Autotests: #5960 autotests display molecules in macro mode basic structures with atoms and bonds (#5983)

* Verify that bond lines between atoms do not overlap in any angle in macro mode

* screen

* Verify that connections between monomers and molecules are maintained correctly in both micro and macro modes

* Verify that switching between micro and macro modes displays molecules without structural changes

* Verify that deleting a bond in macro mode removes the bond while maintaining the integrity of the surrounding structure

* Verify that the structure in macro mode can be saved as a .ket file, and all elements including bonds and atoms are correctly restored when re-loaded

* Peptides - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode

* Bases - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode

* CHEMS - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode

* Nucleotide - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode - Part 1

* Nucleotide - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode - Part 2

* Phosphates - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode
and
HELM results correction

* Sugar - Verify that connection points between monomers and molecules can be created by drawing bonds in macro mode

* phosphate fix

* Nucleotide fix

* Peptide fix

* phosphate fix

* Sugar fix

* CHEMs fix

* Bases fix

* Some fixes

Author: AlexeyGirin

ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts

@@ -42,11 +42,7 @@ test.beforeAll(async ({ browser }) => {
 });
 
 test.afterEach(async () => {
-  await page.keyboard.press('Escape');
-  await page.keyboard.press('Escape');
-  // await page.keyboard.press('Control+0');
   await selectClearCanvasTool(page);
-  // await page.keyboard.press('Control+0');
 });
 
 test.afterAll(async ({ browser }) => {

ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts

@@ -347,77 +347,72 @@ const correctHELMStrings: IHELMString[] = [
     helmDescription: '48. RNA(RA) with single inline Extended SMILES (A)',
     HELMString:
       'RNA1{R([C1(C2=C(N=CN=1)N%91C=N2)N.[*:1]%91 |$;;;;;;;;;;_R1$|])}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
     pageReloadNeeded: true,
+    differentHELMExport:
+      'RNA1{R([C1(N)=NC=NC2N([*:1])C=NC1=2 |$;;;;;;;_R1;;;$|])}$$$$V2.0',
   },
   {
     helmDescription: '49. RNA(RAP) with single inline Extended SMILES (A)',
     HELMString:
       'RNA1{R([C1(C2=C(N=CN=1)N%91C=N2)N.[*:1]%91 |$;;;;;;;;;;_R1$|])P}$$$$V2.0',
-    shouldFail: true,
-    issueNumber:
-      'https://github.com/epam/Indigo/issues/2339, https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport:
+      'RNA1{R([C1(N)=NC=NC2N([*:1])C=NC1=2 |$;;;;;;;_R1;;;$|])P}$$$$V2.0',
   },
   {
     helmDescription: '50. RNA(RP) with single inline Extended SMILES (P)',
     HELMString: 'RNA1{R[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport: 'RNA1{R[P([*:1])(=O)(O)O |$;_R1;;;$|]}$$$$V2.0',
   },
   {
     helmDescription: '51. RNA(RP) with single inline Extended SMILES (R)',
     HELMString:
       'RNA1{[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]P}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport:
+      'RNA1{[O1C(CO[*:1])C(O[*:2])C(O)C1[*:3] |$;;;;_R1;;;_R2;;;;_R3$|]P}$$$$V2.0',
   },
   {
     helmDescription: '52. RNA(RAP) with  single inline Extended SMILES (P)',
     HELMString: 'RNA1{R(A)[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport: 'RNA1{R(A)[P([*:1])(=O)(O)O |$;_R1;;;$|]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription:
       '53. RNA(RAP) with  all monomer inline Extended SMILES (RAP)',
     HELMString:
       'RNA1{[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|](A)P}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2339',
+    differentHELMExport:
+      'RNA1{[O1C(CO[*:1])C(O[*:2])C(O)C1[*:3] |$;;;;_R1;;;_R2;;;;_R3$|](A)P}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription:
       '54. Single peptide with inline SMILES (L) without attachment points',
     HELMString: 'PEPTIDE1{[C([C@@H](C(O)=O)N[H])C(C)C]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport: 'PEPTIDE1{[C(C(C)C)C(N[H])C(=O)O]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription: '55. Single peptide with inline Extended SMILES (L)',
     HELMString:
       'PEPTIDE1{[C([C@@H](C%91=O)N%92)C(C)C.[*:2]%91.[*:1]%92 |$;;;;;;;;_R2;_R1$|]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport:
+      'PEPTIDE1{[C(C(C)C)C(N[*:1])C([*:2])=O |$;;;;;;_R1;;_R2;$|]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription:
       '56. Single CHEM with inline SMILES (A6OH) without attachment points',
     HELMString: 'CHEM1{[N([H])CCCCCCO[H]]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport: 'CHEM1{[N(CCCCCCO[H])[H]]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription: '57. Single CHEM with inline Extended SMILES (A6OH)',
     HELMString:
       'CHEM1{[N%91CCCCCCO%92.[*:2]%91.[*:1]%92 |$;;;;;;;;_R2;_R1$|]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport:
+      'CHEM1{[N([*:2])CCCCCCO[*:1] |$;_R2;;;;;;;;_R1$|]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
@@ -427,20 +422,23 @@ const correctHELMStrings: IHELMString[] = [
       '[C%91([C@H](CS%92)N%93)=O.[*:2]%91.[*:1]%93.[*:3]%92 |$;;;;;;_R2;_R1;_R3$|].' +
       '[C%91([C@H](CC(O%92)=O)N%93)=O.[*:1]%93.[*:2]%91.[*:3]%92 |$;;;;;;;;_R1;_R2;_R3$|].' +
       '[C([C@@H](C%91=O)N%92)C(C)C.[*:2]%91.[*:1]%92 |$;;;;;;;;_R2;_R1$|]}$$$$V2.0',
-    shouldFail: true,
-    issueNumber: 'https://github.com/epam/Indigo/issues/2337',
+    differentHELMExport:
+      'PEPTIDE1{[N([*:1])C(C)C([*:2])=O |$;_R1;;;;_R2;$|].' +
+      '[C([*:2])(=O)C(N[*:1])CS[*:3] |$;_R2;;;;_R1;;;_R3$|].' +
+      '[C([*:2])(=O)C(N[*:1])CC(=O)O[*:3] |$;_R2;;;;_R1;;;;;_R3$|].' +
+      '[C(C(C)C)C(N[*:1])C([*:2])=O |$;;;;;;_R1;;_R2;$|]}$$$$V2.0',
     pageReloadNeeded: true,
   },
   {
     helmDescription:
       '59. List of RNAs of inline Extended Smiles (R(A)P, R(C)P, R(G)P)',
     HELMString:
       // eslint-disable-next-line max-len
-      'RNA1{[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(C2=C(N=CN=1)N%91C=N2)N.[*:1]%91 |$;;;;;;;;;;_R1$|])[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]' +
+      'RNA1{[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(C2=C(N=CN=1)N%91C=N2)N.[*:1]%91 |$;;;;;;;;;;_R1$|])[P%91%92(=O)O.[*:2]%91.[*:1]%92 |$;;;_R2;_R1$|].' +
       // eslint-disable-next-line max-len
-      '.[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(N)=NC(=O)N%91C=C1.[*:1]%91 |$;;;;;;;;_R1$|])[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|].' +
+      '[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(N)=NC(=O)N%91C=C1.[*:1]%91 |$;;;;;;;;_R1$|])[P%91%92(=O)O.[*:2]%91.[*:1]%92 |$;;;_R2;_R1$|].' +
       // eslint-disable-next-line max-len
-      '[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(C2=C(N=C(N)N1)N%91C=N2)=O.[*:1]%91 |$;;;;;;;;;;;_R1$|])[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]}$$$$V2.0',
+      '[O1[C@@H]%91[C@H](O)[C@H](O%92)[C@H]1CO%93.[*:3]%91.[*:1]%93.[*:2]%92 |$;;;;;;;;;_R3;_R1;_R2$|]([C1(C2=C(N=C(N)N1)N%91C=N2)=O.[*:1]%91 |$;;;;;;;;;;;_R1$|])[P%91%92(=O)O.[*:2]%91.[*:1]%92 |$;;;_R2;_R1$|]}$$$$V2.0',
     shouldFail: true,
     issueNumber: 'https://github.com/epam/Indigo/issues/2339',
   },

ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts-snapshots/Import-correct-HELM-sequence-59-List-of-RNAs-of-inline-Extended-Smiles-R-A-P-R-C-P-R-G-P-1-chromium-linux.png

@@ -23,8 +23,10 @@ import {
   openFileAndAddToCanvasAsNewProjectMacro,
   Sugars,
   selectAllStructuresOnCanvas,
+  openFileAndAddToCanvasAsNewProject,
 } from '@utils';
 import { pageReload } from '@utils/common/helpers';
+import { FileType, verifyFile2 } from '@utils/files/receiveFileComparisonData';
 import {
   turnOnMacromoleculesEditor,
   zoomWithMouseWheel,
@@ -892,3 +894,31 @@ test.describe('Sugar monomers on the canvas, their connection points and preview
 //     await takeEditorScreenshot(page);
 //   });
 // }
+
+test(`Verify that the structure in macro mode can be saved as a .ket file, and all elements including bonds and atoms are correctly restored when re-loaded`, async () => {
+  /*
+   * Test task: https://github.com/epam/ketcher/issues/5960
+   * Description: Verify that the structure in macro mode can be saved as a .ket file, and all elements including bonds and atoms are correctly restored when re-loaded
+   * Case: 1. Load monomer on Macrolecules mode
+   *       2. Take screenshot to witness original state
+   *       3. Save canvas to KET
+   *       4. Verify that export result equal to template
+   *       5. Load saved KET to the canvas
+   *       6. Take screenshot to witness saved state
+   *        (screenshots have to be equal)
+   */
+
+  const KETFile =
+    'KET/Micro-Macro-Switcher/Complicated structures on the canvas.ket';
+  const KETFileExpected =
+    'tests/test-data/KET/Micro-Macro-Switcher/Complicated structures on the canvas-expected.ket';
+
+  await openFileAndAddToCanvasAsNewProject(KETFile, page);
+  await takeEditorScreenshot(page);
+  await verifyFile2(page, KETFileExpected, FileType.KET);
+  await openFileAndAddToCanvasAsNewProject(
+    KETFileExpected.replace('tests/test-data/', ''),
+    page,
+  );
+  await takeEditorScreenshot(page);
+});

ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts

@@ -0,0 +1,135 @@
+/* eslint-disable no-self-compare */
+/* eslint-disable max-len */
+/* eslint-disable no-magic-numbers */
+import {
+  chooseTab,
+  Tabs,
+  turnOnMacromoleculesEditor,
+  turnOnMicromoleculesEditor,
+} from '@utils/macromolecules';
+import { Page, test } from '@playwright/test';
+import {
+  takeEditorScreenshot,
+  openFileAndAddToCanvasAsNewProject,
+  selectClearCanvasTool,
+  waitForPageInit,
+  selectEraseTool,
+} from '@utils';
+import { clickOnMicroBondByIndex } from '@utils/macromolecules/polymerBond';
+
+let page: Page;
+
+async function configureInitialState(page: Page) {
+  await chooseTab(page, Tabs.Rna);
+}
+
+test.beforeAll(async ({ browser }) => {
+  const context = await browser.newContext();
+  page = await context.newPage();
+
+  await waitForPageInit(page);
+  await turnOnMacromoleculesEditor(page);
+  await configureInitialState(page);
+});
+
+test.afterEach(async () => {
+  await selectClearCanvasTool(page);
+});
+
+test.afterAll(async ({ browser }) => {
+  await Promise.all(browser.contexts().map((context) => context.close()));
+});
+
+test(`Verify that bond lines between atoms do not overlap in any angle in macro mode`, async () => {
+  /*
+   * Test task: https://github.com/epam/ketcher/issues/5960
+   * Description: Verify that bond lines between atoms do not overlap in any angle in macro mode
+   *
+   * Case: 1. Load ket file with structures
+   *       2. Take screenshot to witness canvas was rendered correct
+   */
+  await openFileAndAddToCanvasAsNewProject(
+    'KET/Micro-Macro-Switcher/Micro bonds on macro canvas.ket',
+    page,
+  );
+  await takeEditorScreenshot(page);
+
+  // Test should be skipped if related bug exists
+  test.fixme(
+    true === true,
+    `That test results are wrong because of https://github.com/epam/ketcher/issues/5961 issue(s).`,
+  );
+});
+
+test(`Verify that connections between monomers and molecules are maintained correctly in both micro and macro modes`, async () => {
+  /*
+   * Test task: https://github.com/epam/ketcher/issues/5960
+   * Description: Verify that connections between monomers and molecules are maintained correctly in both micro and macro modes
+   *
+   * Case: 1. Load ket file with structures
+   *       2. Take screenshot to witness canvas was rendered correct at macro
+   *       3. Switch to Micromolecules mode
+   *       4. Take screenshot to witness canvas was rendered correct at micro
+   */
+  await openFileAndAddToCanvasAsNewProject(
+    'KET/Micro-Macro-Switcher/All type of monomers connected to micro.ket',
+    page,
+  );
+  await takeEditorScreenshot(page);
+
+  await turnOnMicromoleculesEditor(page);
+  await takeEditorScreenshot(page);
+
+  await turnOnMacromoleculesEditor(page);
+});
+
+test(`Verify that switching between micro and macro modes displays molecules without structural changes`, async () => {
+  /*
+   * Test task: https://github.com/epam/ketcher/issues/5960
+   * Description: Verify that switching between micro and macro modes displays molecules without structural changes
+   *
+   * Case: 1. Load ket file with structures at Macro
+   *       2. Take screenshot to witness canvas was rendered correct at macro
+   *       3. Switch to Micromolecules mode
+   *       4. Take screenshot to witness canvas was rendered correct at micro
+   *       Canvases should be equal
+   */
+  await turnOnMicromoleculesEditor(page);
+  await openFileAndAddToCanvasAsNewProject(
+    'KET/Micro-Macro-Switcher/Complicated structures on the canvas.ket',
+    page,
+  );
+  await takeEditorScreenshot(page);
+
+  await turnOnMacromoleculesEditor(page);
+  await takeEditorScreenshot(page);
+});
+
+test(`Verify that deleting a bond in macro mode removes the bond while maintaining the integrity of the surrounding structure`, async () => {
+  /*
+   * Test task: https://github.com/epam/ketcher/issues/5960
+   * Description: Verify that deleting a bond in macro mode removes the bond while maintaining the integrity of the surrounding structure
+   *
+   * Case: 1. Load ket file with structures at Macro
+   *       2. Take screenshot to witness initial state
+   *       3. Delete all bonds at the center of every molecule
+   *       4. Take screenshot to witness final state
+   */
+  await openFileAndAddToCanvasAsNewProject(
+    'KET/Micro-Macro-Switcher/All Bonds on Macro.ket',
+    page,
+  );
+  await takeEditorScreenshot(page);
+
+  await selectEraseTool(page);
+  // removing single bond
+  await clickOnMicroBondByIndex(page, 39);
+  // removing double bond
+  await clickOnMicroBondByIndex(page, 45);
+  // removing single up bond
+  await clickOnMicroBondByIndex(page, 51);
+  // removing single down bond
+  await clickOnMicroBondByIndex(page, 51);
+
+  await takeEditorScreenshot(page);
+});