#5403 - Introduce hydrogen bonds in macromolecules mode #5843

rrodionov91 · 2024-10-22T15:37:34Z

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unit-tests written
e2e-tests written
documentation updated
PR name follows the pattern #1234 – issue name
branch name doesn't contain '#'
PR is linked with the issue
base branch (master or release/xx) is correct
task status changed to "Code review"
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svvald · 2024-10-25T13:17:22Z

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -756,7 +781,10 @@ export class DrawingEntitiesManager {
      return _polymerBond;
    }

-    const polymerBond = new PolymerBond(firstMonomer);
+    const isHydrogenBond = bondType === 'hydrogen';


Can we use MACROMOLECULES_BOND_TYPES here?

svvald · 2024-10-25T13:19:38Z

packages/ketcher-core/src/application/editor/tools/Bond.ts

    this.editor = editor;
    this.history = new EditorHistory(this.editor);
+    this.bondType =
+      options.toolName === 'bond-single'


ToolName enum can be used here

svvald · 2024-10-25T13:19:54Z

packages/ketcher-core/src/application/editor/tools/Bond.ts


-  constructor(private editor: CoreEditor) {
+  constructor(private editor: CoreEditor, options: { toolName: string }) {


And passed as a type here

svvald · 2024-10-25T13:21:43Z

packages/ketcher-core/src/application/editor/modes/BaseMode.ts

@@ -126,6 +130,7 @@ export abstract class BaseMode {
            entity.secondMonomer,
            firstAttachmentPoint,
            secondAttachmentPoint,
+            undefined,


Maybe we shouldn't do anything here as it will lead to massive changes, although I don't really like that we need to pass undefined explicitly in the middle of the arguments list, I'd prefer to have some optional argument in the end of the list or pass arguments as an object with optional properties

svvald · 2024-10-25T13:22:18Z

packages/ketcher-core/src/application/editor/operations/drawingEntity/index.ts

@@ -59,6 +61,7 @@ export class DrawingEntityMoveOperation implements Operation {
    // we need to redraw them to apply the correct drawing mode.
    if (
      this.drawingEntity instanceof PolymerBond ||
+      this.drawingEntity instanceof HydrogenBond ||
      this.drawingEntity instanceof MonomerToAtomBond


Maybe some isBond helper method might come in handy here to improve readability

svvald · 2024-10-25T13:27:24Z

packages/ketcher-core/src/domain/entities/BaseMonomer.ts

@@ -220,9 +222,13 @@ export abstract class BaseMonomer extends DrawingEntity {

  public setBond(
    attachmentPointName: AttachmentPointName,
-    bond: PolymerBond | MonomerToAtomBond,
+    bond: PolymerBond | MonomerToAtomBond | HydrogenBond,


Can't we just use BaseBond type here?

svvald · 2024-10-25T13:29:08Z

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

-          polymerBond,
-        ) as AttachmentPointName,
-      ),
+      (_polymerBond?: PolymerBond) =>


It's a bit confusing, polymerBond type is specified as a union in the deletePolymerBond yet here it's just PolymerBond and I didn't see any type narrowing?

svvald · 2024-10-25T13:30:24Z

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -747,6 +771,7 @@ export class DrawingEntitiesManager {
    secondMonomer: BaseMonomer,
    firstMonomerAttachmentPoint: AttachmentPointName,
    secondMonomerAttachmentPoint: AttachmentPointName,
+    bondType?: string,


Perhaps MACROMOLECULES_BOND_TYPES can be used here too?

svvald · 2024-10-25T13:30:43Z

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -818,17 +849,20 @@ export class DrawingEntitiesManager {
    secondMonomer: BaseMonomer,
    firstMonomerAttachmentPoint: AttachmentPointName,
    secondMonomerAttachmentPoint: AttachmentPointName,
+    bondType = 'polymer',


And here too

svvald · 2024-10-25T13:33:01Z

packages/ketcher-macromolecules/src/components/LeftMenuComponent/LeftMenuComponent.tsx

@@ -33,7 +33,7 @@ export function LeftMenuComponent() {
  const activeMenuItems = [activeTool];

  const menuItemChanged = (name) => {
-    editor.events.selectTool.dispatch(name);
+    editor.events.selectTool.dispatch(name, { toolName: name });


It's a bit confusing why we pass the name of the tool twice, is it due to the nested menu items? Can we avoid it somehow? We still have unique tool names in the end

It's because options are passed directly to active tool and then tool can use them. So toolName option is used in Bond tool to create appropriate bond type

…n sequence and molecules modes - added hiding of hydrogen bonds for expanded monomers

- fixed build - updated screenshots

- updated screenshots

- updated browserlist

auto-assign bot requested review from AlexeyGirin, NataliaLoginova and svvald October 22, 2024 15:37

auto-assign bot assigned rrodionov91 Oct 22, 2024

rrodionov91 linked an issue Oct 22, 2024 that may be closed by this pull request

Introduce hydrogen bonds in macromolecules mode #5403

Closed

rrodionov91 force-pushed the 5403-Introduce_hydrogen_bonds_in_macromolecules_mode branch 3 times, most recently from 909fca2 to 3eb7308 Compare October 25, 2024 12:19

svvald requested changes Oct 25, 2024

View reviewed changes

rrodionov91 added 10 commits October 28, 2024 15:00

- created BaseBond for PolymerBond and MonomerToAtomBond.

4557b40

- added hydrogen bond renderer

d548c05

- added hydrogen bonds serialization/deserialization and displaying i…

ddf2284

…n sequence and molecules modes - added hiding of hydrogen bonds for expanded monomers

#5403 - Introduce hydrogen bonds in macromolecules mode

f61d1a2

- fixed bond deletion

fc20687

- fixed build - updated screenshots

- fixed rna presets

053e762

- updated screenshots

- updated screenshots

3b66955

- updated screenshots

5a91b0a

- updated browserlist

- fixes after review

d9beb4e

- updated screenshot

84b85d4

rrodionov91 force-pushed the 5403-Introduce_hydrogen_bonds_in_macromolecules_mode branch from 3eb7308 to 84b85d4 Compare October 28, 2024 14:00

LankyVeer0h approved these changes Oct 28, 2024

View reviewed changes

svvald approved these changes Oct 28, 2024

View reviewed changes

rrodionov91 merged commit c55cc66 into master Oct 28, 2024
5 checks passed

rrodionov91 deleted the 5403-Introduce_hydrogen_bonds_in_macromolecules_mode branch October 28, 2024 18:04

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#5403 - Introduce hydrogen bonds in macromolecules mode #5843

#5403 - Introduce hydrogen bonds in macromolecules mode #5843

rrodionov91 commented Oct 22, 2024 •

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rrodionov91 Oct 28, 2024


		constructor(private editor: CoreEditor) {
		constructor(private editor: CoreEditor, options: { toolName: string }) {

#5403 - Introduce hydrogen bonds in macromolecules mode #5843

#5403 - Introduce hydrogen bonds in macromolecules mode #5843

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rrodionov91 commented Oct 22, 2024 • edited Loading

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rrodionov91 commented Oct 22, 2024 •

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