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N

neighbors() - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Returns neighbors.
neighbors() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
Returns neighbors.
newInstanceWithIDs(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Returns deep copy of the molecule
next() - Method in class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerAtomPermutor
 
nextCandidate() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns the next candidate match.
nextCandidate() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns the next candidate match.
nextCandidate() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns the next candidate match.
nextState(Match) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns a state in which the atoms in match have been added to the current mapping.
nextState(Match) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns a state in which the atoms in match have been added to the current mapping.
nextState(Match) - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns a state in which the atoms in match have been added to the current mapping.
NodeBuilder - Class in org.openscience.smsd.algorithm.vflib.builder
Class for building/storing nodes (atoms) in the graph with atom query capabilities.
NodeBuilder(AtomMatcher) - Constructor for class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Construct a node for a query atom
nodes() - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns nodes of the query.
nodes() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns nodes of the query.
NonterminalLigand<A> - Class in uk.ac.ebi.centres.ligand
 
NonterminalLigand(MutableDescriptor, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.NonterminalLigand
 
NonterminalLigand(ConnectionProvider<A>, MutableDescriptor, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.NonterminalLigand
 
NonterminalLigand(ConnectionProvider<A>, MutableDescriptor, Set<A>, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.NonterminalLigand
 
NonterminalLigand(MutableDescriptor, Set<A>, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.NonterminalLigand
 
norm1() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
One norm
norm2() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Two norm
norm2() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Two norm
normalize(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Normalizes the vectors of this matrix.
normF() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Frobenius norm
normInf() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Infinity norm
not_null(Object) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.FingerprintSubset
Helper function to test for a null object and throw an exception if one is found.
numberOfAtoms() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
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