public class ExtendedFingerprinter extends Fingerprinter implements IFingerprinter
IAtomContainer
, that
extends the Fingerprinter
with additional bits describing ring
features.Fingerprinter
DEFAULT_SEARCH_DEPTH, DEFAULT_SIZE
Constructor and Description |
---|
ExtendedFingerprinter()
Creates a fingerprint generator of length
DEFAULT_SIZE
and with a search depth of DEFAULT_SEARCH_DEPTH . |
ExtendedFingerprinter(int size) |
ExtendedFingerprinter(int size,
int searchDepth)
Constructs a fingerprint generator that creates fingerprints of
the given size, using a generation algorithm with the given search
depth.
|
Modifier and Type | Method and Description |
---|---|
IBitFingerprint |
getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
IBitFingerprint |
getBitFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
ICountFingerprint |
getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer . |
Map<String,Integer> |
getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
int |
getSize()
Returns the size (or length) of the fingerprint.
|
encodePaths, findPathes, getBitFingerprint, getBondSymbol, getParameters, getSearchDepth, setHashPseudoAtoms, setPathLimit
getFingerprint, getVersionDescription
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFingerprint, getVersionDescription
public ExtendedFingerprinter()
DEFAULT_SIZE
and with a search depth of DEFAULT_SEARCH_DEPTH
.public ExtendedFingerprinter(int size)
public ExtendedFingerprinter(int size, int searchDepth)
size
- The desired size of the fingerprintsearchDepth
- The desired depth of searchpublic IBitFingerprint getBitFingerprint(IAtomContainer container) throws CDKException
getBitFingerprint
in interface IFingerprinter
getBitFingerprint
in class Fingerprinter
container
- The AtomContainer for which a Fingerprint is generatedIAtomContainer
.CDKException
- may be thrown if there is an error during aromaticity detection
or (for key based fingerprints) if there is a SMARTS parsing errorpublic Map<String,Integer> getRawFingerprint(IAtomContainer iAtomContainer) throws CDKException
getRawFingerprint
in interface IFingerprinter
getRawFingerprint
in class Fingerprinter
iAtomContainer
- IAtomContainer for which the fingerprint should be calculated.CDKException
public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, List<IRingSet> rslist) throws CDKException
atomContainer
- The AtomContainer for which a Fingerprint is
generatedringSet
- An SSSR RingSet of ac (if not available, use
getExtendedFingerprint(AtomContainer ac),
which does the calculation)rslist
- A list of all ring systems in acCDKException
- for example if input can not be cloned.public int getSize()
getSize
in interface IFingerprinter
getSize
in class Fingerprinter
public ICountFingerprint getCountFingerprint(IAtomContainer container) throws CDKException
IAtomContainer
.getCountFingerprint
in interface IFingerprinter
getCountFingerprint
in class Fingerprinter
container
- IAtomContainer
for which the fingerprint should be calculated.CDKException
- if there is an error during aromaticity detection
or (for key based fingerprints) if there is a SMARTS parsing error.Copyright © 2017. All Rights Reserved.