public class RBlastMoleculeSignature extends BaseMoleculeSignature
atomContainer
Constructor and Description |
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RBlastMoleculeSignature(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
Make an object that acts as a factory for atom signatures and can also
produce molecule signatures.
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Modifier and Type | Method and Description |
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int |
getAtomCount() |
RBlastAtomSignature |
getAtomSignature(int atomIndex) |
RBlastAtomSignature |
getAtomSignature(int atomIndex,
int height) |
org.openscience.cdk.interfaces.IAtomContainer |
getFragment(int atomIndex,
int height)
Get a fragment of the underlying molecule.
|
java.lang.String |
getMoleculeCanonicalSignatureString()
Get the canonical signature string for the entire molecule.
|
java.lang.String |
getSignatureStringForAtom(int atomIndex)
Get the canonical signature string for a particular atom.
|
java.lang.String |
getSignatureStringForAtom(int atomIndex,
int height) |
java.lang.String |
getSmilesForAtomSignature(int atomIndex,
int height) |
java.lang.String |
getSmilesForAtomSignature(int atomIndex,
int height,
ICanonicalMoleculeLabeller labeller)
Get a fragment as a smiles with the atoms ordered by canonical signature.
|
boolean |
isBondSensitive() |
boolean |
isUseAromatics() |
boolean |
isUseCharge() |
org.openscience.cdk.interfaces.IAtomContainer |
makeMoleculeFromSignature(java.lang.String signatureString)
Convert a signature string into a molecule.
|
void |
setBondSensitive(boolean isBondSensitive) |
void |
setUseAromatics(boolean useAromatics) |
void |
setUseCharge(boolean useCharge) |
getVertexCount, signatureForVertex, signatureStringForVertex, signatureStringForVertex
getCanonicalLabels, getGraphSignature, getHeight, getMaximalSignature, getMinimalSignature, getSortedSignatures, getSymmetryClasses, getSymmetryClasses, getVertexSignatures, getVertexSignatureStrings, isCanonicallyLabelled, reconstructCanonicalEdgeString, reconstructCanonicalGraph, toCanonicalString, toFullString
public RBlastMoleculeSignature(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- public int getAtomCount()
public boolean isUseAromatics()
public void setUseAromatics(boolean useAromatics)
useAromatics
- if true, will use aromatic symbolspublic boolean isUseCharge()
public void setUseCharge(boolean useCharge)
useCharge
- if true, charge symbols will be outputpublic boolean isBondSensitive()
public void setBondSensitive(boolean isBondSensitive)
isBondSensitive
- if true, bond order symbols will be usedpublic java.lang.String getMoleculeCanonicalSignatureString()
public java.lang.String getSignatureStringForAtom(int atomIndex)
atomIndex
- public java.lang.String getSignatureStringForAtom(int atomIndex, int height)
atomIndex
- height
- public RBlastAtomSignature getAtomSignature(int atomIndex)
atomIndex
- public RBlastAtomSignature getAtomSignature(int atomIndex, int height)
atomIndex
- height
- public java.lang.String getSmilesForAtomSignature(int atomIndex, int height)
atomIndex
- height
- public java.lang.String getSmilesForAtomSignature(int atomIndex, int height, ICanonicalMoleculeLabeller labeller)
atomIndex
- height
- labeller
- public org.openscience.cdk.interfaces.IAtomContainer getFragment(int atomIndex, int height)
atomIndex
- height
- public org.openscience.cdk.interfaces.IAtomContainer makeMoleculeFromSignature(java.lang.String signatureString)
signatureString
-