Package | Description |
---|---|
uk.ac.ebi.reactionblast.signature | |
uk.ac.ebi.reactionblast.tools.bulk | |
uk.ac.ebi.reactionblast.tools.labelling |
Modifier and Type | Class and Description |
---|---|
class |
FixedLabeller |
class |
IdentityLabellingAdaptor |
class |
RBlastAtomSignatureLabellingAdaptor |
class |
RBlastMoleculeSignatureLabellingAdaptor |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
RBlastMoleculeSignature.getSmilesForAtomSignature(int atomIndex,
int height,
ICanonicalMoleculeLabeller labeller)
Get a fragment as a smiles with the atoms ordered by canonical signature.
|
Constructor and Description |
---|
RBlastSmilesGenerator(boolean useAromaticityFlag,
ICanonicalMoleculeLabeller labeller) |
Constructor and Description |
---|
MoleculeCanonicalizationTransformation(ICanonicalMoleculeLabeller labeller) |
Modifier and Type | Class and Description |
---|---|
class |
InChiMoleculeLabeller
Canonically labels (permutes) an atom container according to the SMILES
canonicalization algorithm.
|
class |
RBlastMoleculeLabeller |
class |
SignatureMoleculeLabeller
Canonically labels (permutes) an atom container according to the signature
canonicalization algorithm.
|
class |
SmilesMoleculeLabeller
Canonically labels (permutes) an atom container according to the SMILES
canonicalization algorithm.
|
Modifier and Type | Method and Description |
---|---|
protected org.openscience.cdk.interfaces.IAtomContainerSet |
AbstractReactionLabeller.canoniseAtomContainerSet(org.openscience.cdk.interfaces.IAtomContainerSet moleculeSet,
ICanonicalMoleculeLabeller labeller,
java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap) |
org.openscience.cdk.interfaces.IReaction |
AbstractReactionLabeller.labelReaction(org.openscience.cdk.interfaces.IReaction reaction,
ICanonicalMoleculeLabeller labeller) |