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#5670 – Reimplement algorithm for expansion based on "lines" approach
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@svvald
svvald committed Dec 20, 2024
1 parent e832f82 commit e11cdb1
Showing 1 changed file with 105 additions and 207 deletions.
312 changes: 105 additions & 207 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 @@ -26,21 +26,21 @@ import {
SGroupDelete,
SGroupRemoveFromHierarchy,
} from '../operations';
import { Pile, SGroup, SGroupAttachmentPoint, Vec2 } from 'domain/entities';
import { atomGetAttr, atomGetDegree, atomGetSGroups } from './utils';
import {Pile, SGroup, SGroupAttachmentPoint, Vec2} from 'domain/entities';
import {atomGetAttr, atomGetDegree, atomGetSGroups} from './utils';

import { Action } from './action';
import { Coordinates, SgContexts } from '..';
import { uniq } from 'lodash/fp';
import { fromAtomsAttrs } from './atom';
import {Action} from './action';
import {SgContexts} from '..';
import {uniq} from 'lodash/fp';
import {fromAtomsAttrs} from './atom';
import {
SGroupAttachmentPointAdd,
SGroupAttachmentPointRemove,
} from 'application/editor/operations/sgroup/sgroupAttachmentPoints';
import Restruct from 'application/render/restruct/restruct';
import assert from 'assert';
import { MonomerMicromolecule } from 'domain/entities/monomerMicromolecule';
import { isNumber } from 'lodash';
import {MonomerMicromolecule} from 'domain/entities/monomerMicromolecule';
import {isNumber} from 'lodash';

export function fromSeveralSgroupAddition(
restruct: Restruct,
Expand Down Expand Up @@ -157,29 +157,9 @@ export function setExpandMonomerSGroup(
const sGroupBBox = SGroup.getObjBBox(sGroupAtoms, restruct.molecule);
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 sGroupCenter = sGroup.isContracted()
? sGroup.getContractedPosition(restruct.molecule).position
: sGroup.pp;

const visitedAtoms = new Set<number>();
const visitedSGroups = new Set<number>();
Expand Down Expand Up @@ -240,129 +220,123 @@ export function setExpandMonomerSGroup(
prepareSubStructure(atomId, index);
});

const handledAtoms = new Set<number>();
const handledBonds = new Set<number>();
const sameLine = new Set<number>([sgid]);
const complementaryLine = new Set<number>();

let expandedMonomersInLine = [...sGroupsToMove.values()].some((sGroupIds) => {
return sGroupIds.some((sGroupId) => {
const anotherSGroup = restruct.molecule.sgroups.get(sGroupId);
if (!anotherSGroup) {
return false;
sGroupsToMove.forEach((sGroupIds) => {
sGroupIds.forEach((sGroupId) => {
const movableSGroup = restruct.molecule.sgroups.get(sGroupId);
if (!movableSGroup) {
return;
}

const movableSGroupCenter = movableSGroup.isContracted()
? movableSGroup.getContractedPosition(restruct.molecule).position
: movableSGroup?.pp;
if (!sGroupCenter || !movableSGroupCenter) {
return;
}

const sGroupCenter = sGroup.isContracted() ? sGroup.getContractedPosition(
restruct.molecule,
).position : sGroup.pp;
const anotherSGroupCenter = anotherSGroup.isContracted() ? anotherSGroup.getContractedPosition(
restruct.molecule,
).position : anotherSGroup?.pp;
if (!anotherSGroupCenter || !sGroupCenter) {
return false;
const SAME_LINE_THRESHOLD = 0.5;
const inOneLine = (movableSGroupCenter.y < sGroupCenter.y + SAME_LINE_THRESHOLD &&
movableSGroupCenter.y > sGroupCenter.y - SAME_LINE_THRESHOLD);

if (inOneLine) {
sameLine.add(sGroupId);
return;
}

const MOVE_THRESHOLD = 0.5;
const inOneLine = (anotherSGroupCenter.y < sGroupCenter.y + MOVE_THRESHOLD &&
anotherSGroupCenter.y > sGroupCenter.y - MOVE_THRESHOLD);
const WIDE_LINE_THRESHOLD = 2;
const inWideLine = (movableSGroupCenter.y < sGroupCenter.y + WIDE_LINE_THRESHOLD &&
movableSGroupCenter.y > sGroupCenter.y - WIDE_LINE_THRESHOLD);

return inOneLine && anotherSGroup.isExpanded();
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))
);
});

const hasComplementaryBondToMainLine = movableSGroupBondsToOutside.size === 1 &&
[...sameLine.values()].some((sGroupId) => {
const mainLineSGroup = restruct.molecule.sgroups.get(sGroupId);
if (!mainLineSGroup) {
return false;
}

const mainLineSGroupAtoms = SGroup.getAtoms(restruct, mainLineSGroup);
const bond = [...movableSGroupBondsToOutside.values()][0];
return mainLineSGroupAtoms.includes(bond.begin) || mainLineSGroupAtoms.includes(bond.end);
});

if (inWideLine && hasComplementaryBondToMainLine) {
complementaryLine.add(sGroupId);
}
});
});

const largestHeightInLine = [...sameLine.values()].reduce((acc, sGroupId) => {
const sGroupInLine = restruct.molecule.sgroups.get(sGroupId);
if (!sGroupInLine) {
return acc;
}

if (sGroupInLine.isContracted()) {
return acc;
}

const sGroupInLineAtoms = SGroup.getAtoms(restruct, sGroupInLine);
const sGroupInLineBBox = SGroup.getObjBBox(sGroupInLineAtoms, restruct.molecule);
const sGroupInLineHeight = sGroupInLineBBox.p1.y - sGroupInLineBBox.p0.y;

return Math.max(acc, sGroupInLineHeight);
}, 0);
const baseVerticalOffset = largestHeightInLine > sGroupHeight
? 0
: (sGroupHeight - largestHeightInLine) / 2;
const horizontalOffset = sGroupWidth / 2;

const handledAtoms = new Set<number>();
sGroupsToMove.forEach((sGroupIds) => {
if (sGroupsToMove.size === 1) {
return;
}

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

const sGroupCenter = sGroup.isContracted() ? sGroup.getContractedPosition(
restruct.molecule,
).position : sGroup.pp;
const movableSGroupCenter = movableSGroup.isContracted() ? movableSGroup.getContractedPosition(
restruct.molecule,
).position : movableSGroup?.pp;
if (!movableSGroupCenter || !sGroupCenter) {
const movableSGroupCenter = movableSGroup.isContracted()
? movableSGroup.getContractedPosition(restruct.molecule).position
: movableSGroup?.pp;
if (!sGroupCenter || !movableSGroupCenter) {
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))
);
});

const movableSGroupBBox = SGroup.getObjBBox(sGroupAtoms, restruct.molecule);
const movableSGroupWidth = movableSGroupBBox.p1.x - movableSGroupBBox.p0.x;
const movableSGroupHeight = movableSGroupBBox.p1.y - movableSGroupBBox.p0.y;

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

const MOVE_THRESHOLD = 0.5;
const BIG_THRESHOLD = 2;

const movableSGroupAbove = movableSGroupCenter.y < sGroupCenter.y;
const movableSGroupHeightToUse = movableSGroupAbove ? movableSGroupHeight : -movableSGroupHeight;
// For collapsing move vertically always if there is still expanded monomer in line
const isMoveVertically = attrs.expanded ?
((movableSGroup.isContracted() ? movableSGroupCenter.y : movableSGroupCenter.y + movableSGroupHeightToUse / 2) <
sGroupCenter.y + movableSGroupHeight / 2 + MOVE_THRESHOLD) &&
((movableSGroup.isContracted() ? movableSGroupCenter.y : movableSGroupCenter.y + movableSGroupHeightToUse / 2) >
sGroupCenter.y - movableSGroupHeight / 2 - MOVE_THRESHOLD) :
!expandedMonomersInLine;

// 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 =
movableSGroupCenter.x > sGroupCenter.x + MOVE_THRESHOLD;
const isMoveLeft =
movableSGroupCenter.x < sGroupCenter.x - MOVE_THRESHOLD;
if (!isVerticalMovementStarted) {
isVerticalMovementStarted = !isMoveHorizontally && isMoveVertically;
}
console.log('isVerticalMovementStarted', isVerticalMovementStarted);
const moveDown = movableSGroupCenter.y > sGroupCenter.y;
const moveUp = movableSGroupCenter.y < sGroupCenter.y;
const moveRight =
movableSGroupCenter.x > sGroupCenter.x;
const moveLeft =
movableSGroupCenter.x < sGroupCenter.x;
const moveHorizontally = sameLine.has(sGroupId) || complementaryLine.has(sGroupId);
const complementaryBelowInitialSgroup = complementaryLine.has(sGroupId) && movableSGroupCenter.x === sGroupCenter.x;
const moveVertically = complementaryBelowInitialSgroup || !moveHorizontally;

const moveVector = new Vec2(
((!isMoveHorizontally || isVerticalMovementStarted ? 0 : 1) *
(isMoveRight ? 1 : isMoveLeft ? -1 : 0) *
sGroupWidth) /
2,
((isVerticalMovementStarted ? 1 : 0) *
(isMoveDown ? 1 : isMoveUp ? -1 : 0) *
sGroupHeight) /
2,
(moveHorizontally ? 1 : 0) *
(moveRight ? 1 : moveLeft ? -1 : 0) * horizontalOffset,
(moveVertically ? 1 : 0) *
(moveDown ? 1 : moveUp ? -1 : 0) * baseVerticalOffset
);
const finalMoveVector = attrs.expanded
? moveVector
: moveVector.negated();

const movableSGroupAtoms = SGroup.getAtoms(restruct, movableSGroup);
movableSGroupAtoms.forEach((aid) => {
action.addOp(new AtomMove(aid, finalMoveVector));
handledAtoms.add(aid);
Expand All @@ -372,19 +346,16 @@ export function setExpandMonomerSGroup(
});

atomsToMove.forEach((atomIds, key) => {
// if (handledAtoms.has(key)) {
// return;
// }
if (handledAtoms.has(key)) {
return;
}

const sGroups = sGroupsToMove.get(key) ?? [];
const subStructBBox = SGroup.getObjBBox(atomIds, restruct.molecule, true);
const subStructCenter =
sGroups.length === -100
? restruct.molecule.sgroups.get(sGroups[0]).pp
: new Vec2(
subStructBBox.p0.x + (subStructBBox.p1.x - subStructBBox.p0.x) / 2,
subStructBBox.p0.y + (subStructBBox.p1.y - subStructBBox.p0.y) / 2,
);
const subStructCenter = new Vec2(
subStructBBox.p0.x + (subStructBBox.p1.x - subStructBBox.p0.x) / 2,
subStructBBox.p0.y + (subStructBBox.p1.y - subStructBBox.p0.y) / 2,
);
const sGroupCenter = new Vec2(
sGroupBBox.p0.x + (sGroupBBox.p1.x - sGroupBBox.p0.x) / 2,
sGroupBBox.p0.y + (sGroupBBox.p1.y - sGroupBBox.p0.y) / 2,
Expand All @@ -395,81 +366,8 @@ export function setExpandMonomerSGroup(
(direction.y * sGroupHeight) / 2,
);

const canvas = document.querySelector('.Ketcher-root svg');
// const structureRectangle = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'rect',
// );
// structureRectangle.setAttribute('x', `${subStructBBox.p0.x * 40}`);
// structureRectangle.setAttribute('y', `${subStructBBox.p0.y * 40}`);
// structureRectangle.setAttribute(
// 'width',
// `${(subStructBBox.p1.x - subStructBBox.p0.x) * 40}`,
// );
// structureRectangle.setAttribute(
// 'height',
// `${(subStructBBox.p1.y - subStructBBox.p0.y) * 40}`,
// );
// structureRectangle.setAttribute('fill', 'none');
// structureRectangle.setAttribute('stroke', 'red');
// structureRectangle.setAttribute('stroke-width', '2');
// canvas?.appendChild(structureRectangle);
//
// const structureCenter = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'circle',
// );
// structureCenter.setAttribute('cx', `${subStructCenter.x * 40}`);
// structureCenter.setAttribute('cy', `${subStructCenter.y * 40}`);
// structureCenter.setAttribute('r', '5');
// structureCenter.setAttribute('fill', 'red');
// canvas?.appendChild(structureCenter);

// const sgroupRectangle = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'rect',
// );
// sgroupRectangle.setAttribute('x', `${sGroupBBox.p0.x * 40}`);
// sgroupRectangle.setAttribute('y', `${sGroupBBox.p0.y * 40}`);
// sgroupRectangle.setAttribute(
// 'width',
// `${(sGroupBBox.p1.x - sGroupBBox.p0.x) * 40}`,
// );
// sgroupRectangle.setAttribute(
// 'height',
// `${(sGroupBBox.p1.y - sGroupBBox.p0.y) * 40}`,
// );
// sgroupRectangle.setAttribute('fill', 'none');
// sgroupRectangle.setAttribute('stroke', 'blue');
// sgroupRectangle.setAttribute('stroke-width', '2');
// canvas?.appendChild(sgroupRectangle);
//
// const sgroupCenter = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'circle',
// );
// sgroupCenter.setAttribute('cx', `${sGroupCenter.x * 40}`);
// sgroupCenter.setAttribute('cy', `${sGroupCenter.y * 40}`);
// sgroupCenter.setAttribute('r', '5');
// sgroupCenter.setAttribute('fill', 'blue');
// canvas?.appendChild(sgroupCenter);
//
// const sgroupPP = document.createElementNS(
// 'http://www.w3.org/2000/svg',
// 'circle',
// );
// sgroupPP.setAttribute('cx', `${sGroup.pp.x * 40}`);
// sgroupPP.setAttribute('cy', `${sGroup.pp.y * 40}`);
// sgroupPP.setAttribute('r', '5');
// sgroupPP.setAttribute('fill', 'green');
// canvas?.appendChild(sgroupPP);

const finalMoveVector = attrs.expanded ? moveVector : moveVector.negated();

if (handledAtoms.has(key)) {
return;
}

atomIds.forEach((atomId) => {
action.addOp(new AtomMove(atomId, finalMoveVector));
});
Expand Down

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