smiles-drawer

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>Graph.js - Documentation</title> <script src="scripts/prettify/prettify.js"></script> <script src="scripts/prettify/lang-css.js"></script>  <link type="text/css" rel="stylesheet" href="styles/prettify.css"> <link type="text/css" rel="stylesheet" href="styles/jsdoc.css"> </head> <body> <input type="checkbox" id="nav-trigger" class="nav-trigger" /> <label for="nav-trigger" class="navicon-button x"> <div class="navicon"></div> </label> <label for="nav-trigger" class="overlay"></label> <nav> <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="ArrayHelper.html">ArrayHelper</a><ul class='methods'><li data-type='method'><a href="ArrayHelper.html#.clone">clone</a></li><li data-type='method'><a href="ArrayHelper.html#.contains">contains</a></li><li data-type='method'><a href="ArrayHelper.html#.containsAll">containsAll</a></li><li data-type='method'><a href="ArrayHelper.html#.count">count</a></li><li data-type='method'><a href="ArrayHelper.html#.deepCopy">deepCopy</a></li><li data-type='method'><a href="ArrayHelper.html#.each">each</a></li><li data-type='method'><a href="ArrayHelper.html#.equals">equals</a></li><li data-type='method'><a href="ArrayHelper.html#.get">get</a></li><li data-type='method'><a href="ArrayHelper.html#.intersection">intersection</a></li><li data-type='method'><a href="ArrayHelper.html#.merge">merge</a></li><li data-type='method'><a href="ArrayHelper.html#.print">print</a></li><li data-type='method'><a href="ArrayHelper.html#.remove">remove</a></li><li data-type='method'><a href="ArrayHelper.html#.removeAll">removeAll</a></li><li data-type='method'><a href="ArrayHelper.html#.removeUnique">removeUnique</a></li><li data-type='method'><a href="ArrayHelper.html#.sortByAtomicNumberDesc">sortByAtomicNumberDesc</a></li><li data-type='method'><a href="ArrayHelper.html#.toggle">toggle</a></li><li data-type='method'><a href="ArrayHelper.html#.unique">unique</a></li></ul></li><li><a href="Atom.html">Atom</a><ul class='methods'><li data-type='method'><a href="Atom.html#addAnchoredRing">addAnchoredRing</a></li><li data-type='method'><a href="Atom.html#addNeighbouringElement">addNeighbouringElement</a></li><li data-type='method'><a href="Atom.html#attachPseudoElement">attachPseudoElement</a></li><li data-type='method'><a href="Atom.html#backupRings">backupRings</a></li><li data-type='method'><a href="Atom.html#getAtomicNumber">getAtomicNumber</a></li><li data-type='method'><a href="Atom.html#getAttachedPseudoElements">getAttachedPseudoElements</a></li><li data-type='method'><a href="Atom.html#getAttachedPseudoElementsCount">getAttachedPseudoElementsCount</a></li><li data-type='method'><a href="Atom.html#getMaxBonds">getMaxBonds</a></li><li data-type='method'><a href="Atom.html#getRingbondCount">getRingbondCount</a></li><li data-type='method'><a href="Atom.html#haveCommonRingbond">haveCommonRingbond</a></li><li data-type='method'><a href="Atom.html#isHeteroAtom">isHeteroAtom</a></li><li data-type='method'><a href="Atom.html#neighbouringElementsEqual">neighbouringElementsEqual</a></li><li data-type='method'><a href="Atom.html#restoreRings">restoreRings</a></li></ul></li><li><a href="CanvasWrapper.html">CanvasWrapper</a><ul class='methods'><li data-type='method'><a href="CanvasWrapper.html#clear">clear</a></li><li data-type='method'><a href="CanvasWrapper.html#drawAromaticityRing">drawAromaticityRing</a></li><li data-type='method'><a href="CanvasWrapper.html#drawBall">drawBall</a></li><li data-type='method'><a href="CanvasWrapper.html#drawCircle">drawCircle</a></li><li data-type='method'><a href="CanvasWrapper.html#drawDashedWedge">drawDashedWedge</a></li><li data-type='method'><a href="CanvasWrapper.html#drawDebugPoint">drawDebugPoint</a></li><li data-type='method'><a href="CanvasWrapper.html#drawDebugText">drawDebugText</a></li><li data-type='method'><a href="CanvasWrapper.html#drawLine">drawLine</a></li><li data-type='method'><a href="CanvasWrapper.html#drawPoint">drawPoint</a></li><li data-type='method'><a href="CanvasWrapper.html#drawText">drawText</a></li><li data-type='method'><a href="CanvasWrapper.html#drawWedge">drawWedge</a></li><li data-type='method'><a href="CanvasWrapper.html#getChargeText">getChargeText</a></li><li data-type='method'><a href="CanvasWrapper.html#getColor">getColor</a></li><li data-type='method'><a href="CanvasWrapper.html#reset">reset</a></li><li data-type='method'><a href="CanvasWrapper.html#scale">scale</a></li><li data-type='method'><a href="CanvasWrapper.html#setTheme">setTheme</a></li><li data-type='method'><a href="CanvasWrapper.html#updateSize">updateSize</a></li></ul></li><li><a href="Drawer.html">Drawer</a><ul class='methods'><li data-type='method'><a href="Drawer.html#addRing">addRing</a></li><li data-type='method'><a href="Drawer.html#addRingConnection">addRingConnection</a></li><li data-type='method'><a href="Drawer.html#annotateStereochemistry">annotateStereochemistry</a></li><li data-type='method'><a href="Drawer.html#areVerticesInSameRing">areVerticesInSameRing</a></li><li data-type='method'><a href="Drawer.html#backupRingInformation">backupRingInformation</a></li><li data-type='method'><a href="Drawer.html#chooseSide">chooseSide</a></li><li data-type='method'><a href="Drawer.html#createBridgedRing">createBridgedRing</a></li><li data-type='method'><a href="Drawer.html#createNextBond">createNextBond</a></li><li data-type='method'><a href="Drawer.html#createRing">createRing</a></li><li data-type='method'><a href="Drawer.html#draw">draw</a></li><li data-type='method'><a href="Drawer.html#drawEdge">drawEdge</a></li><li data-type='method'><a href="Drawer.html#drawEdges">drawEdges</a></li><li data-type='method'><a href="Drawer.html#drawVertices">drawVertices</a></li><li data-type='method'><a href="Drawer.html#edgeRingCount">edgeRingCount</a></li><li data-type='method'><a href="Drawer.html#extend">extend</a></li><li data-type='method'><a href="Drawer.html#getBridgedRingRings">getBridgedRingRings</a></li><li data-type='method'><a href="Drawer.html#getBridgedRings">getBridgedRings</a></li><li data-type='method'><a href="Drawer.html#getClosestVertex">getClosestVertex</a></li><li data-type='method'><a href="Drawer.html#getCommonRingbondNeighbour">getCommonRingbondNeighbour</a></li><li data-type='method'><a href="Drawer.html#getCommonRings">getCommonRings</a></li><li data-type='method'><a href="Drawer.html#getCurrentCenterOfMass">getCurrentCenterOfMass</a></li><li data-type='method'><a href="Drawer.html#getCurrentCenterOfMassInNeigbourhood">getCurrentCenterOfMassInNeigbourhood</a></li><li data-type='method'><a href="Drawer.html#getEdgeNormals">getEdgeNormals</a></li><li data-type='method'><a href="Drawer.html#getFusedRings">getFusedRings</a></li><li data-type='method'><a href="Drawer.html#getHeavyAtomCount">getHeavyAtomCount</a></li><li data-type='method'><a href="Drawer.html#getLargestOrAromaticCommonRing">getLargestOrAromaticCommonRing</a></li><li data-type='method'><a href="Drawer.html#getLastVertexWithAngle">getLastVertexWithAngle</a></li><li data-type='method'><a href="Drawer.html#getMolecularFormula">getMolecularFormula</a></li><li data-type='method'><a href="Drawer.html#getNonRingNeighbours">getNonRingNeighbours</a></li><li data-type='method'><a href="Drawer.html#getOverlapScore">getOverlapScore</a></li><li data-type='method'><a href="Drawer.html#getRing">getRing</a></li><li data-type='method'><a href="Drawer.html#getRingbondType">getRingbondType</a></li><li data-type='method'><a href="Drawer.html#getRingConnection">getRingConnection</a></li><li data-type='method'><a href="Drawer.html#getRingConnections">getRingConnections</a></li><li data-type='method'><a href="Drawer.html#getRingCount">getRingCount</a></li><li data-type='method'><a href="Drawer.html#getSpiros">getSpiros</a></li><li data-type='method'><a href="Drawer.html#getSubringCenter">getSubringCenter</a></li><li data-type='method'><a href="Drawer.html#getSubtreeOverlapScore">getSubtreeOverlapScore</a></li><li data-type='method'><a href="Drawer.html#getTotalOverlapScore">getTotalOverlapScore</a></li><li data-type='method'><a href="Drawer.html#getVerticesAt">getVerticesAt</a></li><li data-type='method'><a href="Drawer.html#hasBridgedRing">hasBridgedRing</a></li><li data-type='method'><a href="Drawer.html#initPseudoElements">initPseudoElements</a></li><li data-type='method'><a href="Drawer.html#initRings">initRings</a></li><li data-type='method'><a href="Drawer.html#isEdgeInRing">isEdgeInRing</a></li><li data-type='method'><a href="Drawer.html#isEdgeRotatable">isEdgeRotatable</a></li><li data-type='method'><a href="Drawer.html#isPartOfBridgedRing">isPartOfBridgedRing</a></li><li data-type='method'><a href="Drawer.html#isPointInRing">isPointInRing</a></li><li data-type='method'><a href="Drawer.html#isRingAromatic">isRingAromatic</a></li><li data-type='method'><a href="Drawer.html#position">position</a></li><li data-type='method'><a href="Drawer.html#printRingInfo">printRingInfo</a></li><li data-type='method'><a href="Drawer.html#removeRing">removeRing</a></li><li data-type='method'><a href="Drawer.html#removeRingConnection">removeRingConnection</a></li><li data-type='method'><a href="Drawer.html#removeRingConnectionsBetween">removeRingConnectionsBetween</a></li><li data-type='method'><a href="Drawer.html#resolvePrimaryOverlaps">resolvePrimaryOverlaps</a></li><li data-type='method'><a href="Drawer.html#resolveSecondaryOverlaps">resolveSecondaryOverlaps</a></li><li data-type='method'><a href="Drawer.html#restoreRingInformation">restoreRingInformation</a></li><li data-type='method'><a href="Drawer.html#rotateDrawing">rotateDrawing</a></li><li data-type='method'><a href="Drawer.html#rotateSubtree">rotateSubtree</a></li><li data-type='method'><a href="Drawer.html#setRingCenter">setRingCenter</a></li><li data-type='method'><a href="Drawer.html#visitStereochemistry">visitStereochemistry</a></li></ul></li><li><a href="Edge.html">Edge</a><ul class='methods'><li data-type='method'><a href="Edge.html#setBondType">setBondType</a></li></ul></li><li><a href="Graph.html">Graph</a><ul class='methods'><li data-type='method'><a href="Graph.html#._ccCountDfs">_ccCountDfs</a></li><li data-type='method'><a href="Graph.html#._ccGetDfs">_ccGetDfs</a></li><li data-type='method'><a href="Graph.html#.getConnectedComponentCount">getConnectedComponentCount</a></li><li data-type='method'><a href="Graph.html#.getConnectedComponents">getConnectedComponents</a></li><li data-type='method'><a href="Graph.html#_bridgeDfs">_bridgeDfs</a></li><li data-type='method'><a href="Graph.html#_init">_init</a></li><li data-type='method'><a href="Graph.html#addEdge">addEdge</a></li><li data-type='method'><a href="Graph.html#addVertex">addVertex</a></li><li data-type='method'><a href="Graph.html#clear">clear</a></li><li data-type='method'><a href="Graph.html#getAdjacencyList">getAdjacencyList</a></li><li data-type='method'><a href="Graph.html#getAdjacencyMatrix">getAdjacencyMatrix</a></li><li data-type='method'><a href="Graph.html#getBridges">getBridges</a></li><li data-type='method'><a href="Graph.html#getComponentsAdjacencyMatrix">getComponentsAdjacencyMatrix</a></li><li data-type='method'><a href="Graph.html#getDistanceMatrix">getDistanceMatrix</a></li><li data-type='method'><a href="Graph.html#getEdge">getEdge</a></li><li data-type='method'><a href="Graph.html#getEdgeList">getEdgeList</a></li><li data-type='method'><a href="Graph.html#getEdges">getEdges</a></li><li data-type='method'><a href="Graph.html#getSubgraphAdjacencyList">getSubgraphAdjacencyList</a></li><li data-type='method'><a href="Graph.html#getSubgraphAdjacencyMatrix">getSubgraphAdjacencyMatrix</a></li><li data-type='method'><a href="Graph.html#getSubgraphDistanceMatrix">getSubgraphDistanceMatrix</a></li><li data-type='method'><a href="Graph.html#getTreeDepth">getTreeDepth</a></li><li data-type='method'><a href="Graph.html#getVertexList">getVertexList</a></li><li data-type='method'><a href="Graph.html#hasEdge">hasEdge</a></li><li data-type='method'><a href="Graph.html#kkLayout">kkLayout</a></li><li data-type='method'><a href="Graph.html#traverseBF">traverseBF</a></li><li data-type='method'><a href="Graph.html#traverseTree">traverseTree</a></li></ul></li><li><a href="Line.html">Line</a><ul class='methods'><li data-type='method'><a href="Line.html#clone">clone</a></li><li data-type='method'><a href="Line.html#getAngle">getAngle</a></li><li data-type='method'><a href="Line.html#getLeftChiral">getLeftChiral</a></li><li data-type='method'><a href="Line.html#getLeftElement">getLeftElement</a></li><li data-type='method'><a href="Line.html#getLeftVector">getLeftVector</a></li><li data-type='method'><a href="Line.html#getLength">getLength</a></li><li data-type='method'><a href="Line.html#getRightChiral">getRightChiral</a></li><li data-type='method'><a href="Line.html#getRightElement">getRightElement</a></li><li data-type='method'><a href="Line.html#getRightVector">getRightVector</a></li><li data-type='method'><a href="Line.html#rotate">rotate</a></li><li data-type='method'><a href="Line.html#rotateToXAxis">rotateToXAxis</a></li><li data-type='method'><a href="Line.html#setLeftVector">setLeftVector</a></li><li data-type='method'><a href="Line.html#setRightVector">setRightVector</a></li><li data-type='method'><a href="Line.html#shorten">shorten</a></li><li data-type='method'><a href="Line.html#shortenFrom">shortenFrom</a></li><li data-type='method'><a href="Line.html#shortenLeft">shortenLeft</a></li><li data-type='method'><a href="Line.html#shortenRight">shortenRight</a></li><li data-type='method'><a href="Line.html#shortenTo">shortenTo</a></li></ul></li><li><a href="MathHelper.html">MathHelper</a><ul class='methods'><li data-type='method'><a href="MathHelper.html#.apothem">apothem</a></li><li data-type='method'><a href="MathHelper.html#.centralAngle">centralAngle</a></li><li data-type='method'><a href="MathHelper.html#.innerAngle">innerAngle</a></li><li data-type='method'><a href="MathHelper.html#.meanAngle">meanAngle</a></li><li data-type='method'><a href="MathHelper.html#.parityOfPermutation">parityOfPermutation</a></li><li data-type='method'><a href="MathHelper.html#.polyCircumradius">polyCircumradius</a></li><li data-type='method'><a href="MathHelper.html#.round">round</a></li><li data-type='method'><a href="MathHelper.html#.toDeg">toDeg</a></li><li data-type='method'><a href="MathHelper.html#.toRad">toRad</a></li></ul></li><li><a href="Ring.html">Ring</a><ul class='methods'><li data-type='method'><a href="Ring.html#clone">clone</a></li><li data-type='method'><a href="Ring.html#contains">contains</a></li><li data-type='method'><a href="Ring.html#eachMember">eachMember</a></li><li data-type='method'><a href="Ring.html#getAngle">getAngle</a></li><li data-type='method'><a href="Ring.html#getDoubleBondCount">getDoubleBondCount</a></li><li data-type='method'><a href="Ring.html#getOrderedNeighbours">getOrderedNeighbours</a></li><li data-type='method'><a href="Ring.html#getPolygon">getPolygon</a></li><li data-type='method'><a href="Ring.html#getSize">getSize</a></li><li data-type='method'><a href="Ring.html#isBenzeneLike">isBenzeneLike</a></li></ul></li><li><a href="RingConnection.html">RingConnection</a><ul class='methods'><li data-type='method'><a href="RingConnection.html#.getNeighbours">getNeighbours</a></li><li data-type='method'><a href="RingConnection.html#.getVertices">getVertices</a></li><li data-type='method'><a href="RingConnection.html#.isBridge">isBridge</a></li><li data-type='method'><a href="RingConnection.html#addVertex">addVertex</a></li><li data-type='method'><a href="RingConnection.html#containsRing">containsRing</a></li><li data-type='method'><a href="RingConnection.html#isBridge">isBridge</a></li><li data-type='method'><a href="RingConnection.html#updateOther">updateOther</a></li></ul></li><li><a href="SSSR.html">SSSR</a><ul class='methods'><li data-type='method'><a href="SSSR.html#.areSetsEqual">areSetsEqual</a></li><li data-type='method'><a href="SSSR.html#.bondsToAtoms">bondsToAtoms</a></li><li data-type='method'><a href="SSSR.html#.getBondCount">getBondCount</a></li><li data-type='method'><a href="SSSR.html#.getEdgeCount">getEdgeCount</a></li><li data-type='method'><a href="SSSR.html#.getEdgeList">getEdgeList</a></li><li data-type='method'><a href="SSSR.html#.getPathIncludedDistanceMatrices">getPathIncludedDistanceMatrices</a></li><li data-type='method'><a href="SSSR.html#.getRingCandidates">getRingCandidates</a></li><li data-type='method'><a href="SSSR.html#.getRings">getRings</a></li><li data-type='method'><a href="SSSR.html#.getSSSR">getSSSR</a></li><li data-type='method'><a href="SSSR.html#.isSupersetOf">isSupersetOf</a></li><li data-type='method'><a href="SSSR.html#.matrixToString">matrixToString</a></li><li data-type='method'><a href="SSSR.html#.pathSetsContain">pathSetsContain</a></li></ul></li><li><a href="Vector2.html">Vector2</a><ul class='methods'><li data-type='method'><a href="Vector2.html#add">add</a></li><li data-type='method'><a href="Vector2.html#angle">angle</a></li><li data-type='method'><a href="Vector2.html#clockwise">clockwise</a></li><li data-type='method'><a href="Vector2.html#clone">clone</a></li><li data-type='method'><a href="Vector2.html#distance">distance</a></li><li data-type='method'><a href="Vector2.html#distanceSq">distanceSq</a></li><li data-type='method'><a href="Vector2.html#divide">divide</a></li><li data-type='method'><a href="Vector2.html#getRotateAwayFromAngle">getRotateAwayFromAngle</a></li><li data-type='method'><a href="Vector2.html#getRotateToAngle">getRotateToAngle</a></li><li data-type='method'><a href="Vector2.html#getRotateTowardsAngle">getRotateTowardsAngle</a></li><li data-type='method'><a href="Vector2.html#invert">invert</a></li><li data-type='method'><a href="Vector2.html#isInPolygon">isInPolygon</a></li><li data-type='method'><a href="Vector2.html#length">length</a></li><li data-type='method'><a href="Vector2.html#lengthSq">lengthSq</a></li><li data-type='method'><a href="Vector2.html#multiply">multiply</a></li><li data-type='method'><a href="Vector2.html#multiplyScalar">multiplyScalar</a></li><li data-type='method'><a href="Vector2.html#normalize">normalize</a></li><li data-type='method'><a href="Vector2.html#normalized">normalized</a></li><li data-type='method'><a href="Vector2.html#relativeClockwise">relativeClockwise</a></li><li data-type='method'><a href="Vector2.html#rotate">rotate</a></li><li data-type='method'><a href="Vector2.html#rotateAround">rotateAround</a></li><li data-type='method'><a href="Vector2.html#rotateAwayFrom">rotateAwayFrom</a></li><li data-type='method'><a href="Vector2.html#rotateTo">rotateTo</a></li><li data-type='method'><a href="Vector2.html#sameSideAs">sameSideAs</a></li><li data-type='method'><a href="Vector2.html#subtract">subtract</a></li><li data-type='method'><a href="Vector2.html#toString">toString</a></li><li data-type='method'><a href="Vector2.html#whichSide">whichSide</a></li><li data-type='method'><a href="Vector2.html#.add">add</a></li><li data-type='method'><a href="Vector2.html#.angle">angle</a></li><li data-type='method'><a href="Vector2.html#.averageDirection">averageDirection</a></li><li data-type='method'><a href="Vector2.html#.divide">divide</a></li><li data-type='method'><a href="Vector2.html#.divideScalar">divideScalar</a></li><li data-type='method'><a href="Vector2.html#.dot">dot</a></li><li data-type='method'><a href="Vector2.html#.midpoint">midpoint</a></li><li data-type='method'><a href="Vector2.html#.multiply">multiply</a></li><li data-type='method'><a href="Vector2.html#.multiplyScalar">multiplyScalar</a></li><li data-type='method'><a href="Vector2.html#.normals">normals</a></li><li data-type='method'><a href="Vector2.html#.scalarProjection">scalarProjection</a></li><li data-type='method'><a href="Vector2.html#.subtract">subtract</a></li><li data-type='method'><a href="Vector2.html#.threePointangle">threePointangle</a></li><li data-type='method'><a href="Vector2.html#.units">units</a></li></ul></li><li><a href="Vertex.html">Vertex</a><ul class='methods'><li data-type='method'><a href="Vertex.html#addChild">addChild</a></li><li data-type='method'><a href="Vertex.html#addRingbondChild">addRingbondChild</a></li><li data-type='method'><a href="Vertex.html#clone">clone</a></li><li data-type='method'><a href="Vertex.html#equals">equals</a></li><li data-type='method'><a href="Vertex.html#getAngle">getAngle</a></li><li data-type='method'><a href="Vertex.html#getDrawnNeighbours">getDrawnNeighbours</a></li><li data-type='method'><a href="Vertex.html#getNeighbourCount">getNeighbourCount</a></li><li data-type='method'><a href="Vertex.html#getNeighbours">getNeighbours</a></li><li data-type='method'><a href="Vertex.html#getNextInRing">getNextInRing</a></li><li data-type='method'><a href="Vertex.html#getSpanningTreeNeighbours">getSpanningTreeNeighbours</a></li><li data-type='method'><a href="Vertex.html#getTextDirection">getTextDirection</a></li><li data-type='method'><a href="Vertex.html#isTerminal">isTerminal</a></li><li data-type='method'><a href="Vertex.html#setParentVertexId">setParentVertexId</a></li><li data-type='method'><a href="Vertex.html#setPosition">setPosition</a></li><li data-type='method'><a href="Vertex.html#setPositionFromVector">setPositionFromVector</a></li></ul></li></ul> </nav> <div id="main"> <h1 class="page-title">Graph.js</h1> <section> <article> <pre class="prettyprint source linenums"><code>//@ts-check const MathHelper = require('./MathHelper') const Vector2 = require('./Vector2') const Vertex = require('./Vertex') const Edge = require('./Edge') const Ring = require('./Ring') const Atom = require('./Atom') /** * A class representing the molecular graph. * * @property {Vertex[]} vertices The vertices of the graph. * @property {Edge[]} edges The edges of this graph. * @property {Object} vertexIdsToEdgeId A map mapping vertex ids to the edge between the two vertices. The key is defined as vertexAId + '_' + vertexBId. * @property {Boolean} isometric A boolean indicating whether or not the SMILES associated with this graph is isometric. */ class Graph { /** * The constructor of the class Graph. * * @param {Object} parseTree A SMILES parse tree. * @param {Boolean} [isomeric=false] A boolean specifying whether or not the SMILES is isomeric. */ constructor(parseTree, isomeric = false) { this.vertices = Array(); this.edges = Array(); this.vertexIdsToEdgeId = {}; this.isomeric = isomeric; // Used for the bridge detection algorithm this._time = 0; this._init(parseTree); } /** * PRIVATE FUNCTION. Initializing the graph from the parse tree. * * @param {Object} node The current node in the parse tree. * @param {Number} parentVertexId=null The id of the previous vertex. * @param {Boolean} isBranch=false Whether or not the bond leading to this vertex is a branch bond. Branches are represented by parentheses in smiles (e.g. CC(O)C). */ _init(node, order = 0, parentVertexId = null, isBranch = false) { // Create a new vertex object let atom = new Atom(node.atom.element ? node.atom.element : node.atom, node.bond); atom.branchBond = node.branchBond; atom.ringbonds = node.ringbonds; atom.bracket = node.atom.element ? node.atom : null; let vertex = new Vertex(atom); let parentVertex = this.vertices[parentVertexId]; this.addVertex(vertex); // Add the id of this node to the parent as child if (parentVertexId !== null) { vertex.setParentVertexId(parentVertexId); vertex.value.addNeighbouringElement(parentVertex.value.element); parentVertex.addChild(vertex.id); parentVertex.value.addNeighbouringElement(atom.element); // In addition create a spanningTreeChildren property, which later will // not contain the children added through ringbonds parentVertex.spanningTreeChildren.push(vertex.id); // Add edge between this node and its parent let edge = new Edge(parentVertexId, vertex.id, 1); let vertexId = null; if (isBranch) { edge.setBondType(vertex.value.branchBond || '-'); vertexId = vertex.id; edge.setBondType(vertex.value.branchBond || '-'); vertexId = vertex.id; } else { edge.setBondType(parentVertex.value.bondType || '-'); vertexId = parentVertex.id; } let edgeId = this.addEdge(edge); } let offset = node.ringbondCount + 1; if (atom.bracket) { offset += atom.bracket.hcount; } let stereoHydrogens = 0; if (atom.bracket && atom.bracket.chirality) { atom.isStereoCenter = true; stereoHydrogens = atom.bracket.hcount; for (var i = 0; i < stereoHydrogens; i++) { this._init({ atom: 'H', isBracket: 'false', branches: Array(), branchCount: 0, ringbonds: Array(), ringbondCount: false, next: null, hasNext: false, bond: '-' }, i, vertex.id, true); } } for (var i = 0; i < node.branchCount; i++) { this._init(node.branches[i], i + offset, vertex.id, true); } if (node.hasNext) { this._init(node.next, node.branchCount + offset, vertex.id); } } /** * Clears all the elements in this graph (edges and vertices). */ clear() { this.vertices = Array(); this.edges = Array(); this.vertexIdsToEdgeId = {}; } /** * Add a vertex to the graph. * * @param {Vertex} vertex A new vertex. * @returns {Number} The vertex id of the new vertex. */ addVertex(vertex) { vertex.id = this.vertices.length; this.vertices.push(vertex); return vertex.id; } /** * Add an edge to the graph. * * @param {Edge} edge A new edge. * @returns {Number} The edge id of the new edge. */ addEdge(edge) { let source = this.vertices[edge.sourceId]; let target = this.vertices[edge.targetId]; edge.id = this.edges.length; this.edges.push(edge); this.vertexIdsToEdgeId[edge.sourceId + '_' + edge.targetId] = edge.id; this.vertexIdsToEdgeId[edge.targetId + '_' + edge.sourceId] = edge.id; edge.isPartOfAromaticRing = source.value.isPartOfAromaticRing && target.value.isPartOfAromaticRing; source.value.bondCount += edge.weight; target.value.bondCount += edge.weight; source.edges.push(edge.id); target.edges.push(edge.id); return edge.id; } /** * Returns the edge between two given vertices. * * @param {Number} vertexIdA A vertex id. * @param {Number} vertexIdB A vertex id. * @returns {(Edge|null)} The edge or, if no edge can be found, null. */ getEdge(vertexIdA, vertexIdB) { let edgeId = this.vertexIdsToEdgeId[vertexIdA + '_' + vertexIdB]; return edgeId === undefined ? null : this.edges[edgeId]; } /** * Returns the ids of edges connected to a vertex. * * @param {Number} vertexId A vertex id. * @returns {Number[]} An array containing the ids of edges connected to the vertex. */ getEdges(vertexId) { let edgeIds = Array(); let vertex = this.vertices[vertexId]; for (var i = 0; i < vertex.neighbours.length; i++) { edgeIds.push(this.vertexIdsToEdgeId[vertexId + '_' + vertex.neighbours[i]]); } return edgeIds; } /** * Check whether or not two vertices are connected by an edge. * * @param {Number} vertexIdA A vertex id. * @param {Number} vertexIdB A vertex id. * @returns {Boolean} A boolean indicating whether or not two vertices are connected by an edge. */ hasEdge(vertexIdA, vertexIdB) { return this.vertexIdsToEdgeId[vertexIdA + '_' + vertexIdB] !== undefined } /** * Returns an array containing the vertex ids of this graph. * * @returns {Number[]} An array containing all vertex ids of this graph. */ getVertexList() { let arr = [this.vertices.length]; for (var i = 0; i < this.vertices.length; i++) { arr[i] = this.vertices[i].id; } return arr; } /** * Returns an array containing source, target arrays of this graphs edges. * * @returns {Array[]} An array containing source, target arrays of this graphs edges. Example: [ [ 2, 5 ], [ 6, 9 ] ]. */ getEdgeList() { let arr = Array(this.edges.length); for (var i = 0; i < this.edges.length; i++) { arr[i] = [this.edges[i].sourceId, this.edges[i].targetId]; } return arr; } /** * Get the adjacency matrix of the graph. * * @returns {Array[]} The adjancency matrix of the molecular graph. */ getAdjacencyMatrix() { let length = this.vertices.length; let adjacencyMatrix = Array(length); for (var i = 0; i < length; i++) { adjacencyMatrix[i] = new Array(length); adjacencyMatrix[i].fill(0); } for (var i = 0; i < this.edges.length; i++) { let edge = this.edges[i]; adjacencyMatrix[edge.sourceId][edge.targetId] = 1; adjacencyMatrix[edge.targetId][edge.sourceId] = 1; } return adjacencyMatrix; } /** * Get the adjacency matrix of the graph with all bridges removed (thus the components). Thus the remaining vertices are all part of ring systems. * * @returns {Array[]} The adjancency matrix of the molecular graph with all bridges removed. */ getComponentsAdjacencyMatrix() { let length = this.vertices.length; let adjacencyMatrix = Array(length); let bridges = this.getBridges(); for (var i = 0; i < length; i++) { adjacencyMatrix[i] = new Array(length); adjacencyMatrix[i].fill(0); } for (var i = 0; i < this.edges.length; i++) { let edge = this.edges[i]; adjacencyMatrix[edge.sourceId][edge.targetId] = 1; adjacencyMatrix[edge.targetId][edge.sourceId] = 1; } for (var i = 0; i < bridges.length; i++) { adjacencyMatrix[bridges[i][0]][bridges[i][1]] = 0; adjacencyMatrix[bridges[i][1]][bridges[i][0]] = 0; } return adjacencyMatrix; } /** * Get the adjacency matrix of a subgraph. * * @param {Number[]} vertexIds An array containing the vertex ids contained within the subgraph. * @returns {Array[]} The adjancency matrix of the subgraph. */ getSubgraphAdjacencyMatrix(vertexIds) { let length = vertexIds.length; let adjacencyMatrix = Array(length); for (var i = 0; i < length; i++) { adjacencyMatrix[i] = new Array(length); adjacencyMatrix[i].fill(0); for (var j = 0; j < length; j++) { if (i === j) { continue; } if (this.hasEdge(vertexIds[i], vertexIds[j])) { adjacencyMatrix[i][j] = 1; } } } return adjacencyMatrix; } /** * Get the distance matrix of the graph. * * @returns {Array[]} The distance matrix of the graph. */ getDistanceMatrix() { let length = this.vertices.length; let adja = this.getAdjacencyMatrix(); let dist = Array(length); for (var i = 0; i < length; i++) { dist[i] = Array(length); dist[i].fill(Infinity); } for (var i = 0; i < length; i++) { for (var j = 0; j < length; j++) { if (adja[i][j] === 1) { dist[i][j] = 1; } } } for (var k = 0; k < length; k++) { for (var i = 0; i < length; i++) { for (var j = 0; j < length; j++) { if (dist[i][j] > dist[i][k] + dist[k][j]) { dist[i][j] = dist[i][k] + dist[k][j] } } } } return dist; } /** * Get the distance matrix of a subgraph. * * @param {Number[]} vertexIds An array containing the vertex ids contained within the subgraph. * @returns {Array[]} The distance matrix of the subgraph. */ getSubgraphDistanceMatrix(vertexIds) { let length = vertexIds.length; let adja = this.getSubgraphAdjacencyMatrix(vertexIds); let dist = Array(length); for (var i = 0; i < length; i++) { dist[i] = Array(length); dist[i].fill(Infinity); } for (var i = 0; i < length; i++) { for (var j = 0; j < length; j++) { if (adja[i][j] === 1) { dist[i][j] = 1; } } } for (var k = 0; k < length; k++) { for (var i = 0; i < length; i++) { for (var j = 0; j < length; j++) { if (dist[i][j] > dist[i][k] + dist[k][j]) { dist[i][j] = dist[i][k] + dist[k][j] } } } } return dist; } /** * Get the adjacency list of the graph. * * @returns {Array[]} The adjancency list of the graph. */ getAdjacencyList() { let length = this.vertices.length; let adjacencyList = Array(length); for (var i = 0; i < length; i++) { adjacencyList[i] = []; for (var j = 0; j < length; j++) { if (i === j) { continue; } if (this.hasEdge(this.vertices[i].id, this.vertices[j].id)) { adjacencyList[i].push(j); } } } return adjacencyList; } /** * Get the adjacency list of a subgraph. * * @param {Number[]} vertexIds An array containing the vertex ids contained within the subgraph. * @returns {Array[]} The adjancency list of the subgraph. */ getSubgraphAdjacencyList(vertexIds) { let length = vertexIds.length; let adjacencyList = Array(length); for (var i = 0; i < length; i++) { adjacencyList[i] = Array(); for (var j = 0; j < length; j++) { if (i === j) { continue; } if (this.hasEdge(vertexIds[i], vertexIds[j])) { adjacencyList[i].push(j); } } } return adjacencyList; } /** * Returns an array containing the edge ids of bridges. A bridge splits the graph into multiple components when removed. * * @returns {Number[]} An array containing the edge ids of the bridges. */ getBridges() { let length = this.vertices.length; let visited = new Array(length); let disc = new Array(length); let low = new Array(length); let parent = new Array(length); let adj = this.getAdjacencyList(); let outBridges = Array(); visited.fill(false); parent.fill(null); this._time = 0; for (var i = 0; i < length; i++) { if (!visited[i]) { this._bridgeDfs(i, visited, disc, low, parent, adj, outBridges); } } return outBridges; } /** * Traverses the graph in breadth-first order. * * @param {Number} startVertexId The id of the starting vertex. * @param {Function} callback The callback function to be called on every vertex. */ traverseBF(startVertexId, callback) { let length = this.vertices.length; let visited = new Array(length); visited.fill(false); var queue = [startVertexId]; while (queue.length > 0) { // JavaScripts shift() is O(n) ... bad JavaScript, bad! let u = queue.shift(); let vertex = this.vertices[u]; callback(vertex); for (var i = 0; i < vertex.neighbours.length; i++) { let v = vertex.neighbours[i] if (!visited[v]) { visited[v] = true; queue.push(v); } } } } /** * Get the depth of a subtree in the direction opposite to the vertex specified as the parent vertex. * * @param {Number} vertexId A vertex id. * @param {Number} parentVertexId The id of a neighbouring vertex. * @returns {Number} The depth of the sub-tree. */ getTreeDepth(vertexId, parentVertexId) { if (vertexId === null || parentVertexId === null) { return 0; } let neighbours = this.vertices[vertexId].getSpanningTreeNeighbours(parentVertexId); let max = 0; for (var i = 0; i < neighbours.length; i++) { let childId = neighbours[i]; let d = this.getTreeDepth(childId, vertexId); if (d > max) { max = d; } } return max + 1; } /** * Traverse a sub-tree in the graph. * * @param {Number} vertexId A vertex id. * @param {Number} parentVertexId A neighbouring vertex. * @param {Function} callback The callback function that is called with each visited as an argument. * @param {Number} [maxDepth=Number.MAX_SAFE_INTEGER] The maximum depth of the recursion. * @param {Boolean} [ignoreFirst=false] Whether or not to ignore the starting vertex supplied as vertexId in the callback. * @param {Number} [depth=1] The current depth in the tree. * @param {Uint8Array} [visited=null] An array holding a flag on whether or not a node has been visited. */ traverseTree(vertexId, parentVertexId, callback, maxDepth = Number.MAX_SAFE_INTEGER, ignoreFirst = false, depth = 1, visited = null) { if (visited === null) { visited = new Uint8Array(this.vertices.length); } if (depth > maxDepth + 1 || visited[vertexId] === 1) { return; } visited[vertexId] = 1; let vertex = this.vertices[vertexId]; let neighbours = vertex.getNeighbours(parentVertexId); if (!ignoreFirst || depth > 1) { callback(vertex); } for (var i = 0; i < neighbours.length; i++) { this.traverseTree(neighbours[i], vertexId, callback, maxDepth, ignoreFirst, depth + 1, visited); } } /** * Positiones the (sub)graph using Kamada and Kawais algorithm for drawing general undirected graphs. https://pdfs.semanticscholar.org/b8d3/bca50ccc573c5cb99f7d201e8acce6618f04.pdf * * @param {Number[]} vertexIds An array containing vertexIds to be placed using the force based layout. * @param {Vector2} center The center of the layout. * @param {Number} startVertexId A vertex id. Should be the starting vertex - e.g. the first to be positioned and connected to a previously place vertex. * @param {Ring} ring The bridged ring associated with this force-based layout. */ kkLayout(vertexIds, center, startVertexId, ring, bondLength) { let edgeStrength = bondLength; // Add vertices that are directly connected to the ring var i = vertexIds.length; while (i--) { let vertex = this.vertices[vertexIds[i]]; var j = vertex.neighbours.length; } let matDist = this.getSubgraphDistanceMatrix(vertexIds); let length = vertexIds.length; // Initialize the positions. Place all vertices on a ring around the center let radius = MathHelper.polyCircumradius(500, length); let angle = MathHelper.centralAngle(length); let a = 0.0; let arrPositionX = new Float32Array(length); let arrPositionY = new Float32Array(length); let arrPositioned = Array(length); i = length; while (i--) { let vertex = this.vertices[vertexIds[i]]; if (!vertex.positioned) { arrPositionX[i] = center.x + Math.cos(a) * radius; arrPositionY[i] = center.y + Math.sin(a) * radius; } else { arrPositionX[i] = vertex.position.x; arrPositionY[i] = vertex.position.y; } arrPositioned[i] = vertex.positioned; a += angle; } // Create the matrix containing the lengths let matLength = Array(length); i = length; while (i--) { matLength[i] = new Array(length); var j = length; while (j--) { matLength[i][j] = bondLength * matDist[i][j]; } } // Create the matrix containing the spring strenghts let matStrength = Array(length); i = length; while (i--) { matStrength[i] = Array(length); var j = length; while (j--) { matStrength[i][j] = edgeStrength * Math.pow(matDist[i][j], -2.0); } } // Create the matrix containing the energies let matEnergy = Array(length); let arrEnergySumX = new Float32Array(length); let arrEnergySumY = new Float32Array(length); i = length; while (i--) { matEnergy[i] = Array(length); } i = length; let ux, uy, dEx, dEy, vx, vy, denom; while (i--) { ux = arrPositionX[i]; uy = arrPositionY[i]; dEx = 0.0; dEy = 0.0; let j = length; while (j--) { if (i === j) { continue; } vx = arrPositionX[j]; vy = arrPositionY[j]; denom = 1.0 / Math.sqrt((ux - vx) * (ux - vx) + (uy - vy) * (uy - vy)); matEnergy[i][j] = [ matStrength[i][j] * ((ux - vx) - matLength[i][j] * (ux - vx) * denom), matStrength[i][j] * ((uy - vy) - matLength[i][j] * (uy - vy) * denom) ] matEnergy[j][i] = matEnergy[i][j]; dEx += matEnergy[i][j][0]; dEy += matEnergy[i][j][1]; } arrEnergySumX[i] = dEx; arrEnergySumY[i] = dEy; } // Utility functions, maybe inline them later let energy = function (index) { return [arrEnergySumX[index] * arrEnergySumX[index] + arrEnergySumY[index] * arrEnergySumY[index], arrEnergySumX[index], arrEnergySumY[index]]; } let highestEnergy = function () { let maxEnergy = 0.0; let maxEnergyId = 0; let maxDEX = 0.0; let maxDEY = 0.0 i = length; while (i--) { let [delta, dEX, dEY] = energy(i); if (delta > maxEnergy && arrPositioned[i] === false) { maxEnergy = delta; maxEnergyId = i; maxDEX = dEX; maxDEY = dEY; } } return [maxEnergyId, maxEnergy, maxDEX, maxDEY]; } let update = function (index, dEX, dEY) { let dxx = 0.0; let dyy = 0.0; let dxy = 0.0; let ux = arrPositionX[index]; let uy = arrPositionY[index]; let arrL = matLength[index]; let arrK = matStrength[index]; i = length; while (i--) { if (i === index) { continue; } let vx = arrPositionX[i]; let vy = arrPositionY[i]; let l = arrL[i]; let k = arrK[i]; let m = (ux - vx) * (ux - vx); let denom = 1.0 / Math.pow(m + (uy - vy) * (uy - vy), 1.5); dxx += k * (1 - l * (uy - vy) * (uy - vy) * denom); dyy += k * (1 - l * m * denom); dxy += k * (l * (ux - vx) * (uy - vy) * denom); } // Prevent division by zero if (dxx === 0) { dxx = 0.1; } if (dyy === 0) { dyy = 0.1; } if (dxy === 0) { dxy = 0.1; } let dy = (dEX / dxx + dEY / dxy); dy /= (dxy / dxx - dyy / dxy); // had to split this onto two lines because the syntax highlighter went crazy. let dx = -(dxy * dy + dEX) / dxx; arrPositionX[index] += dx; arrPositionY[index] += dy; // Update the energies let arrE = matEnergy[index]; dEX = 0.0; dEY = 0.0; ux = arrPositionX[index]; uy = arrPositionY[index]; let vx, vy, prevEx, prevEy, denom; i = length; while (i--) { if (index === i) { continue; } vx = arrPositionX[i]; vy = arrPositionY[i]; // Store old energies prevEx = arrE[i][0]; prevEy = arrE[i][1]; denom = 1.0 / Math.sqrt((ux - vx) * (ux - vx) + (uy - vy) * (uy - vy)); dx = arrK[i] * ((ux - vx) - arrL[i] * (ux - vx) * denom); dy = arrK[i] * ((uy - vy) - arrL[i] * (uy - vy) * denom); arrE[i] = [dx, dy]; dEX += dx; dEY += dy; arrEnergySumX[i] += dx - prevEx; arrEnergySumY[i] += dy - prevEy; } arrEnergySumX[index] = dEX; arrEnergySumY[index] = dEY; } // Setting parameters let threshold = 0.1; let innerThreshold = 0.1; let maxIteration = 2000; let maxInnerIteration = 50; let maxEnergy = 1e9; // Setting up variables for the while loops let maxEnergyId = 0; let dEX = 0.0; let dEY = 0.0; let delta = 0.0; let iteration = 0; let innerIteration = 0; while (maxEnergy > threshold && maxIteration > iteration) { iteration++; [maxEnergyId, maxEnergy, dEX, dEY] = highestEnergy(); delta = maxEnergy; innerIteration = 0; while (delta > innerThreshold && maxInnerIteration > innerIteration) { innerIteration++; update(maxEnergyId, dEX, dEY); [delta, dEX, dEY] = energy(maxEnergyId); } } i = length; while (i--) { let index = vertexIds[i]; let vertex = this.vertices[index]; vertex.position.x = arrPositionX[i]; vertex.position.y = arrPositionY[i]; vertex.positioned = true; vertex.forcePositioned = true; } } /** * PRIVATE FUNCTION used by getBridges(). */ _bridgeDfs(u, visited, disc, low, parent, adj, outBridges) { visited[u] = true; disc[u] = low[u] = ++this._time; for (var i = 0; i < adj[u].length; i++) { let v = adj[u][i]; if (!visited[v]) { parent[v] = u; this._bridgeDfs(v, visited, disc, low, parent, adj, outBridges); low[u] = Math.min(low[u], low[v]); // If low > disc, we have a bridge if (low[v] > disc[u]) { outBridges.push([u, v]); } } else if (v !== parent[u]) { low[u] = Math.min(low[u], disc[v]); } } } /** * Returns the connected components of the graph. * * @param {Array[]} adjacencyMatrix An adjacency matrix. * @returns {Set[]} Connected components as sets. */ static getConnectedComponents(adjacencyMatrix) { let length = adjacencyMatrix.length; let visited = new Array(length); let components = new Array(); let count = 0; visited.fill(false); for (var u = 0; u < length; u++) { if (!visited[u]) { let component = Array(); visited[u] = true; component.push(u); count++; Graph._ccGetDfs(u, visited, adjacencyMatrix, component); if (component.length > 1) { components.push(component); } } } return components; } /** * Returns the number of connected components for the graph. * * @param {Array[]} adjacencyMatrix An adjacency matrix. * @returns {Number} The number of connected components of the supplied graph. */ static getConnectedComponentCount(adjacencyMatrix) { let length = adjacencyMatrix.length; let visited = new Array(length); let count = 0; visited.fill(false); for (var u = 0; u < length; u++) { if (!visited[u]) { visited[u] = true; count++; Graph._ccCountDfs(u, visited, adjacencyMatrix); } } return count; } /** * PRIVATE FUNCTION used by getConnectedComponentCount(). */ static _ccCountDfs(u, visited, adjacencyMatrix) { for (var v = 0; v < adjacencyMatrix[u].length; v++) { let c = adjacencyMatrix[u][v]; if (!c || visited[v] || u === v) { continue; } visited[v] = true; Graph._ccCountDfs(v, visited, adjacencyMatrix); } } /** * PRIVATE FUNCTION used by getConnectedComponents(). */ static _ccGetDfs(u, visited, adjacencyMatrix, component) { for (var v = 0; v < adjacencyMatrix[u].length; v++) { let c = adjacencyMatrix[u][v]; if (!c || visited[v] || u === v) { continue; } visited[v] = true; component.push(v); Graph._ccGetDfs(v, visited, adjacencyMatrix, component); } } } module.exports = Graph</code></pre> </article> </section> </div> <br class="clear"> <footer> Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Tue Jun 26 2018 08:07:40 GMT+0200 (W. Europe Summer Time) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme. </footer> <script>prettyPrint();</script> <script src="scripts/linenumber.js"></script> </body> </html>