Backmerge: #6235 – Incorrect representation of hydrogens for alias ch…

…arge valence and radical properties in macro mode (#6262)

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

@@ -294,6 +294,11 @@ export class MacromoleculesConverter {
       reStruct?.bonds.set(bondId, new ReBond(bond));
     });
 
+    struct.findConnectedComponents();
+    struct.setImplicitHydrogen();
+    struct.setStereoLabelsToAtoms();
+    struct.markFragments();
+
     return { struct, reStruct, conversionErrorMessage };
   }
 

packages/ketcher-core/src/application/render/renderers/AtomRenderer.ts

@@ -1,5 +1,5 @@
 import { BaseRenderer } from 'application/render/renderers/BaseRenderer';
-import { Atom } from 'domain/entities/CoreAtom';
+import { Atom, AtomRadical } from 'domain/entities/CoreAtom';
 import { Coordinates } from 'application/editor/shared/coordinates';
 import { CoreEditor, ZoomTool } from 'application/editor';
 import { AtomLabel, ElementColor, Elements } from 'domain/constants';
@@ -163,7 +163,7 @@ export class AtomRenderer extends BaseRenderer {
     const isAtomInMiddleOfChain = (atomNeighborsHalfEdges?.length || 0) >= 2;
     const hasCharge = this.atom.hasCharge;
     const hasRadical = this.atom.hasRadical;
-    const hasAlias = this.atom.properties.alias;
+    const hasAlias = this.atom.hasAlias;
     const hasExplicitValence = this.atom.hasExplicitValence;
     const hasExplicitIsotope = this.atom.hasExplicitIsotope;
 
@@ -263,24 +263,27 @@ export class AtomRenderer extends BaseRenderer {
       textElement
         ?.append('tspan')
         .attr('dy', this.atom.hasExplicitIsotope ? 4 : 0)
-        .text(this.atom.properties.alias || this.atom.label);
+        .text(this.labelText);
     }
 
-    if (hydrogenAmount > 0) {
+    if (!this.atom.hasAlias && hydrogenAmount > 0) {
       textElement
         ?.append('tspan')
-        .attr('dy', this.atom.hasExplicitIsotope ? 4 : 0)
+        .attr(
+          'dy',
+          this.atom.hasExplicitIsotope && shouldHydrogenBeOnLeft ? 4 : 0,
+        )
         .text('H');
-    }
 
-    if (hydrogenAmount > 1) {
-      textElement?.append('tspan').text(hydrogenAmount).attr('dy', 3);
+      if (hydrogenAmount > 1) {
+        textElement?.append('tspan').text(hydrogenAmount).attr('dy', 3);
+      }
     }
 
     if (shouldHydrogenBeOnLeft) {
       textElement
         ?.append('tspan')
-        .text(this.atom.properties.alias || this.atom.label)
+        .text(this.labelText)
         .attr('dy', hydrogenAmount > 1 ? -3 : 0);
     }
 
@@ -345,7 +348,7 @@ export class AtomRenderer extends BaseRenderer {
         ?.append('tspan')
         .text(
           (Math.abs(charge) > 1 ? Math.abs(charge) : '') +
-            (charge > 0 ? '+' : '-'),
+            (charge > 0 ? '+' : '–'),
         )
         .attr('fill', this.labelColor)
         .attr('dy', -4);
@@ -362,7 +365,7 @@ export class AtomRenderer extends BaseRenderer {
     this.radicalElement = this.rootElement?.append('g');
 
     switch (radical) {
-      case 1:
+      case AtomRadical.Single:
         this.radicalElement
           ?.append('circle')
           .attr('cx', 3)
@@ -376,15 +379,15 @@ export class AtomRenderer extends BaseRenderer {
           .attr('r', 2)
           .attr('fill', this.labelColor);
         break;
-      case 2:
+      case AtomRadical.Doublet:
         this.radicalElement
           ?.append('circle')
           .attr('cx', 0)
           .attr('cy', -10)
           .attr('r', 2)
           .attr('fill', this.labelColor);
         break;
-      case 3:
+      case AtomRadical.Triplet:
         this.radicalElement
           ?.append('path')
           .attr('d', `M 0 -5 L 2 -10 L 4 -5 M -6 -5 L -4 -10 L -2 -5`)
@@ -413,6 +416,12 @@ export class AtomRenderer extends BaseRenderer {
       const explicitIsotope = this.atom.properties.isotope as number;
 
       this.textElement
+        /*
+         * TODO: Currently it's always appended in front of the atom (1H3C or 1CH3), however, in micro mode isotope is placed before the exact atom, not the hydrogen (H31C or 1CH3)
+         * While the latter is displayed correctly, the former has to be fixed. Can go through all the tspans and use label tspan instead of :first-child here
+         * However, now it leads to the atom properties being positioned incorrectly due to 'dy' attribute being relative to the previous tspan
+         * Probably we could consider another approach for positioning the atom properties?
+         */
         ?.insert('tspan', ':first-child')
         .text(explicitIsotope)
         .attr('fill', this.labelColor)

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

@@ -8,11 +8,18 @@ import { AtomRenderer } from 'application/render/renderers/AtomRenderer';
 import { isNumber } from 'lodash';
 import { MonomerToAtomBond } from './MonomerToAtomBond';
 
+export enum AtomRadical {
+  None,
+  Single,
+  Doublet,
+  Triplet,
+}
+
 export interface AtomProperties {
   charge?: number | null;
   explicitValence?: number;
   isotope?: number | null;
-  radical?: number;
+  radical?: AtomRadical;
   alias?: string | null;
 }
 export class Atom extends DrawingEntity {
@@ -86,6 +93,10 @@ export class Atom extends DrawingEntity {
     return connectionsAmount;
   }
 
+  public get hasAlias() {
+    return Boolean(this.properties.alias);
+  }
+
   public get hasRadical() {
     return isNumber(this.properties.radical) && this.properties.radical !== 0;
   }
@@ -105,14 +116,108 @@ export class Atom extends DrawingEntity {
     return isNumber(this.properties.isotope) && this.properties.isotope >= 0;
   }
 
+  private get radicalAmount() {
+    switch (this.properties.radical) {
+      case AtomRadical.Single:
+      case AtomRadical.Triplet:
+        return 2;
+      case AtomRadical.Doublet:
+        return 1;
+      default:
+        return 0;
+    }
+  }
+
+  private get valenceWithoutHydrogen() {
+    const charge = this.properties.charge || 0;
+    const label = this.label;
+    const element = Elements.get(this.label);
+    // if (!element) {
+    //   // query atom, skip
+    //   this.implicitH = 0;
+    //   return 0;
+    // }
+
+    const elementGroupNumber = element?.group;
+    const radicalAmount = this.radicalAmount;
+    const connectionAmount = this.calculateConnections();
+    const absoluteCharge = Math.abs(charge);
+
+    if (elementGroupNumber === 3) {
+      if (
+        label === AtomLabel.B ||
+        label === AtomLabel.Al ||
+        label === AtomLabel.Ga ||
+        label === AtomLabel.In
+      ) {
+        if (charge === -1) {
+          if (radicalAmount + connectionAmount <= 4) {
+            return radicalAmount + connectionAmount;
+          }
+        }
+      }
+    } else if (elementGroupNumber === 5) {
+      if (label === AtomLabel.N || label === AtomLabel.P) {
+        if (charge === 1 || charge === 2) {
+          return radicalAmount + connectionAmount;
+        }
+      } else if (
+        label === AtomLabel.Sb ||
+        label === AtomLabel.Bi ||
+        label === AtomLabel.As
+      ) {
+        if (charge === 1 || charge === 2) {
+          return radicalAmount + connectionAmount;
+        }
+      }
+    } else if (elementGroupNumber === 6) {
+      if (label === AtomLabel.O) {
+        if (charge >= 1) {
+          return radicalAmount + connectionAmount;
+        }
+      } else if (
+        label === AtomLabel.S ||
+        label === AtomLabel.Se ||
+        label === AtomLabel.Po
+      ) {
+        if (charge === 1) {
+          return radicalAmount + connectionAmount;
+        }
+      }
+    } else if (elementGroupNumber === 7) {
+      if (
+        label === AtomLabel.Cl ||
+        label === AtomLabel.Br ||
+        label === AtomLabel.I ||
+        label === AtomLabel.At
+      ) {
+        if (charge === 1) {
+          return radicalAmount + connectionAmount;
+        }
+      }
+    }
+
+    return radicalAmount + connectionAmount + absoluteCharge;
+  }
+
   calculateValence() {
+    if (this.hasExplicitValence) {
+      const valence = this.properties.explicitValence as number;
+      const hydrogenAmount = valence - this.valenceWithoutHydrogen;
+
+      return {
+        valence,
+        hydrogenAmount,
+      };
+    }
+
     const label = this.label;
     const element = Elements.get(label);
     const elementGroupNumber = element?.group;
     const connectionAmount = this.calculateConnections();
-    const radicalAmount = this.properties.radical || 0;
-    const absCharge = 0;
+    const radicalAmount = this.radicalAmount;
     const charge = this.properties.charge || 0;
+    const absCharge = Math.abs(charge);
     let valence = connectionAmount;
     let hydrogenAmount = 0;
 
@@ -358,6 +463,7 @@ export class Atom extends DrawingEntity {
       if (connectionAmount + radicalAmount + absCharge === 0) valence = 1;
       else hydrogenAmount = -1;
     }
+
     // if (Atom.isHeteroAtom(label) && this.implicitHCount !== null) {
     //   hydrogenAmount = this.implicitHCount;
     // }

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

@@ -1981,6 +1981,7 @@ export class DrawingEntitiesManager {
         monomerToNewMonomer.get(atom.monomer) as BaseMonomer,
         atom.atomIdInMicroMode,
         atom.label,
+        atom.properties,
       );
       const addedAtom = atomAddCommand.operations[0].atom as Atom;