#225 – moved CIP rendering logic to Atom class

epam · Mar 20, 2023 · c608227 · c608227
1 parent bf2eaf9
commit c608227
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Showing 6 changed files with 72 additions and 3 deletions.
diff --git a/packages/ketcher-core/src/application/render/restruct/reatom.ts b/packages/ketcher-core/src/application/render/restruct/reatom.ts
@@ -135,7 +135,7 @@ class ReAtom extends ReObject {
 
   show(restruct: ReStruct, aid: number, options: any): void {
     // eslint-disable-line max-statements
-    const atom = restruct.molecule.atoms.get(aid)
+    const atom = restruct.molecule.atoms.get(aid)!
     const sgroups = restruct.molecule.sgroups
     const functionalGroups = restruct.molecule.functionalGroups
     const render = restruct.render
@@ -402,7 +402,58 @@ class ReAtom extends ReObject {
 
       restruct.addReObjectPath(LayerMap.hovering, this.visel, path)
     }
+
+    if (atom.cip) {
+      this.drawCIPLabel(atom, render.ctab)
+    }
   }
+
+  drawCIPLabel(atom: Atom, restruct: ReStruct) {
+    const render = restruct.render
+    const { options, paper } = render
+    const path = paper.set()
+
+    const cipLabelPosition = atom.pp.scaled(options.scale)
+    const cipValuePath = getCIPValuePath({
+      paper,
+      cipLabelPosition,
+      atom,
+      options
+    })
+    const box = util.relBox(cipValuePath.getBBox())
+
+    cipValuePath.translateAbs(0.5 * box.width, -0.5 * box.height)
+    path.push(cipValuePath.toBack())
+
+    restruct.addReObjectPath(LayerMap.data, this.visel, path, null, true)
+  }
+}
+
+function getCIPValuePath({
+  paper,
+  cipLabelPosition,
+  atom,
+  options
+}: {
+  paper
+  cipLabelPosition: Vec2
+  atom: Atom
+  options
+}) {
+  const text = paper
+    .text(cipLabelPosition.x, cipLabelPosition.y, `(${atom.cip})`)
+    .attr({
+      font: options.font,
+      'font-size': options.fontsz
+    })
+  const box = text.getBBox()
+  const path = paper.set()
+  const rect = paper
+    .rect(box.x - 1, box.y - 1, box.width + 2, box.height + 2, 3, 3)
+    .attr({ fill: '#0f0', stroke: '#fff', opacity: 1 })
+  path.push(rect.toBack(), text.toBack())
+
+  return path
 }
 
 function getStereoAtomColor(options, stereoLabel) {

diff --git a/packages/ketcher-core/src/domain/entities/atom.ts b/packages/ketcher-core/src/domain/entities/atom.ts
@@ -53,6 +53,13 @@ export enum StereoLabel {
   Or = 'or'
 }
 
+export enum CIP {
+  S = 'S',
+  R = 'R',
+  s = 's',
+  r = 'r'
+}
+
 export interface AtomAttributes {
   stereoParity?: number
   stereoLabel?: string | null
@@ -69,6 +76,7 @@ export interface AtomAttributes {
   rglabel?: string | null
   charge?: number
   radical?: number
+  cip?: CIP | null
   isotope?: number
   alias?: string | null
   pseudo?: string
@@ -101,6 +109,7 @@ export class Atom {
     label: 'C',
     isotope: 0,
     radical: 0,
+    cip: null,
     charge: 0,
     explicitValence: -1,
     ringBondCount: 0,
@@ -125,6 +134,7 @@ export class Atom {
   isotope: number
   hCount: number
   radical: number
+  cip: CIP | null
   charge: number
   explicitValence: number
   ringBondCount: number
@@ -153,6 +163,7 @@ export class Atom {
     this.alias = getValueOrDefault(attributes.alias, Atom.attrlist.alias)
     this.isotope = getValueOrDefault(attributes.isotope, Atom.attrlist.isotope)
     this.radical = getValueOrDefault(attributes.radical, Atom.attrlist.radical)
+    this.cip = getValueOrDefault(attributes.cip, Atom.attrlist.cip)
     this.charge = getValueOrDefault(attributes.charge, Atom.attrlist.charge)
     this.rglabel = getValueOrDefault(attributes.rglabel, Atom.attrlist.rglabel)
     this.attpnt = getValueOrDefault(attributes.attpnt, Atom.attrlist.attpnt)

diff --git a/packages/ketcher-core/src/domain/entities/functionalGroup.ts b/packages/ketcher-core/src/domain/entities/functionalGroup.ts
@@ -16,6 +16,7 @@
 import { ReSGroup } from 'application/render'
 import assert from 'assert'
 import { FunctionalGroupsProvider } from '../helpers'
+import { Atom } from './atom'
 import { Bond } from './bond'
 import { Pool } from './pool'
 import { SGroup } from './sgroup'
@@ -235,7 +236,7 @@ export class FunctionalGroup {
   }
 
   static isAtomInContractedFunctionalGroup(
-    atom,
+    atom: Atom,
     sgroups,
     functionalGroups,
     sgroupsFromReStruct: boolean

diff --git a/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts b/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts
@@ -68,6 +68,7 @@ export function atomToStruct(source) {
   ifDef(params, 'explicitValence', source.explicitValence)
   ifDef(params, 'isotope', source.isotope)
   ifDef(params, 'radical', source.radical)
+  ifDef(params, 'cip', source.cip)
   ifDef(params, 'attpnt', source.attachmentPoints)
   // stereo
   ifDef(params, 'stereoLabel', source.stereoLabel)

diff --git a/packages/ketcher-react/src/script/editor/tool/select.ts b/packages/ketcher-react/src/script/editor/tool/select.ts
@@ -304,7 +304,7 @@ class SelectTool {
       )
       const atomFromStruct = atomId !== null && struct.atoms.get(atomId)?.a
       if (
-        atomId !== null &&
+        atomFromStruct &&
         !FunctionalGroup.isAtomInContractedFunctionalGroup(
           // TODO: examine if this code is really needed, seems like its a hack
           atomFromStruct,

diff --git a/packages/ketcher-react/src/script/ui/data/schema/struct-schema.js b/packages/ketcher-react/src/script/ui/data/schema/struct-schema.js
@@ -66,6 +66,11 @@ export const atom = {
       ],
       default: 0
     },
+    cip: {
+      title: 'CIP',
+      type: 'string',
+      enum: ['R', 'S', 'r', 's']
+    },
     ringBondCount: {
       title: 'Ring bond count',
       enum: [0, -2, -1, 2, 3, 4],