#632 Adding a stereo flag when opening the structure (#655)

* Move isCorrectStereoCenter func to core * Move isStereoCanter from Struct to helpers/utils * Rename ValidateStereo tp StereoValidator
epam · Jul 19, 2021 · 3295523 · 3295523
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commit 3295523
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Showing 12 changed files with 125 additions and 90 deletions.
diff --git a/packages/ketcher-core/src/domain/entities/Struct.ts b/packages/ketcher-core/src/domain/entities/Struct.ts
@@ -33,6 +33,11 @@ import { SimpleObject } from './SimpleObject'
 import { Text } from './Text'
 import { Vec2 } from './Vec2'
 
+export type Neighbor = {
+  aid: number
+  bid: number
+}
+
 function arrayAddIfMissing(array, item) {
   for (var i = 0; i < array.length; ++i) {
     if (array[i] === item) return false
@@ -923,6 +928,16 @@ export class Struct {
     }
   }
 
+  atomGetNeighbors(aid: number): Array<Neighbor> | undefined {
+    return this.atoms.get(aid)?.neighbors.map(nei => {
+      const hb = this.halfBonds.get(nei)!
+      return {
+        aid: hb.end,
+        bid: hb.bid
+      }
+    })
+  }
+
   getComponents() {
     // eslint-disable-line max-statements
     /* saver */

diff --git a/packages/ketcher-core/src/domain/helpers/index.ts b/packages/ketcher-core/src/domain/helpers/index.ts
@@ -1 +1,2 @@
 export * from './Scale'
+export * from './utils/StereoValidator'
diff --git a/packages/ketcher-core/src/domain/helpers/utils/StereoValidator.ts b/packages/ketcher-core/src/domain/helpers/utils/StereoValidator.ts
@@ -0,0 +1,49 @@
+import { Bond } from '../../entities/Bond'
+import { Struct, Neighbor } from '../../entities/Struct'
+
+function isCorrectStereoCenter(
+  bond: Bond,
+  beginNeighs: Array<Neighbor> | undefined,
+  endNeighs: Array<Neighbor> | undefined,
+  struct: Struct
+) {
+  const beginAtom = struct.atoms.get(bond.begin)
+
+  let EndAtomNeigh: number | undefined = NaN
+
+  if (endNeighs?.length === 2) {
+    EndAtomNeigh =
+      endNeighs[0].aid === bond.begin ? endNeighs[1].aid : endNeighs[0].aid
+  }
+
+  if (bond.stereo > 0) {
+    if (
+      endNeighs?.length === 1 &&
+      beginNeighs?.length === 2 &&
+      Number(beginAtom?.implicitH) % 2 === 0
+    ) {
+      return false
+    }
+
+    if (
+      endNeighs?.length === 2 &&
+      beginNeighs?.length === 2 &&
+      Number(beginAtom?.implicitH) % 2 === 0 &&
+      struct.atomGetNeighbors(EndAtomNeigh)?.length === 1
+    ) {
+      return false
+    }
+
+    if (beginNeighs?.length === 1) {
+      return false
+    }
+
+    return true
+  } else {
+    return false
+  }
+}
+
+export const StereoValidator = {
+  isCorrectStereoCenter
+}
diff --git a/packages/ketcher-core/src/domain/serializers/mol/Molfile.ts b/packages/ketcher-core/src/domain/serializers/mol/Molfile.ts
@@ -19,6 +19,8 @@ import { Elements } from 'domain/constants'
 import common from './common'
 import utils from './utils'
 
+import { StereoValidator } from 'domain/helpers/utils/StereoValidator'
+
 const END_V2000 = '2D 1   1.00000     0.00000     0'
 
 type Mapping = {
@@ -52,7 +54,27 @@ export class Molfile {
     }
     ret.initHalfBonds()
     ret.initNeighbors()
+    ret.setImplicitHydrogen()
+
+    ret.bonds.forEach(bond => {
+      const beginNeighs = ret.atomGetNeighbors(bond.begin)
+      const endNeighs = ret.atomGetNeighbors(bond.end)
+      if (bond.stereo) {
+        if (
+          !StereoValidator.isCorrectStereoCenter(
+            bond,
+            beginNeighs,
+            endNeighs,
+            ret
+          )
+        ) {
+          ret.atoms.get(bond.begin).stereoLabel = null
+        }
+      }
+    })
+
     ret.markFragments()
+
     return ret
   }
 

diff --git a/packages/ketcher-react/src/script/editor/actions/atom.js b/packages/ketcher-react/src/script/editor/actions/atom.js
@@ -29,12 +29,7 @@ import {
   SGroupAtomAdd,
   CalcImplicitH
 } from '../operations'
-import {
-  atomGetAttr,
-  atomGetDegree,
-  atomGetNeighbors,
-  atomGetSGroups
-} from './utils'
+import { atomGetAttr, atomGetDegree, atomGetSGroups } from './utils'
 import { fromRGroupFragment, fromUpdateIfThen } from './rgroup'
 import { removeAtomFromSgroupIfNeeded, removeSgroupIfNeeded } from './sgroup'
 import { fromBondStereoUpdate } from './bond'
@@ -72,11 +67,11 @@ export function fromAtomsAttrs(restruct, ids, attrs, reset) {
 
       switch (key) {
         case 'stereoLabel':
-          if ('stereoLabel' in attrs)
+          if (key in attrs && value)
             action.addOp(new AtomAttr(aid, key, value).perform(restruct))
           break
         case 'stereoParity':
-          if ('stereoParity' in attrs)
+          if (key in attrs && value)
             action.addOp(new AtomAttr(aid, key, value).perform(restruct))
           break
         default:
@@ -96,7 +91,7 @@ export function fromAtomsAttrs(restruct, ids, attrs, reset) {
 
     action.addOp(new CalcImplicitH([aid]).perform(restruct))
 
-    const atomNeighbors = atomGetNeighbors(restruct, aid)
+    const atomNeighbors = restruct.molecule.atomGetNeighbors(aid)
     const bond = restruct.molecule.bonds.get(atomNeighbors[0]?.bid)
     if (bond) {
       action.mergeWith(fromBondStereoUpdate(restruct, bond))
@@ -165,7 +160,7 @@ export function fromAtomMerge(restruct, srcId, dstId) {
 
   const action = new Action()
 
-  const atomNeighbors = atomGetNeighbors(restruct, srcId)
+  const atomNeighbors = restruct.molecule.atomGetNeighbors(srcId)
   atomNeighbors.forEach(nei => {
     const bond = restruct.molecule.bonds.get(nei.bid)
 

diff --git a/packages/ketcher-react/src/script/editor/actions/bond.ts b/packages/ketcher-react/src/script/editor/actions/bond.ts
@@ -14,7 +14,14 @@
  * limitations under the License.
  ***************************************************************************/
 
-import { Atom, Bond, StereoLabel, Vec2 } from 'ketcher-core'
+import {
+  Atom,
+  Bond,
+  StereoLabel,
+  Vec2,
+  Neighbor,
+  StereoValidator
+} from 'ketcher-core'
 import {
   AtomAdd,
   AtomAttr,
@@ -24,7 +31,7 @@ import {
   CalcImplicitH,
   FragmentAdd
 } from '../operations'
-import { atomForNewBond, atomGetAttr, atomGetNeighbors } from './utils'
+import { atomForNewBond, atomGetAttr } from './utils'
 import {
   fromAtomMerge,
   fromStereoAtomAttrs,
@@ -179,11 +186,6 @@ function fromBondFlipping(restruct: ReStruct, id: number): Action {
   return action.perform(restruct)
 }
 
-type Neighbor = {
-  aid: Number
-  bid: Number
-}
-
 export function fromBondStereoUpdate(
   restruct: ReStruct,
   bond: Bond,
@@ -218,13 +220,21 @@ export function fromBondStereoUpdate(
 
   fragmentStereoBonds.forEach((bond: Bond | undefined) => {
     if (bond) {
-      const beginNeighs: Array<Neighbor> = atomGetNeighbors(
-        restruct,
+      const beginNeighs: Array<Neighbor> | undefined = struct.atomGetNeighbors(
         bond.begin
       )
-      const endNeighs: Array<Neighbor> = atomGetNeighbors(restruct, bond.end)
+      const endNeighs: Array<Neighbor> | undefined = struct.atomGetNeighbors(
+        bond.end
+      )
 
-      if (isCorrectStereoCenter(bond, beginNeighs, endNeighs, restruct)) {
+      if (
+        StereoValidator.isCorrectStereoCenter(
+          bond,
+          beginNeighs,
+          endNeighs,
+          struct
+        )
+      ) {
         const stereoLabel = struct.atoms.get(bond.begin)?.stereoLabel
         if (
           stereoLabel == null ||
@@ -273,53 +283,6 @@ export function fromBondStereoUpdate(
   return action
 }
 
-// TODO the function for calculating the stereocenter should be for the atom, not for bond
-function isCorrectStereoCenter(
-  bond: Bond,
-  beginNeighs: Array<Neighbor>,
-  endNeighs: Array<Neighbor>,
-  restruct: ReStruct
-) {
-  const struct = restruct.molecule
-  const beginAtom = struct.atoms.get(bond.begin)
-
-  let EndAtomNeigh: Number = NaN
-
-  if (endNeighs.length === 2) {
-    EndAtomNeigh =
-      endNeighs[0].aid === bond.begin ? endNeighs[1].aid : endNeighs[0].aid
-  }
-
-  if (bond.stereo > 0) {
-    if (
-      endNeighs.length === 1 &&
-      beginNeighs.length === 2 &&
-      Number(beginAtom?.implicitH) % 2 === 0
-    ) {
-      return false
-    }
-
-    if (bond.stereo > 0) {
-      if (
-        endNeighs.length === 2 &&
-        beginNeighs.length === 2 &&
-        Number(beginAtom?.implicitH) % 2 === 0 &&
-        atomGetNeighbors(restruct, EndAtomNeigh).length === 1
-      ) {
-        return false
-      }
-    }
-
-    if (beginNeighs.length === 1) {
-      return false
-    }
-
-    return true
-  } else {
-    return false
-  }
-}
-
 function getStereoParity(stereo: Number): number | null {
   let newAtomParity: number | null = null
   switch (stereo) {

diff --git a/packages/ketcher-react/src/script/editor/actions/erase.js b/packages/ketcher-react/src/script/editor/actions/erase.js
@@ -26,7 +26,7 @@ import {
   TextDelete
 } from '../operations'
 import { fromBondStereoUpdate } from '../actions/bond'
-import { atomGetDegree, atomGetNeighbors } from './utils'
+import { atomGetDegree } from './utils'
 import {
   fromSgroupDeletion,
   removeAtomFromSgroupIfNeeded,
@@ -116,7 +116,7 @@ export function fromFragmentDeletion(restruct, selection) {
   })
 
   selection.atoms.forEach(aid => {
-    atomGetNeighbors(restruct, aid).forEach(nei => {
+    restruct.molecule.atomGetNeighbors(aid).forEach(nei => {
       if (selection.bonds.indexOf(nei.bid) === -1) {
         selection.bonds = selection.bonds.concat([nei.bid])
       }

diff --git a/packages/ketcher-react/src/script/editor/actions/fragment.js b/packages/ketcher-react/src/script/editor/actions/fragment.js
@@ -29,7 +29,7 @@ import {
  * limitations under the License.
  ***************************************************************************/
 import { Pile, RGroup, Vec2 } from 'ketcher-core'
-import { atomGetNeighbors, getRelSgroupsBySelection } from './utils'
+import { getRelSgroupsBySelection } from './utils'
 import { fromRGroupFragment, fromUpdateIfThen } from './rgroup'
 
 import Action from '../shared/action'
@@ -158,7 +158,7 @@ function processAtom(restruct, aid, frid, newfrid) {
   while (queue.length > 0) {
     const id = queue.shift()
 
-    atomGetNeighbors(restruct, id).forEach(nei => {
+    restruct.molecule.atomGetNeighbors(id).forEach(nei => {
       if (
         restruct.molecule.atoms.get(nei.aid).fragment === frid &&
         !usedIds.has(nei.aid)

diff --git a/packages/ketcher-react/src/script/editor/actions/utils.js b/packages/ketcher-react/src/script/editor/actions/utils.js
@@ -26,16 +26,6 @@ export function atomGetDegree(restruct, aid) {
   return restruct.atoms.get(aid).a.neighbors.length
 }
 
-export function atomGetNeighbors(restruct, aid) {
-  return restruct.atoms.get(aid)?.a.neighbors.map(nei => {
-    const hb = restruct.molecule.halfBonds.get(nei)
-    return {
-      aid: hb.end,
-      bid: hb.bid
-    }
-  })
-}
-
 export function atomGetSGroups(restruct, aid) {
   return Array.from(restruct.atoms.get(aid).a.sgs)
 }
@@ -71,7 +61,7 @@ export function atomForNewBond(restruct, id) {
   const neighbours = []
   const pos = atomGetPos(restruct, id)
 
-  atomGetNeighbors(restruct, id).forEach(nei => {
+  restruct.molecule.atomGetNeighbors(id).forEach(nei => {
     const neiPos = atomGetPos(restruct, nei.aid)
 
     if (Vec2.dist(pos, neiPos) < 0.1) return
@@ -112,14 +102,14 @@ export function atomForNewBond(restruct, id) {
       maxAngle = -((4 * Math.PI) / 3)
 
       // zig-zag
-      const nei = atomGetNeighbors(restruct, id)[0]
+      const nei = restruct.molecule.atomGetNeighbors(id)[0]
       if (atomGetDegree(restruct, nei.aid) > 1) {
         const neiNeighbours = []
         const neiPos = atomGetPos(restruct, nei.aid)
         const neiV = Vec2.diff(pos, neiPos)
         const neiAngle = Math.atan2(neiV.y, neiV.x)
 
-        atomGetNeighbors(restruct, nei.aid).forEach(neiNei => {
+        restruct.molecule.atomGetNeighbors(nei.aid).forEach(neiNei => {
           const neiNeiPos = atomGetPos(restruct, neiNei.aid)
 
           if (neiNei.bid === nei.bid || Vec2.dist(neiPos, neiNeiPos) < 0.1)

diff --git a/packages/ketcher-react/src/script/editor/operations/atom/AtomAttr.ts b/packages/ketcher-react/src/script/editor/operations/atom/AtomAttr.ts
@@ -14,8 +14,8 @@
  * limitations under the License.
  ***************************************************************************/
 
- import { BaseOperation } from '../base'
- import { OperationType } from '../OperationType'
+import { BaseOperation } from '../base'
+import { OperationType } from '../OperationType'
 import Restruct from '../../../render/restruct'
 
 type Data = {

diff --git a/packages/ketcher-react/src/script/editor/operations/bond/index.ts b/packages/ketcher-react/src/script/editor/operations/bond/index.ts
@@ -14,9 +14,9 @@
  * limitations under the License.
  ***************************************************************************/
 
- import Restruct, { ReBond } from '../../../render/restruct'
+import Restruct, { ReBond } from '../../../render/restruct'
 
- import { BaseOperation } from '../base'
+import { BaseOperation } from '../base'
 import { Bond } from 'ketcher-core'
 import { OperationType } from '../OperationType'
 

diff --git a/packages/ketcher-react/src/script/editor/operations/calcimplicitH.ts b/packages/ketcher-react/src/script/editor/operations/calcimplicitH.ts
@@ -22,7 +22,7 @@ export class CalcImplicitH extends BaseOperation {
   atomIds: Array<number>
 
   constructor(aids: Array<number>) {
-    super(OperationType.CALC_IMPLICIT_H, 5)
+    super(OperationType.CALC_IMPLICIT_H, 10)
     this.atomIds = aids
   }
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		export * from './Scale'
		export * from './utils/StereoValidator'