smiles-drawer

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>Vertex - 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">Vertex</h1> <section> <header> <h2> Vertex </h2> <div class="class-description"><p>A class representing a vertex.</p></div> </header> <article> <div class="container-overview"> <h2>Constructor</h2> <h4 class="name" id="Vertex"><span class="type-signature"></span>new Vertex<span class="signature">(value, x<span class="signature-attributes">opt</span>, y<span class="signature-attributes">opt</span>)</span><span class="type-signature"></span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line27">line 27</a> </li></ul></dd> </dl> <h5 class="subsection-title">Properties:</h5> <table class="props"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>id</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The id of this vertex.</p></td> </tr> <tr> <td class="name"><code>value</code></td> <td class="type"> <span class="param-type"><a href="Atom.html">Atom</a></span> </td> <td class="description last"><p>The atom associated with this vertex.</p></td> </tr> <tr> <td class="name"><code>position</code></td> <td class="type"> <span class="param-type"><a href="Vector2.html">Vector2</a></span> </td> <td class="description last"><p>The position of this vertex.</p></td> </tr> <tr> <td class="name"><code>previousPosition</code></td> <td class="type"> <span class="param-type"><a href="Vector2.html">Vector2</a></span> </td> <td class="description last"><p>The position of the previous vertex.</p></td> </tr> <tr> <td class="name"><code>parentVertexId</code></td> <td class="type"> <span class="param-type">Number</span> | <span class="param-type">null</span> </td> <td class="description last"><p>The id of the previous vertex.</p></td> </tr> <tr> <td class="name"><code>children</code></td> <td class="type"> <span class="param-type">Array.<Number></span> </td> <td class="description last"><p>The ids of the children of this vertex.</p></td> </tr> <tr> <td class="name"><code>spanningTreeChildren</code></td> <td class="type"> <span class="param-type">Array.<Number></span> </td> <td class="description last"><p>The ids of the children of this vertex as defined in the spanning tree defined by the SMILES.</p></td> </tr> <tr> <td class="name"><code>edges</code></td> <td class="type"> <span class="param-type">Array.<Number></span> </td> <td class="description last"><p>The ids of edges associated with this vertex.</p></td> </tr> <tr> <td class="name"><code>positioned</code></td> <td class="type"> <span class="param-type">Boolean</span> </td> <td class="description last"><p>A boolean indicating whether or not this vertex has been positioned.</p></td> </tr> <tr> <td class="name"><code>angle</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The angle of this vertex.</p></td> </tr> <tr> <td class="name"><code>dir</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The direction of this vertex.</p></td> </tr> <tr> <td class="name"><code>neighbourCount</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The number of neighbouring vertices.</p></td> </tr> <tr> <td class="name"><code>neighbours</code></td> <td class="type"> <span class="param-type">Array.<Number></span> </td> <td class="description last"><p>The vertex ids of neighbouring vertices.</p></td> </tr> <tr> <td class="name"><code>neighbouringElements</code></td> <td class="type"> <span class="param-type">Array.<String></span> </td> <td class="description last"><p>The element symbols associated with neighbouring vertices.</p></td> </tr> <tr> <td class="name"><code>forcePositioned</code></td> <td class="type"> <span class="param-type">Boolean</span> </td> <td class="description last"><p>A boolean indicating whether or not this vertex was positioned using a force-based approach.</p></td> </tr> </tbody> </table> <div class="description"> <p>The constructor for the class Vertex.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th>Attributes</th> <th>Default</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>value</code></td> <td class="type"> <span class="param-type"><a href="Atom.html">Atom</a></span> </td> <td class="attributes"> </td> <td class="default"> </td> <td class="description last"><p>The value associated with this vertex.</p></td> </tr> <tr> <td class="name"><code>x</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="attributes"> <optional><br> </td> <td class="default"> <code>0</code> </td> <td class="description last"><p>The initial x coordinate of the positional vector of this vertex.</p></td> </tr> <tr> <td class="name"><code>y</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="attributes"> <optional><br> </td> <td class="default"> <code>0</code> </td> <td class="description last"><p>The initial y coordinate of the positional vector of this vertex.</p></td> </tr> </tbody> </table> </div> <h3 class="subsection-title">Methods</h3> <h4 class="name" id="addChild"><span class="type-signature"></span>addChild<span class="signature">(vertexId)</span><span class="type-signature"></span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line80">line 80</a> </li></ul></dd> </dl> <div class="description"> <p>Add a child vertex id to this vertex.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertexId</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The id of a vertex to be added as a child to this vertex.</p></td> </tr> </tbody> </table> <h4 class="name" id="addRingbondChild"><span class="type-signature"></span>addRingbondChild<span class="signature">(vertexId, ringbondIndex)</span><span class="type-signature"></span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line95">line 95</a> </li></ul></dd> </dl> <div class="description"> <p>Add a child vertex id to this vertex as the second child of the neighbours array, except this vertex is the first vertex of the SMILE string, then it is added as the first. This is used to get the correct ordering of neighbours for parity calculations. If a hydrogen is implicitly attached to the chiral center, insert as the third child.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertexId</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The id of a vertex to be added as a child to this vertex.</p></td> </tr> <tr> <td class="name"><code>ringbondIndex</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The index of the ringbond.</p></td> </tr> </tbody> </table> <h4 class="name" id="clone"><span class="type-signature"></span>clone<span class="signature">()</span><span class="type-signature"> → {<a href="Vertex.html">Vertex</a>}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line166">line 166</a> </li></ul></dd> </dl> <div class="description"> <p>Clones this vertex and returns the clone.</p> </div> <h5>Returns:</h5> <div class="param-desc"> <p>A clone of this vertex.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type"><a href="Vertex.html">Vertex</a></span> </dd> </dl> <h4 class="name" id="equals"><span class="type-signature"></span>equals<span class="signature">(vertex)</span><span class="type-signature"> → {Boolean}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line186">line 186</a> </li></ul></dd> </dl> <div class="description"> <p>Returns true if this vertex and the supplied vertex both have the same id, else returns false.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertex</code></td> <td class="type"> <span class="param-type"><a href="Vertex.html">Vertex</a></span> </td> <td class="description last"><p>The vertex to check.</p></td> </tr> </tbody> </table> <h5>Returns:</h5> <div class="param-desc"> <p>A boolean indicating whether or not the two vertices have the same id.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Boolean</span> </dd> </dl> <h4 class="name" id="getAngle"><span class="type-signature"></span>getAngle<span class="signature">(referenceVector<span class="signature-attributes">opt</span>, returnAsDegrees<span class="signature-attributes">opt</span>)</span><span class="type-signature"> → {Number}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line197">line 197</a> </li></ul></dd> </dl> <div class="description"> <p>Returns the angle of this vertexes positional vector. If a reference vector is supplied in relations to this vector, else in relations to the coordinate system.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th>Attributes</th> <th>Default</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>referenceVector</code></td> <td class="type"> <span class="param-type"><a href="Vector2.html">Vector2</a></span> </td> <td class="attributes"> <optional><br> </td> <td class="default"> <code>null</code> </td> <td class="description last"><p>The reference vector.</p></td> </tr> <tr> <td class="name"><code>returnAsDegrees</code></td> <td class="type"> <span class="param-type">Boolean</span> </td> <td class="attributes"> <optional><br> </td> <td class="default"> <code>false</code> </td> <td class="description last"><p>If true, returns angle in degrees, else in radians.</p></td> </tr> </tbody> </table> <h5>Returns:</h5> <div class="param-desc"> <p>The angle of this vertex.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Number</span> </dd> </dl> <h4 class="name" id="getDrawnNeighbours"><span class="type-signature"></span>getDrawnNeighbours<span class="signature">(vertices)</span><span class="type-signature"> → {Array.<Number>}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line274">line 274</a> </li></ul></dd> </dl> <div class="description"> <p>Returns an array of ids of neighbouring vertices that will be drawn (vertex.value.isDrawn === true).</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertices</code></td> <td class="type"> <span class="param-type">Array.<<a href="Vertex.html">Vertex</a>></span> </td> <td class="description last"><p>An array containing the vertices associated with the current molecule.</p></td> </tr> </tbody> </table> <h5>Returns:</h5> <div class="param-desc"> <p>An array containing the ids of neighbouring vertices that will be drawn.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Array.<Number></span> </dd> </dl> <h4 class="name" id="getNeighbourCount"><span class="type-signature"></span>getNeighbourCount<span class="signature">()</span><span class="type-signature"> → {Number}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line291">line 291</a> </li></ul></dd> </dl> <div class="description"> <p>Returns the number of neighbours of this vertex.</p> </div> <h5>Returns:</h5> <div class="param-desc"> <p>The number of neighbours.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Number</span> </dd> </dl> <h4 class="name" id="getNeighbours"><span class="type-signature"></span>getNeighbours<span class="signature">(vertexId<span class="signature-attributes">opt</span>)</span><span class="type-signature"> → {Array.<Number>}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line252">line 252</a> </li></ul></dd> </dl> <div class="description"> <p>Returns an array of ids of neighbouring vertices.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th>Attributes</th> <th>Default</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertexId</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="attributes"> <optional><br> </td> <td class="default"> <code>null</code> </td> <td class="description last"><p>If a value is supplied, the vertex with this id is excluded from the returned indices.</p></td> </tr> </tbody> </table> <h5>Returns:</h5> <div class="param-desc"> <p>An array containing the ids of neighbouring vertices.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Array.<Number></span> </dd> </dl> <h4 class="name" id="getNextInRing"><span class="type-signature"></span>getNextInRing<span class="signature">(vertices, ringId, previousVertexId)</span><span class="type-signature"> → {Number}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a>, <a href="Vertex.js.html#line327">line 327</a> </li></ul></dd> </dl> <div class="description"> <p>Gets the next vertex in the ring in opposide direction to the supplied vertex id.</p> </div> <h5>Parameters:</h5> <table class="params"> <thead> <tr> <th>Name</th> <th>Type</th> <th class="last">Description</th> </tr> </thead> <tbody> <tr> <td class="name"><code>vertices</code></td> <td class="type"> <span class="param-type">Array.<<a href="Vertex.html">Vertex</a>></span> </td> <td class="description last"><p>The array of vertices for the current molecule.</p></td> </tr> <tr> <td class="name"><code>ringId</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The id of the ring containing this vertex.</p></td> </tr> <tr> <td class="name"><code>previousVertexId</code></td> <td class="type"> <span class="param-type">Number</span> </td> <td class="description last"><p>The id of the previous vertex. The next vertex will be opposite from the vertex with this id as seen from this vertex.</p></td> </tr> </tbody> </table> <h5>Returns:</h5> <div class="param-desc"> <p>The id of the next vertex in the ring.</p> </div> <dl class="param-type"> <dt> Type </dt> <dd> <span class="param-type">Number</span> </dd> </dl> <h4 class="name" id="getSpanningTreeNeighbours"><span class="type-signature"></span>getSpanningTreeNeighbours<span class="signature">(vertexId<span class="signature-attributes">opt</span>)</span><span class="type-signature"> → {Array.<Number>}</span></h4> <dl class="details"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="Vertex.js.html">Vertex.js</a