- 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
-