Uses of Interface
org.jmol.util.Node
Packages that use Node
Package
Description
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
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Uses of Node in org.jmol.api
Methods in org.jmol.api that return NodeMethods in org.jmol.api with parameters of type NodeModifier and TypeMethodDescriptionSmilesMatcherInterface.compileSearchTarget
(Node[] atoms, int atomCount, BS bitSet) int[][]
SmilesMatcherInterface.getCorrelationMaps
(String pattern, Node[] atoms, int ac, BS bsSelected, int flags) void
SmilesMatcherInterface.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) BS[]
SmilesMatcherInterface.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) SmilesMatcherInterface.polyhedronToSmiles
(Node center, int[][] faces, int atomCount, P3[] points, int flags, String details) -
Uses of Node in org.jmol.modelset
Classes in org.jmol.modelset that implement NodeMethods in org.jmol.modelset with parameters of type Node -
Uses of Node in org.jmol.smiles
Classes in org.jmol.smiles that implement NodeModifier and TypeClassDescriptionclass
This class represents an atom in aSmilesMolecule
.Methods in org.jmol.smiles that return NodeModifier and TypeMethodDescriptionNode[]
SmilesStereo.getAlleneAtoms
(boolean haveTopo, SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom pAtom1) Node[]
SmilesAtom.getMatchingAtom()
Returns the matching atom or null.Methods in org.jmol.smiles with parameters of type NodeModifier and TypeMethodDescriptionSmilesMatcher.compileSearchTarget
(Node[] atoms, int atomCount, BS bsSelected) static int
SmilesStereo.getAtropicStereoFlag
(Node[] nodes) SmilesMatcher.getAtropisomerKeys
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) called by SmilesParser to get nn in ^nn- base on match to actual structureint[][]
SmilesMatcher.getCorrelationMaps
(String pattern, Node[] atoms, int atomCount, BS bsSelected, int flags) Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.void
SmilesMatcher.getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> ret, Lst<BS>[] vRings) called by ForceFieldMMFF.setAtomTypes onlyinternal to Jmol -- called by org.jmol.Viewer.getSmilesBS[]
SmilesMatcher.getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) Returns a vector of bitsets indicating which atoms match the pattern.boolean
SmilesAtom.isCrossLinked
(Node node) SmilesMatcher.polyhedronToSmiles
(Node center, int[][] faces, int atomCount, P3[] points, int flags, String details) Generate a topological SMILES string from a set of facesvoid
void
SmilesAtom.setMatchingAtom
(Node jmolAtom, int index) Sets the number of a matching atom in a molecule.boolean
SmilesStereo.setTopoCoordinates
(SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom sAtom2, Node[] cAtoms, boolean isNot) -
Uses of Node in org.jmol.util
Fields in org.jmol.util declared as NodeMethods in org.jmol.util that return NodeModifier and TypeMethodDescriptionstatic Node
Edge.getAtropismNode
(int order, Node a1, boolean isFirst) Methods in org.jmol.util with parameters of type NodeModifier and TypeMethodDescriptionstatic final JmolMolecule[]
JmolMolecule.addMolecule
(JmolMolecule[] molecules, int iMolecule, Node[] atoms, int iAtom, BS bsBranch, int modelIndex, int indexInModel, BS bsExclude) static Node
Edge.getAtropismNode
(int order, Node a1, boolean isFirst) static BS
JmolMolecule.getBranchBitSet
(Node[] atoms, int atomIndex, BS bsToTest, Lst<BS> biobranches, int atomIndexNot, boolean allowCyclic, boolean allowBioResidue) given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.static BS
JmolMolecule.getBranchesForInversion
(Node[] at, int atomIndex, BS bsToTest) static String
JmolMolecule.getMolecularFormulaAtoms
(Node[] atoms, BS bsSelected, float[] wts, boolean isEmpirical) static final JmolMolecule[]
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.boolean
Node.isCrossLinked
(Node node) -
Uses of Node in org.jmol.viewer
Methods in org.jmol.viewer that return NodeMethods in org.jmol.viewer with parameters of type NodeModifier and TypeMethodDescriptionViewer.getSmartsMatchForNodes
(String smarts, Node[] atoms) BS[]
Viewer.getSubstructureSetArrayForNodes
(String pattern, Node[] nodes, int flags)