#5490 - Update indigo to 1.24.0-rc.2 in browser module (#5523)

- also updated ketcher to 2.25.0-rc.2 - fixed monomerFactory to rely on MonomerClass field - fixed screenshots
epam · Sep 18, 2024 · 371321b · 371321b
1 parent 14444b6
commit 371321b
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts
@@ -397,6 +397,7 @@ const correctHELMStrings: IHELMString[] = [
       'RNA1{[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|](A)P}$$$$V2.0',
     shouldFail: true,
     issueNumber: 'https://github.com/epam/Indigo/issues/2339',
+    pageReloadNeeded: true,
   },
   {
     helmDescription:

diff --git a/...le-peti-e8f4f-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png b/...le-peti-e8f4f-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...i-char--d41d6-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png b/...i-char--d41d6-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...le-RNAs-87b49-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png b/...le-RNAs-87b49-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...i-char--050cf-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png b/...i-char--050cf-presents-an-AND-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...le-RNAs-d5feb-at-the-proportion-of-that-element-is-unknown-1-chromium-linux.png b/...le-RNAs-d5feb-at-the-proportion-of-that-element-is-unknown-1-chromium-linux.png
diff --git a/...i-char--c8418-at-the-proportion-of-that-element-is-unknown-1-chromium-linux.png b/...i-char--c8418-at-the-proportion-of-that-element-is-unknown-1-chromium-linux.png
diff --git a/...mple-pept-e1213--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png b/...mple-pept-e1213--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...lti-char--7a592--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png b/...lti-char--7a592--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...mple-RNAs-a09b2--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png b/...mple-RNAs-a09b2--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...lti-char--356cc--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png b/...lti-char--356cc--excluding-OR-relationship-of-the-monomers-1-chromium-linux.png
diff --git a/...le-pept-d7357-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png b/...le-pept-d7357-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png
diff --git a/...i-char--497a3-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png b/...i-char--497a3-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png
diff --git a/...le-RNAs-45bd1-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png b/...le-RNAs-45bd1-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png
diff --git a/...i-char--a3e4a-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png b/...i-char--a3e4a-it-the-probability-of-the-element-is-unknown-1-chromium-linux.png
diff --git a/...LM-sequence-50-RNA-RP-with-single-inline-Extended-SMILES-P-1-chromium-linux.png b/...LM-sequence-50-RNA-RP-with-single-inline-Extended-SMILES-P-1-chromium-linux.png
diff --git a/...LM-sequence-51-RNA-RP-with-single-inline-Extended-SMILES-R-1-chromium-linux.png b/...LM-sequence-51-RNA-RP-with-single-inline-Extended-SMILES-R-1-chromium-linux.png
diff --git a/...M-sequence-52-RNA-RAP-with-single-inline-Extended-SMILES-P-1-chromium-linux.png b/...M-sequence-52-RNA-RAP-with-single-inline-Extended-SMILES-P-1-chromium-linux.png
diff --git a/...nce-53-RNA-RAP-with-all-monomer-inline-Extended-SMILES-RAP-1-chromium-linux.png b/...nce-53-RNA-RAP-with-all-monomer-inline-Extended-SMILES-RAP-1-chromium-linux.png
diff --git a/...gle-peptide-with-inline-SMILES-L-without-attachment-points-1-chromium-linux.png b/...gle-peptide-with-inline-SMILES-L-without-attachment-points-1-chromium-linux.png
diff --git a/...M-sequence-55-Single-peptide-with-inline-Extended-SMILES-L-1-chromium-linux.png b/...M-sequence-55-Single-peptide-with-inline-Extended-SMILES-L-1-chromium-linux.png
diff --git a/...gle-CHEM-with-inline-SMILES-A6OH-without-attachment-points-1-chromium-linux.png b/...gle-CHEM-with-inline-SMILES-A6OH-without-attachment-points-1-chromium-linux.png
diff --git a/...M-sequence-57-Single-CHEM-with-inline-Extended-SMILES-A6OH-1-chromium-linux.png b/...M-sequence-57-Single-CHEM-with-inline-Extended-SMILES-A6OH-1-chromium-linux.png
diff --git a/...uence-58-List-of-peptide-of-inline-Extended-Smiles-A-C-D-L-1-chromium-linux.png b/...uence-58-List-of-peptide-of-inline-Extended-Smiles-A-C-D-L-1-chromium-linux.png
diff --git a/...9-List-of-RNAs-of-inline-Extended-Smiles-R-A-P-R-C-P-R-G-P-1-chromium-linux.png b/...9-List-of-RNAs-of-inline-Extended-Smiles-R-A-P-R-C-P-R-G-P-1-chromium-linux.png
diff --git a/...t-HELM-sequence-40-Probability-is-greater-than-100-PEPTIDE-1-chromium-linux.png b/...t-HELM-sequence-40-Probability-is-greater-than-100-PEPTIDE-1-chromium-linux.png
diff --git a/...RNA-rAp--eda93-e-inline-SMILES-r-without-attachment-points-1-chromium-linux.png b/...RNA-rAp--eda93-e-inline-SMILES-r-without-attachment-points-1-chromium-linux.png
diff --git a/...8-RNA-R-A-P-with-inline-SMILES-A-without-attachment-points-1-chromium-linux.png b/...8-RNA-R-A-P-with-inline-SMILES-A-without-attachment-points-1-chromium-linux.png
diff --git a/...NA-R-A-P-22a0a-e-inline-SMILES-R-without-attachment-points-1-chromium-linux.png b/...NA-R-A-P-22a0a-e-inline-SMILES-R-without-attachment-points-1-chromium-linux.png
diff --git a/...-a-fil-32430-view-display-changes-made-during-modification-1-chromium-linux.png b/...-a-fil-32430-view-display-changes-made-during-modification-1-chromium-linux.png
diff --git a/...iles-from-external-editor-for-dna-peptide-conj-example-mol-1-chromium-linux.png b/...iles-from-external-editor-for-dna-peptide-conj-example-mol-1-chromium-linux.png
diff --git a/...es-from-external-editor-for-dna-peptideSS-conj-example-mol-1-chromium-linux.png b/...es-from-external-editor-for-dna-peptideSS-conj-example-mol-1-chromium-linux.png
diff --git a/...external-editor-for-rna-mod-phosphate-mod-base-example-mol-1-chromium-linux.png b/...external-editor-for-rna-mod-phosphate-mod-base-example-mol-1-chromium-linux.png
diff --git a/...ng-bet-8a35b-A-with-modified-monomer-with-modyfied-monomer-2-chromium-linux.png b/...ng-bet-8a35b-A-with-modified-monomer-with-modyfied-monomer-2-chromium-linux.png
diff --git a/...ng-bet-cbf77-A-with-modified-monomer-with-modyfied-monomer-2-chromium-linux.png b/...ng-bet-cbf77-A-with-modified-monomer-with-modyfied-monomer-2-chromium-linux.png
diff --git a/package-lock.json b/package-lock.json
diff --git a/packages/ketcher-core/__tests__/mock-data.ts b/packages/ketcher-core/__tests__/mock-data.ts
@@ -13,6 +13,7 @@ import { Peptide } from 'domain/entities/Peptide';
 import { PolymerBond } from 'domain/entities/PolymerBond';
 import { MonomerItemType } from 'domain/types';
 import { mockFn } from 'jest-mock-extended';
+import { KetMonomerClass } from 'application/formatters';
 
 const mockAtoms = [
   {
@@ -757,6 +758,7 @@ export const peptideMonomerItem: MonomerItemType = {
     MonomerCode: '',
     MonomerName: '',
     MonomerType: 'PEPTIDE',
+    MonomerClass: KetMonomerClass.AminoAcid,
     Name: '',
     MonomerNaturalAnalogCode: 'A',
   },

diff --git a/packages/ketcher-core/package.json b/packages/ketcher-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-core",
-  "version": "2.25.0-rc.1",
+  "version": "2.25.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-core/src/application/editor/operations/monomer/monomerFactory.ts b/packages/ketcher-core/src/application/editor/operations/monomer/monomerFactory.ts
@@ -1,27 +1,31 @@
 import {
-  PeptideRenderer,
-  ChemRenderer,
+  AmbiguousMonomerRenderer,
   BaseMonomerRenderer,
+  ChemRenderer,
+  PeptideRenderer,
+  PhosphateRenderer,
   RNABaseRenderer,
   SugarRenderer,
-  PhosphateRenderer,
   UnresolvedMonomerRenderer,
   UnsplitNucleotideRenderer,
-  AmbiguousMonomerRenderer,
 } from 'application/render/renderers';
 import { MonomerOrAmbiguousType } from 'domain/types';
 import {
-  Peptide,
+  AmbiguousMonomer,
   Chem,
-  Sugar,
+  Peptide,
   Phosphate,
   RNABase,
+  Sugar,
   UnresolvedMonomer,
   UnsplitNucleotide,
-  AmbiguousMonomer,
 } from 'domain/entities';
 import { KetMonomerClass } from 'application/formatters/types/ket';
 import { isAmbiguousMonomerLibraryItem } from 'domain/helpers/monomers';
+import {
+  rnaDnaNaturalAnalogues,
+  unknownNaturalAnalogues,
+} from 'domain/constants/monomers';
 
 type DerivedClass<T> = new (...args: unknown[]) => T;
 export const MONOMER_CONST = {
@@ -65,39 +69,49 @@ export const monomerFactory = (
     MonomerRenderer = UnresolvedMonomerRenderer;
     ketMonomerClass = KetMonomerClass.CHEM;
   } else if (
-    monomer.props.MonomerType === MONOMER_CONST.CHEM ||
-    (monomer.props.MonomerType === MONOMER_CONST.RNA &&
-      (monomer.props.MonomerClass === MONOMER_CONST.MODDNA ||
-        monomer.props.MonomerClass === MONOMER_CONST.DNA))
-  ) {
-    Monomer = Chem;
-    MonomerRenderer = ChemRenderer;
-    ketMonomerClass = KetMonomerClass.CHEM;
-  } else if (
-    monomer.props.MonomerClass === MONOMER_CONST.RNA ||
-    monomer.props.MonomerClass === MONOMER_CONST.DNA
+    monomer.props.MonomerClass === KetMonomerClass.RNA ||
+    monomer.props.MonomerClass === KetMonomerClass.DNA
   ) {
     Monomer = UnsplitNucleotide;
     MonomerRenderer = UnsplitNucleotideRenderer;
     ketMonomerClass = KetMonomerClass.RNA;
-  } else if (monomer.props.MonomerType === MONOMER_CONST.PEPTIDE) {
+  } else if (
+    monomer.props.MonomerClass === KetMonomerClass.AminoAcid ||
+    monomer.props.MonomerType === MONOMER_CONST.PEPTIDE
+  ) {
     Monomer = Peptide;
     MonomerRenderer = PeptideRenderer;
     ketMonomerClass = KetMonomerClass.AminoAcid;
+  } else if (
+    monomer.props.MonomerClass === KetMonomerClass.Sugar ||
+    (monomer.props.MonomerType === MONOMER_CONST.RNA &&
+      monomer.props.MonomerNaturalAnalogCode === MONOMER_CONST.R)
+  ) {
+    Monomer = Sugar;
+    MonomerRenderer = SugarRenderer;
+    ketMonomerClass = KetMonomerClass.Sugar;
+  } else if (
+    monomer.props.MonomerClass === KetMonomerClass.Phosphate ||
+    (monomer.props.MonomerType === MONOMER_CONST.RNA &&
+      monomer.props.MonomerNaturalAnalogCode === MONOMER_CONST.P)
+  ) {
+    Monomer = Phosphate;
+    MonomerRenderer = PhosphateRenderer;
+    ketMonomerClass = KetMonomerClass.Phosphate;
+  } else if (
+    monomer.props.MonomerClass === KetMonomerClass.Base ||
+    (monomer.props.MonomerType === MONOMER_CONST.RNA &&
+      [...rnaDnaNaturalAnalogues, ...unknownNaturalAnalogues].includes(
+        monomer.props.MonomerNaturalAnalogCode,
+      ))
+  ) {
+    Monomer = RNABase;
+    MonomerRenderer = RNABaseRenderer;
+    ketMonomerClass = KetMonomerClass.Base;
   } else {
-    if (monomer.props.MonomerNaturalAnalogCode === MONOMER_CONST.R) {
-      Monomer = Sugar;
-      MonomerRenderer = SugarRenderer;
-      ketMonomerClass = KetMonomerClass.Sugar;
-    } else if (monomer.props.MonomerNaturalAnalogCode === MONOMER_CONST.P) {
-      Monomer = Phosphate;
-      MonomerRenderer = PhosphateRenderer;
-      ketMonomerClass = KetMonomerClass.Phosphate;
-    } else {
-      Monomer = RNABase;
-      MonomerRenderer = RNABaseRenderer;
-      ketMonomerClass = KetMonomerClass.Base;
-    }
+    Monomer = Chem;
+    MonomerRenderer = ChemRenderer;
+    ketMonomerClass = KetMonomerClass.CHEM;
   }
 
   return [Monomer, MonomerRenderer, ketMonomerClass];

diff --git a/packages/ketcher-core/src/domain/constants/monomers.ts b/packages/ketcher-core/src/domain/constants/monomers.ts
@@ -15,6 +15,7 @@ export enum RNA_DNA_NON_MODIFIED_PART {
 }
 
 export const rnaDnaNaturalAnalogues = ['A', 'T', 'G', 'C', 'U'];
+export const unknownNaturalAnalogues = ['.', 'X'];
 export const peptideNaturalAnalogues = [
   'A',
   'C',

diff --git a/packages/ketcher-macromolecules/package.json b/packages/ketcher-macromolecules/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-macromolecules",
-  "version": "2.25.0-rc.1",
+  "version": "2.25.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-macromolecules/src/testMockData/monomerPresets.ts b/packages/ketcher-macromolecules/src/testMockData/monomerPresets.ts
@@ -1,6 +1,7 @@
 import {
   AttachmentPointName,
   KetConnectionType,
+  KetMonomerClass,
   KetMonomerGroupTemplateClass,
   KetTemplateType,
   MonomerItemType,
@@ -278,6 +279,7 @@ const phosphate = {
     Name: 'Phosphate',
     MonomerNaturalAnalogCode: 'P',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Phosphate,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -291,6 +293,7 @@ const ribose = {
     Name: 'Ribose',
     MonomerNaturalAnalogCode: 'R',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Sugar,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -304,6 +307,7 @@ const thymine = {
     Name: 'Thymine',
     MonomerNaturalAnalogCode: 'T',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Base,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -317,6 +321,7 @@ const cytosine = {
     Name: 'Cytosine',
     MonomerNaturalAnalogCode: 'C',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Base,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -330,6 +335,7 @@ const uracil = {
     Name: 'Uracil',
     MonomerNaturalAnalogCode: 'U',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Base,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -343,6 +349,7 @@ const adenine = {
     Name: 'Adenine',
     MonomerNaturalAnalogCode: 'A',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Base,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',
@@ -356,6 +363,7 @@ const guanine = {
     Name: 'Guanine',
     MonomerNaturalAnalogCode: 'G',
     MonomerType: '',
+    MonomerClass: KetMonomerClass.Base,
     BranchMonomer: '',
     MonomerCaps: {},
     MonomerCode: '',

diff --git a/packages/ketcher-react/package.json b/packages/ketcher-react/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-react",
-  "version": "2.25.0-rc.1",
+  "version": "2.25.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-standalone/package.json b/packages/ketcher-standalone/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-standalone",
-  "version": "2.25.0-rc.1",
+  "version": "2.25.0-rc.2",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "indigo-ketcher": "1.24.0-rc.1",
+    "indigo-ketcher": "1.24.0-rc.2",
     "ketcher-core": "*"
   },
   "devDependencies": {