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#5245 - Replacement of peptide at the end of sequence on preset w/out base works wrong #5274

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merged 2 commits into from
Aug 12, 2024
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#5245 - Replacement of peptide at the end of sequence on preset w/out base works wrong #5274

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b2ba743
#5245 - Replacement of peptide at the end of sequence on preset w/out…
rrodionov91 Aug 9, 2024
b2888c5
- fixed conditions sequence in rna addition method for sequence mode
rrodionov91 Aug 9, 2024
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135 changes: 66 additions & 69 deletions packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1290,6 +1290,7 @@ export class SequenceMode extends BaseMode {
selectionRange.some((nodeSelection) =>
[preset.sugar, preset.base, preset.phosphate].some(
(monomer) =>
monomer &&
!this.checkIfNewMonomerCouldEstablishConnections(
nodeSelection,
monomer,
Expand Down Expand Up @@ -1364,6 +1365,53 @@ export class SequenceMode extends BaseMode {
}
}

private createRnaPresetNode(preset: IRnaPreset, position: Vec2) {
const editor = CoreEditor.provideEditorInstance();
const { base: rnaBase, sugar, phosphate } = preset;

if (!sugar) {
return;
}

const rnaPresetAddResult = editor.drawingEntitiesManager.addRnaPreset({
sugar,
sugarPosition: position,
rnaBase,
rnaBasePosition: position,
phosphate,
phosphatePosition: position,
});

const sugarMonomer = rnaPresetAddResult.monomers.find(
(monomer) => monomer instanceof Sugar,
) as Sugar;
const rnaBaseMonomer = rnaPresetAddResult.monomers.find(
(monomer) => monomer instanceof RNABase,
) as RNABase;
const phosphateMonomer = rnaPresetAddResult.monomers.find(
(monomer) => monomer instanceof Phosphate,
) as Phosphate;

let newPresetNode: Nucleotide | Nucleoside | LinkerSequenceNode;

if (!rnaBase) {
newPresetNode = new LinkerSequenceNode(sugarMonomer);
} else if (!phosphateMonomer) {
newPresetNode = new Nucleoside(sugarMonomer, rnaBaseMonomer);
} else {
newPresetNode = new Nucleotide(
sugarMonomer,
rnaBaseMonomer,
phosphateMonomer,
);
}

return {
newPresetNode,
rnaPresetAddModelChanges: rnaPresetAddResult.command,
};
}

private replaceSelectionWithPreset(
preset: IRnaPreset,
selection: NodeSelection,
Expand All @@ -1389,44 +1437,15 @@ export class SequenceMode extends BaseMode {
});
});

const { base: rnaBase, sugar, phosphate } = preset;
const rnaAdditionResult = this.createRnaPresetNode(preset, position);

if (!rnaBase || !sugar) {
if (!rnaAdditionResult) {
return;
}

const monomerAddCommand = editor.drawingEntitiesManager.addRnaPreset({
sugar,
sugarPosition: position,
rnaBase,
rnaBasePosition: position,
phosphate,
phosphatePosition: position,
});

const sugarMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof Sugar,
) as Sugar;
const rnaBaseMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof RNABase,
) as RNABase;
const phosphateMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof Phosphate,
) as Phosphate;

modelChanges.merge(monomerAddCommand.command);

let newPresetNode: Nucleotide | Nucleoside;
if (phosphateMonomer) {
newPresetNode = new Nucleotide(
sugarMonomer,
rnaBaseMonomer,
phosphateMonomer,
);
} else {
newPresetNode = new Nucleoside(sugarMonomer, rnaBaseMonomer);
}
const { newPresetNode, rnaPresetAddModelChanges } = rnaAdditionResult;

modelChanges.merge(rnaPresetAddModelChanges);
modelChanges.merge(
this.insertNewSequenceFragment(
newPresetNode,
Expand All @@ -1439,7 +1458,11 @@ export class SequenceMode extends BaseMode {

// TODO: This check breaks some side chains (e.g. Sugar-to-Sugar for Nucleotides), need another way of preserving connections
const monomerForSideConnections =
newPresetNode instanceof Nucleotide ? phosphateMonomer : sugarMonomer;
newPresetNode instanceof Nucleotide
? newPresetNode.phosphate
: newPresetNode instanceof Nucleoside
? newPresetNode.sugar
: newPresetNode.monomer;

sideChainConnections?.forEach((sideConnectionData) => {
const {
Expand Down Expand Up @@ -1545,45 +1568,19 @@ export class SequenceMode extends BaseMode {
} else {
const newNodePosition = this.getNewNodePosition();

const { base: rnaBase, sugar, phosphate } = preset;
const rnaAdditionResult = this.createRnaPresetNode(
preset,
newNodePosition,
);

if (!rnaBase || !sugar) {
if (!rnaAdditionResult) {
return;
}

const monomerAddCommand = editor.drawingEntitiesManager.addRnaPreset({
sugar,
sugarPosition: newNodePosition,
rnaBase,
rnaBasePosition: newNodePosition,
phosphate,
phosphatePosition: newNodePosition,
});

const sugarMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof Sugar,
) as Sugar;
const rnaBaseMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof RNABase,
) as RNABase;
const phosphateMonomer = monomerAddCommand.monomers.find(
(monomer) => monomer instanceof Phosphate,
) as Phosphate;

modelChanges.merge(monomerAddCommand.command);

let newPresetNode: Nucleotide | Nucleoside;
if (phosphateMonomer) {
newPresetNode = new Nucleotide(
sugarMonomer,
rnaBaseMonomer,
phosphateMonomer,
);
} else {
newPresetNode = new Nucleoside(sugarMonomer, rnaBaseMonomer);
}

modelChanges.merge(this.insertNewSequenceFragment(newPresetNode));
modelChanges.merge(rnaAdditionResult.rnaPresetAddModelChanges);
modelChanges.merge(
this.insertNewSequenceFragment(rnaAdditionResult.newPresetNode),
);

modelChanges.addOperation(new ReinitializeModeOperation());
editor.renderersContainer.update(modelChanges);
Expand Down
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