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#5236 - Replace monomer from library at view mode goes wrong for all types of monomer converded to @ symbol #5478

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#5236 - Replace monomer from library at view mode goes wrong for all types of monomer converded to @ symbol #5478

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152 changes: 117 additions & 35 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 @@ -1095,6 +1095,46 @@ export class SequenceMode extends BaseMode {
const hasNextNodeInChain =
selection.node.lastMonomerInNode.attachmentPointsToBonds.R2;

let newSequenceNode;

if (selection.node instanceof LinkerSequenceNode) {
const addedMonomers: BaseMonomer[] = [];

selection.node.monomers.forEach((_, monomerIndex) => {
const monomerAddCommand = editor.drawingEntitiesManager.addMonomer(
monomerItem,
position,
);
const newMonomer = monomerAddCommand.operations[0]
.monomer as BaseMonomer;

modelChanges.merge(monomerAddCommand);
addedMonomers.push(newMonomer);

if (monomerIndex > 0) {
modelChanges.merge(
editor.drawingEntitiesManager.createPolymerBond(
addedMonomers[monomerIndex - 1],
newMonomer,
AttachmentPointName.R2,
AttachmentPointName.R1,
),
);
}
});

newSequenceNode = new LinkerSequenceNode(addedMonomers[0]);
} else {
const monomerAddCommand = editor.drawingEntitiesManager.addMonomer(
monomerItem,
position,
);
const newMonomer = monomerAddCommand.operations[0].monomer as BaseMonomer;
modelChanges.merge(monomerAddCommand);

newSequenceNode = new MonomerSequenceNode(newMonomer);
}

selection.node.monomers.forEach((monomer) => {
modelChanges.merge(editor.drawingEntitiesManager.deleteMonomer(monomer));
monomer.forEachBond((polymerBond) => {
Expand All @@ -1104,17 +1144,9 @@ export class SequenceMode extends BaseMode {
});
});

const monomerAddCommand = editor.drawingEntitiesManager.addMonomer(
monomerItem,
position,
);
const newMonomer = monomerAddCommand.operations[0].monomer as BaseMonomer;
const newMonomerSequenceNode = new MonomerSequenceNode(newMonomer);

modelChanges.merge(monomerAddCommand);
modelChanges.merge(
this.insertNewSequenceFragment(
newMonomerSequenceNode,
newSequenceNode,
nextNode || null,
previousSelectionNode,
Boolean(hasPreviousNodeInChain),
Expand All @@ -1131,7 +1163,7 @@ export class SequenceMode extends BaseMode {
} = sideConnectionData;
if (
!this.isConnectionPossible(
newMonomer,
newSequenceNode.monomer,
firstMonomerAttachmentPointName,
secondMonomer,
secondMonomerAttachmentPointName,
Expand All @@ -1142,15 +1174,15 @@ export class SequenceMode extends BaseMode {

modelChanges.merge(
editor.drawingEntitiesManager.createPolymerBond(
newMonomer,
newSequenceNode.monomer,
secondMonomer,
firstMonomerAttachmentPointName,
secondMonomerAttachmentPointName,
),
);
});

return newMonomerSequenceNode;
return newSequenceNode;
}

private replaceSelectionsWithMonomer(
Expand Down Expand Up @@ -1488,6 +1520,43 @@ export class SequenceMode extends BaseMode {
selection.node.lastMonomerInNode.attachmentPointsToBonds.R2;

const sideChainConnections = this.preserveSideChainConnections(selection);
const newPresetNodes: Array<Nucleoside | Nucleotide | LinkerSequenceNode> =
[];

if (selection.node instanceof LinkerSequenceNode) {
selection.node.monomers.forEach((_, monomerIndex) => {
const newPresetNode = this.createRnaPresetNode(preset, position);

assert(newPresetNode);

const rnaPresetAddModelChanges =
editor.drawingEntitiesManager.addRnaPresetFromNode(newPresetNode);

modelChanges.merge(rnaPresetAddModelChanges);
newPresetNodes.push(newPresetNode);

if (monomerIndex > 0) {
modelChanges.merge(
editor.drawingEntitiesManager.createPolymerBond(
newPresetNodes[monomerIndex - 1].lastMonomerInNode,
newPresetNode.firstMonomerInNode,
AttachmentPointName.R2,
AttachmentPointName.R1,
),
);
}
});
} else {
const newPresetNode = this.createRnaPresetNode(preset, position);

assert(newPresetNode);

const rnaPresetAddModelChanges =
editor.drawingEntitiesManager.addRnaPresetFromNode(newPresetNode);

modelChanges.merge(rnaPresetAddModelChanges);
newPresetNodes.push(newPresetNode);
}

selection.node.monomers.forEach((monomer) => {
modelChanges.merge(editor.drawingEntitiesManager.deleteMonomer(monomer));
Expand All @@ -1498,31 +1567,44 @@ export class SequenceMode extends BaseMode {
});
});

const newPresetNode = this.createRnaPresetNode(preset, position);

assert(newPresetNode);

const rnaPresetAddModelChanges =
editor.drawingEntitiesManager.addRnaPresetFromNode(newPresetNode);

modelChanges.merge(rnaPresetAddModelChanges);
modelChanges.merge(
this.insertNewSequenceFragment(
newPresetNode,
nextNode || null,
previousSelectionNode,
Boolean(hasPreviousNodeInChain),
Boolean(hasNextNodeInChain),
),
);
if (newPresetNodes.length > 1) {
modelChanges.merge(
this.insertNewSequenceFragment(
newPresetNodes[0],
null,
previousSelectionNode,
Boolean(hasPreviousNodeInChain),
Boolean(hasNextNodeInChain),
),
);
modelChanges.merge(
this.insertNewSequenceFragment(
newPresetNodes[newPresetNodes.length - 1],
nextNode,
undefined,
Boolean(hasPreviousNodeInChain),
Boolean(hasNextNodeInChain),
),
);
} else {
modelChanges.merge(
this.insertNewSequenceFragment(
newPresetNodes[0],
nextNode || null,
previousSelectionNode,
Boolean(hasPreviousNodeInChain),
Boolean(hasNextNodeInChain),
),
);
}

// 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
? newPresetNode.phosphate
: newPresetNode instanceof Nucleoside
? newPresetNode.sugar
: newPresetNode.monomer;
newPresetNodes[0] instanceof Nucleotide
? newPresetNodes[0].phosphate
: newPresetNodes[0] instanceof Nucleoside
? newPresetNodes[0].sugar
: newPresetNodes[0].monomer;

sideChainConnections?.forEach((sideConnectionData) => {
const {
Expand Down Expand Up @@ -1551,7 +1633,7 @@ export class SequenceMode extends BaseMode {
);
});

return newPresetNode;
return newPresetNodes.at(-1);
}

private replaceSelectionsWithPreset(
Expand Down
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