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#5670 – Fix vertical/horizontal movement for peptides
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@svvald
svvald committed Dec 24, 2024
1 parent b5029ed commit 94a429b
Showing 1 changed file with 99 additions and 29 deletions.
128 changes: 99 additions & 29 deletions packages/ketcher-core/src/application/editor/actions/sgroup.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -120,15 +120,19 @@ export function setExpandMonomerSGroup(
) {
const action = new Action();

const sGroup = restruct.molecule.sgroups.get(sgid);
assert(sGroup != null);

if (attrs.expanded === sGroup.isExpanded()) {
return action;
}

Object.keys(attrs).forEach((key) => {
action.addOp(new SGroupAttr(sgid, key, attrs[key]));
});

const sgroup = restruct.molecule.sgroups.get(sgid);
assert(sgroup != null);

const sGroupAtoms = SGroup.getAtoms(restruct, sgroup);
const attachmentPoints = sgroup.getAttachmentPoints();
const sGroupAtoms = SGroup.getAtoms(restruct, sGroup);
const attachmentPoints = sGroup.getAttachmentPoints();
const bondsToOutside = restruct.molecule.bonds.filter((_, bond) => {
return (
(sGroupAtoms.includes(bond.begin) && !sGroupAtoms.includes(bond.end)) ||
Expand All @@ -154,6 +158,29 @@ export function setExpandMonomerSGroup(
const sGroupWidth = sGroupBBox.p1.x - sGroupBBox.p0.x;
const sGroupHeight = sGroupBBox.p1.y - sGroupBBox.p0.y;


// const canvas = document.querySelector('.Ketcher-root svg');
// const structureRectangle = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'rect',
// );
// const p0x = sgroup?.pp?.x - 0.5;
// const p0y = sgroup?.pp?.y - 0.5;
// structureRectangle.setAttribute('x', `${p0x * 40}`);
// structureRectangle.setAttribute('y', `${p0y * 40}`);
// structureRectangle.setAttribute(
// 'width',
// `${(p0x + 1) * 40}`,
// );
// structureRectangle.setAttribute(
// 'height',
// `${(p0y + 0.5) * 40}`,
// );
// structureRectangle.setAttribute('fill', 'none');
// structureRectangle.setAttribute('stroke', 'red');
// structureRectangle.setAttribute('stroke-width', '2');
// canvas?.appendChild(structureRectangle);

const visitedAtoms = new Set<number>();
const visitedSGroups = new Set<number>();

Expand All @@ -167,7 +194,7 @@ export function setExpandMonomerSGroup(
visitedAtoms.add(atomId);

const atomSGroups = restruct.atoms.get(atomId)?.a.sgs;
const atomInSGroup = atomSGroups?.size && atomSGroups.size > 0;
const atomInSGroup = atomSGroups && atomSGroups.size > 0;
if (atomInSGroup) {
for (const anotherSGroupId of atomSGroups.values()) {
if (visitedSGroups.has(anotherSGroupId) || anotherSGroupId === sgid) {
Expand Down Expand Up @@ -203,6 +230,7 @@ export function setExpandMonomerSGroup(
return;
}

// TODO: Rewrite recursion to iteration approach as it leads to incorrect movement order for RNA bases
prepareSubStructure(neighborAtomId, subStructureKey);
});
}
Expand All @@ -213,47 +241,89 @@ export function setExpandMonomerSGroup(
});

const handledAtoms = new Set<number>();
let isVerticalMovementStarted = false;
const handledBonds = new Set<number>();

sGroupsToMove.forEach((sGroupIds) => {
if (sGroupsToMove.size === 1) {
return;
}

let isVerticalMovementStarted = false;
sGroupIds.forEach((sGroupId) => {
const collapsedSgroup = restruct.molecule.sgroups.get(sGroupId);
const collapsedSgroupCenter = collapsedSgroup.getContractedPosition(
const movableSGroup = restruct.molecule.sgroups.get(sGroupId);
if (!movableSGroup) {
return;
}

const sGroupCenter = sGroup.isContracted() ? sGroup.getContractedPosition(
restruct.molecule,
).position;
const expandedSGroupCenter = sgroup.getContractedPosition(
).position : sGroup.pp;
const movableSGroupCenter = movableSGroup.isContracted() ? movableSGroup.getContractedPosition(
restruct.molecule,
).position;
const collapsedSGroupAtoms = SGroup.getAtoms(restruct, collapsedSgroup);
).position : movableSGroup?.pp;
if (!movableSGroupCenter || !sGroupCenter) {
return;
}

const movableSGroupAtoms = SGroup.getAtoms(restruct, movableSGroup);
const movableSGroupBondsToOutside = restruct.molecule.bonds.filter((_, bond) => {
return (
(movableSGroupAtoms.includes(bond.begin) && !movableSGroupAtoms.includes(bond.end)) ||
(movableSGroupAtoms.includes(bond.end) && !movableSGroupAtoms.includes(bond.begin))
);
});

// console.log(movableSGroup.data, movableSGroupBondsToOutside);
// movableSGroupBondsToOutside.forEach(bond => handledBonds.add(bond.));

const MOVE_THRESHOLD = 0.5;
const isMoveVertically =
collapsedSgroupCenter.y <
expandedSGroupCenter.y + sGroupHeight / 2 + MOVE_THRESHOLD &&
collapsedSgroupCenter.y >
expandedSGroupCenter.y - sGroupHeight / 2 - MOVE_THRESHOLD;
const isMoveHorizontally =
collapsedSgroupCenter.y < expandedSGroupCenter.y + MOVE_THRESHOLD &&
collapsedSgroupCenter.y > expandedSGroupCenter.y - MOVE_THRESHOLD;
const isMoveDown = collapsedSgroupCenter.y > expandedSGroupCenter.y;
const isMoveUp = collapsedSgroupCenter.y < expandedSGroupCenter.y;
const BIG_THRESHOLD = 2;
// For collapsing move vertically always if there is still expanded monomer in line
const isMoveVertically = attrs.expanded ?
(movableSGroupCenter.y <
sGroupCenter.y + sGroupHeight / 2 + MOVE_THRESHOLD &&
movableSGroupCenter.y >
sGroupCenter.y - sGroupHeight / 2 - MOVE_THRESHOLD) :
true;


// Move horizontally if monomer is in wide area and not having any other connections (for RNAs/DNAs)
const inOneLine = (movableSGroupCenter.y < sGroupCenter.y + MOVE_THRESHOLD &&
movableSGroupCenter.y > sGroupCenter.y - MOVE_THRESHOLD);
const inLargeLine = (movableSGroupCenter.y < sGroupCenter.y + BIG_THRESHOLD &&
movableSGroupCenter.y > sGroupCenter.y - BIG_THRESHOLD);
const hasAdditionalConnections = [...movableSGroupBondsToOutside.keys()].some((bondId) => !handledBonds.has(bondId));
movableSGroupBondsToOutside.forEach((_, bondId) => handledBonds.add(bondId));
console.log(movableSGroup.data);
console.log('moveVertically', isMoveVertically);
console.log('handledBonds', handledBonds, 'bondsToOutside', movableSGroupBondsToOutside);
console.log('oneLine', inOneLine, 'largeLine', inLargeLine, 'additionalConnections', hasAdditionalConnections);
// const isMoveHorizontally =
// (movableSGroupCenter.y < sGroupCenter.y + MOVE_THRESHOLD &&
// movableSGroupCenter.y > sGroupCenter.y - MOVE_THRESHOLD) || (
// movableSGroupCenter.y < sGroupCenter.y + BIG_THRESHOLD &&
// movableSGroupCenter.y > sGroupCenter.y - BIG_THRESHOLD &&
// ![...movableSGroupBondsToOutside.keys()].some((bondId) => handledBonds.has(bondId))
// );
const isMoveHorizontally = inOneLine || (inLargeLine && !hasAdditionalConnections);
console.log('moveHorizontally', isMoveHorizontally);
const isMoveDown = movableSGroupCenter.y > sGroupCenter.y;
const isMoveUp = movableSGroupCenter.y < sGroupCenter.y;
const isMoveRight =
collapsedSgroupCenter.x > expandedSGroupCenter.x + MOVE_THRESHOLD;
movableSGroupCenter.x > sGroupCenter.x + MOVE_THRESHOLD;
const isMoveLeft =
collapsedSgroupCenter.x < expandedSGroupCenter.x - MOVE_THRESHOLD;
movableSGroupCenter.x < sGroupCenter.x - MOVE_THRESHOLD;
if (!isVerticalMovementStarted) {
isVerticalMovementStarted = !isMoveHorizontally && isMoveVertically;
}
console.log(isMoveVertically);
console.log('isVerticalMovementStarted', isVerticalMovementStarted);

const moveVector = new Vec2(
((!isMoveHorizontally ? 0 : 1) *
((!isMoveHorizontally || isVerticalMovementStarted ? 0 : 1) *
(isMoveRight ? 1 : isMoveLeft ? -1 : 0) *
sGroupWidth) /
2,
((isMoveHorizontally || !isVerticalMovementStarted ? 0 : 1) *
((isVerticalMovementStarted ? 1 : 0) *
(isMoveDown ? 1 : isMoveUp ? -1 : 0) *
sGroupHeight) /
2,
Expand All @@ -262,7 +332,7 @@ export function setExpandMonomerSGroup(
? moveVector
: moveVector.negated();

collapsedSGroupAtoms.forEach((aid) => {
movableSGroupAtoms.forEach((aid) => {
action.addOp(new AtomMove(aid, finalMoveVector));
handledAtoms.add(aid);
});
Expand Down

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