#3651 - different coordinate systems are used in micro and macro mode (…

…#3726) Co-authored-by: Konstantin Zharich <[email protected]>
epam · Dec 21, 2023 · d4981dc · d4981dc
1 parent 9e5ad98
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Showing 14 changed files with 81 additions and 41 deletions.
diff --git a/ketcher-autotests/tests/test-data/KET/five-monomers.ket b/ketcher-autotests/tests/test-data/KET/five-monomers.ket
@@ -41,7 +41,7 @@
         "id": "45",
         "position": {
             "x": 7.325,
-            "y": 6.925000000000001
+            "y": -6.925000000000001
         },
         "alias": "A",
         "templateId": "A___Alanine"
@@ -184,7 +184,7 @@
         "id": "46",
         "position": {
             "x": 12.4,
-            "y": 6.775
+            "y": -6.775
         },
         "alias": "25R",
         "templateId": "25R___2,5-Ribose"
@@ -425,7 +425,7 @@
         "id": "47",
         "position": {
             "x": 15.8,
-            "y": 6.675000000000001
+            "y": -6.675000000000001
         },
         "alias": "baA",
         "templateId": "baA___N-benzyl-adenine"
@@ -742,7 +742,7 @@
         "id": "49",
         "position": {
             "x": 22.6,
-            "y": 6.8500000000000005
+            "y": -6.8500000000000005
         },
         "alias": "Test-6-Ch",
         "templateId": "Test-6-Ch___Test-6-AP-Chem"
@@ -1148,7 +1148,7 @@
         "id": "51",
         "position": {
             "x": 19.35,
-            "y": 6.7250000000000005
+            "y": -6.7250000000000005
         },
         "alias": "Test-6-Ph",
         "templateId": "Test-6-Ph___Test-6-AP-Phosphate"

diff --git a/ketcher-autotests/tests/test-data/KET/monomers-and-chem.ket b/ketcher-autotests/tests/test-data/KET/monomers-and-chem.ket
@@ -52,7 +52,7 @@
         "id": "1",
         "position": {
             "x": 7.9750000000000005,
-            "y": 5.9
+            "y": -5.9
         },
         "alias": "A",
         "templateId": "A___Alanine"
@@ -189,7 +189,7 @@
         "id": "3",
         "position": {
             "x": 13.325000000000001,
-            "y": 5.825000000000005
+            "y": -5.825000000000005
         },
         "alias": "Bal",
         "templateId": "Bal___beta-Alanine"
@@ -324,7 +324,7 @@
         "id": "6",
         "position": {
             "x": 8.075000000000003,
-            "y": 10.05
+            "y": -10.05
         },
         "alias": "Az",
         "templateId": "Az___Azide"

diff --git a/ketcher-autotests/tests/test-data/KET/monomers-connected-with-bonds-expected.ket b/ketcher-autotests/tests/test-data/KET/monomers-connected-with-bonds-expected.ket
@@ -52,7 +52,8 @@
         "id": "0",
         "position": {
             "x": 9.850000000000001,
-            "y": 11.279999995231629
+            "y": -11.279999995231629,
+            "z": 0
         },
         "alias": "baA",
         "templateId": "baA___N-benzyl-adenine"
@@ -368,7 +369,8 @@
         "id": "1",
         "position": {
             "x": 9.850000000000001,
-            "y": 8.729999995231628
+            "y": -8.729999995231628,
+            "z": 0
         },
         "alias": "12ddR",
         "templateId": "12ddR___1',2'-Di-Deoxy-Ribose"
@@ -563,7 +565,8 @@
         "id": "2",
         "position": {
             "x": 12.4,
-            "y": 8.729999995231628
+            "y": -8.729999995231628,
+            "z": 0
         },
         "alias": "P",
         "templateId": "P___Phosphate"

diff --git a/ketcher-autotests/tests/test-data/KET/monomers-connected-with-bonds.ket b/ketcher-autotests/tests/test-data/KET/monomers-connected-with-bonds.ket
@@ -52,7 +52,7 @@
       "id": "373",
       "position": {
           "x": 9.850000000000001,
-          "y": 11.279999995231629
+          "y": -11.279999995231629
       },
       "alias": "baA",
       "templateId": "baA___N-benzyl-adenine"
@@ -366,7 +366,7 @@
       "id": "374",
       "position": {
           "x": 9.850000000000001,
-          "y": 8.729999995231628
+          "y": -8.729999995231628
       },
       "alias": "12ddR",
       "templateId": "12ddR___1',2'-Di-Deoxy-Ribose"
@@ -557,7 +557,7 @@
       "id": "376",
       "position": {
           "x": 12.4,
-          "y": 8.729999995231628
+          "y": -8.729999995231628
       },
       "alias": "P",
       "templateId": "P___Phosphate"

diff --git a/ketcher-autotests/tests/test-data/KET/monomers-with-bonds.ket b/ketcher-autotests/tests/test-data/KET/monomers-with-bonds.ket
@@ -308,7 +308,7 @@
         "id": "3",
         "position": {
             "x": 8.200000000000001,
-            "y": 2.475
+            "y": -2.475
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -731,7 +731,7 @@
         "id": "4",
         "position": {
             "x": 10.9,
-            "y": 2.375
+            "y": -2.375
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -741,7 +741,7 @@
         "id": "5",
         "position": {
             "x": 13.725000000000001,
-            "y": 2.275
+            "y": -2.275
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -751,7 +751,7 @@
         "id": "6",
         "position": {
             "x": 7.8500000000000005,
-            "y": 7.300000000000001
+            "y": -7.300000000000001
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -761,7 +761,7 @@
         "id": "7",
         "position": {
             "x": 10.65,
-            "y": 7.1000000000000005
+            "y": -7.1000000000000005
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -771,7 +771,7 @@
         "id": "8",
         "position": {
             "x": 13.725000000000001,
-            "y": 7.1000000000000005
+            "y": -7.1000000000000005
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -781,7 +781,7 @@
         "id": "9",
         "position": {
             "x": 10.825000000000001,
-            "y": 4.7250000000000005
+            "y": -4.7250000000000005
         },
         "alias": "Test-6-P",
         "templateId": "Test-6-P___Test-6-AP-Peptide"
@@ -791,7 +791,7 @@
         "id": "19",
         "position": {
             "x": 2.2,
-            "y": 8.9
+            "y": -8.9
         },
         "alias": "A",
         "templateId": "A___Adenine"
@@ -996,7 +996,7 @@
         "id": "20",
         "position": {
             "x": 2.2,
-            "y": 6.3500000000000005
+            "y": -6.3500000000000005
         },
         "alias": "R",
         "templateId": "R___Ribose"
@@ -1237,7 +1237,7 @@
         "id": "22",
         "position": {
             "x": 4.75,
-            "y": 6.3500000000000005
+            "y": -6.3500000000000005
         },
         "alias": "P",
         "templateId": "P___Phosphate"

diff --git a/ketcher-autotests/tests/test-data/KET/three-monomers-connected-with-bonds.ket b/ketcher-autotests/tests/test-data/KET/three-monomers-connected-with-bonds.ket
@@ -52,7 +52,7 @@
         "id": "76",
         "position": {
             "x": 10.325000000000001,
-            "y": 5.2250000000000005
+            "y": -5.2250000000000005
         },
         "alias": "A",
         "templateId": "A___Alanine"
@@ -195,7 +195,7 @@
         "id": "77",
         "position": {
             "x": 14.525,
-            "y": 5.125
+            "y": -5.125
         },
         "alias": "Edc",
         "templateId": "Edc___S-ethylthiocysteine"
@@ -398,7 +398,7 @@
         "id": "78",
         "position": {
             "x": 19.175,
-            "y": 5.300000000000001
+            "y": -5.300000000000001
         },
         "alias": "A6OH",
         "templateId": "A6OH___6-amino-hexanol"

diff --git a/ketcher-autotests/tests/test-data/KET/three-monomers-not-connected-with-bonds.ket b/ketcher-autotests/tests/test-data/KET/three-monomers-not-connected-with-bonds.ket
@@ -29,7 +29,7 @@
         "id": "36",
         "position": {
             "x": 12.625,
-            "y": 9.575000000000001
+            "y": -9.575000000000001
         },
         "alias": "Bal",
         "templateId": "Bal___beta-Alanine"
@@ -170,7 +170,7 @@
         "id": "37",
         "position": {
             "x": 17.025000000000002,
-            "y": 9.675
+            "y": -9.675
         },
         "alias": "Edc",
         "templateId": "Edc___S-ethylthiocysteine"
@@ -373,7 +373,7 @@
         "id": "38",
         "position": {
             "x": 20.775000000000002,
-            "y": 9.725000000000001
+            "y": -9.725000000000001
         },
         "alias": "Test-6-Ch",
         "templateId": "Test-6-Ch___Test-6-AP-Chem"

diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/monomers-and-chem.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/monomers-and-chem.mol
@@ -1,13 +1,13 @@
 
-  -INDIGO-12152318292D
+  -INDIGO-12202313442D
 
   0  0  0  0  0  0  0  0  0  0  0 V3000
 M  V30 BEGIN CTAB
 M  V30 COUNTS 3 2 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 A 7.975 5.9 0.0 0 CLASS=AA ATTCHORD=(4 2 Br 3 Al)
-M  V30 2 Bal 13.325 5.825 0.0 0 CLASS=AA ATTCHORD=(2 1 Al)
-M  V30 3 Az 8.075 10.05 0.0 0 CLASS=CHEM ATTCHORD=(2 1 Al)
+M  V30 1 A 7.975 -5.9 0.0 0 CLASS=AA ATTCHORD=(4 2 Br 3 Al)
+M  V30 2 Bal 13.325 -5.825 0.0 0 CLASS=AA ATTCHORD=(2 1 Al)
+M  V30 3 Az 8.075 -10.05 0.0 0 CLASS=CHEM ATTCHORD=(2 1 Al)
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2

diff --git a/packages/ketcher-core/src/domain/entities/Axis.ts b/packages/ketcher-core/src/domain/entities/Axis.ts
@@ -0,0 +1,7 @@
+export enum Axis {
+  x = 'x',
+  y = 'y',
+  z = 'z',
+}
+
+export type Axises = 'x' | 'y' | 'z';
diff --git a/packages/ketcher-core/src/domain/entities/index.ts b/packages/ketcher-core/src/domain/entities/index.ts
@@ -43,3 +43,4 @@ export * from './Chem';
 export * from './Sugar';
 export * from './RNABase';
 export * from './Phosphate';
+export * from './Axis';
diff --git a/packages/ketcher-core/src/domain/serializers/ket/fromKet/monomerToDrawingEntity.ts b/packages/ketcher-core/src/domain/serializers/ket/fromKet/monomerToDrawingEntity.ts
@@ -4,13 +4,17 @@ import {
 } from 'application/formatters/types/ket';
 import { Struct, Vec2 } from 'domain/entities';
 import { DrawingEntitiesManager } from 'domain/entities/DrawingEntitiesManager';
+import { switchIntoChemistryCoordSystem } from 'domain/serializers/ket/helpers';
 
 export function monomerToDrawingEntity(
   node: IKetMonomerNode,
   template: IKetMonomerTemplate,
   struct: Struct,
   drawingEntitiesManager: DrawingEntitiesManager,
 ) {
+  const position: Vec2 = switchIntoChemistryCoordSystem(
+    new Vec2(node.position.x, node.position.y),
+  );
   return drawingEntitiesManager.addMonomer(
     {
       struct,
@@ -30,6 +34,6 @@ export function monomerToDrawingEntity(
       attachmentPoints: template.attachmentPoints,
       seqId: node.seqid,
     },
-    new Vec2(node.position.x, node.position.y),
+    position,
   );
 }
diff --git a/packages/ketcher-core/src/domain/serializers/ket/helpers.ts b/packages/ketcher-core/src/domain/serializers/ket/helpers.ts
@@ -14,6 +14,7 @@
  * limitations under the License.
  ***************************************************************************/
 
+import { Vec2, Axis, Axises } from 'domain/entities';
 import { cloneDeepWith, cloneDeep } from 'lodash';
 
 const customizer = (value: any) => {
@@ -34,3 +35,19 @@ export const setMonomerPrefix = (monomerId: number) => `monomer${monomerId}`;
 export const getKetRef = (entityId: string) => {
   return { $ref: entityId };
 };
+
+const rotateCoordAxisBy180Degrees = (position: Vec2, axis: Axises): Vec2 => {
+  const rotatedPosition = {
+    x: position.x,
+    y: position.y,
+    z: position.z,
+  };
+
+  rotatedPosition[axis] = -rotatedPosition[axis];
+
+  return new Vec2(rotatedPosition.x, rotatedPosition.y, rotatedPosition.z);
+};
+
+export const switchIntoChemistryCoordSystem = (position: Vec2) => {
+  return rotateCoordAxisBy180Degrees(position, Axis.y);
+};
diff --git a/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts b/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
@@ -50,6 +50,7 @@ import {
   getKetRef,
   setMonomerPrefix,
   setMonomerTemplatePrefix,
+  switchIntoChemistryCoordSystem,
 } from 'domain/serializers/ket/helpers';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
 import { validate } from 'domain/serializers/ket/validate';
@@ -439,10 +440,9 @@ export class KetSerializer implements Serializer<Struct> {
         fileContent[monomerName] = {
           type: 'monomer',
           id: monomer.id.toString(),
-          position: {
-            x: monomer.position.x,
-            y: monomer.position.y,
-          },
+          position: switchIntoChemistryCoordSystem(
+            new Vec2(monomer.position.x, monomer.position.y),
+          ),
           alias: monomer.label,
           templateId,
           seqid: monomer.monomerItem.seqId,