Atom.attrlist.atomicMass,
+    );
     this.substitutionCount = getValueOrDefault(
       attributes.substitutionCount,
       Atom.attrlist.substitutionCount,

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

@@ -27,6 +27,7 @@ import {
 import { Elements } from 'domain/constants';
 import { ifDef } from 'utilities';
 import { mergeFragmentsToStruct } from './mergeFragmentsToStruct';
+import { AtomAttributeName } from 'application/editor';
 
 export function toRlabel(values) {
   let res = 0;
@@ -82,7 +83,19 @@ export function moleculeToStruct(ketItem: any): Struct {
 
 export function atomToStruct(source) {
   const params: any = {};
-
+  const queryAttribute: AtomAttributeName[] = [
+    'ringBondCount',
+    'substitutionCount',
+    'hCount',
+    'aromaticity',
+    'degree',
+    'ringMembership',
+    'connectivity',
+    'ringSize',
+    'ringConnectivity',
+    'chirality',
+    'atomicMass',
+  ];
   ifDef(params, 'label', source.label);
   ifDef(params, 'alias', source.alias);
   ifDef(params, 'pp', {
@@ -101,10 +114,11 @@ export function atomToStruct(source) {
   ifDef(params, 'stereoParity', source.stereoParity);
   ifDef(params, 'weight', source.weight);
   // query
-  ifDef(params, 'ringBondCount', source.ringBondCount);
-  ifDef(params, 'substitutionCount', source.substitutionCount);
+  queryAttribute.forEach((attributeName) => {
+    ifDef(params, attributeName, source[attributeName]);
+  });
   ifDef(params, 'unsaturatedAtom', Number(Boolean(source.unsaturatedAtom)));
-  ifDef(params, 'hCount', source.hCount);
+
   // reaction
   ifDef(params, 'aam', source.mapping);
   ifDef(params, 'invRet', source.invRet);

packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts

@@ -83,6 +83,15 @@ function atomToKet(source) {
   ifDef(result, 'substitutionCount', source.substitutionCount, 0);
   ifDef(result, 'unsaturatedAtom', !!source.unsaturatedAtom, false);
   ifDef(result, 'hCount', source.hCount, 0);
+  ifDef(result, 'aromaticity', source.aromaticity);
+  ifDef(result, 'degree', source.degree);
+  ifDef(result, 'ringMembership', source.ringMembership);
+  ifDef(result, 'connectivity', source.connectivity);
+  ifDef(result, 'ringSize', source.ringSize);
+  ifDef(result, 'ringConnectivity', source.ringConnectivity);
+  ifDef(result, 'chirality', source.chirality);
+  ifDef(result, 'atomicMass', source.atomicMass, 0);
+
   // reaction
   ifDef(result, 'mapping', parseInt(source.aam), 0);
   ifDef(result, 'invRet', source.invRet, 0);

packages/ketcher-react/src/components/ToggleButtonGroup/ToggleButtonGroup.tsx

@@ -28,7 +28,7 @@ export default function ButtonGroup<T>({
       {buttons.map(({ label, value: buttonValue }) => (
         <ToggleButton
           key={label}
-          value={Number(buttonValue)}
+          value={Number(buttonValue) || ''}
           onClick={(event) => handleChange(event, buttonValue)}
           className={clsx(classes.button, {
             [classes.selected]: buttonValue === value,

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

@@ -86,6 +86,15 @@ export function fromAtom(satom) {
     radical: satom.radical,
     invRet: satom.invRet,
     exactChangeFlag: !!satom.exactChangeFlag,
+    aromaticity: satom.aromaticity,
+    degree: satom.degree,
+    implicitHCount: satom.implicitHCount,
+    ringMembership: satom.ringMembership,
+    ringSize: satom.ringSize,
+    connectivity: satom.connectivity,
+    ringConnectivity: satom.ringConnectivity,
+    chirality: satom.chirality,
+    atomicMass: satom.atomicMass === null ? '' : satom.atomicMass.toString(),
     ringBondCount: satom.ringBondCount,
     substitutionCount: satom.substitutionCount,
     unsaturatedAtom: !!satom.unsaturatedAtom,
@@ -108,6 +117,7 @@ export function toAtom(atom) {
     unsaturatedAtom: +(atom.unsaturatedAtom ?? false),
   });
   if (charge !== undefined) conv.charge = charge;
+  conv.atomicMass = atom.atomicMass === '' ? null : Number(atom.atomicMass);
   return conv;
 }