IAtomContainer. Fingerprints are one-dimensional bit arrays, where bits are set according to a the occurrence of a particular structural feature (See for example the Daylight inc. theory manual for more information). Fingerprints are a means for determining the similarity of chemical structures, some fingerprints (not this one) allow database pre-screening for substructure searches.
A fingerprint is generated for an AtomContainer with this code: It is recommended to use atomtyped container before generating the fingerprints. For example: AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer); AtomContainer molecule = new AtomContainer(); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer); IFingerprinter fingerprinter = new ShortestPathFingerprinter(); IBitFingerprint fingerprint = fingerprinter.getFingerprint(molecule); fingerprint.fingerprintLength(); // returns 1024 by default fingerprint.length(); // returns the highest set bit
The FingerPrinter calculates fingerprint based on the Shortest Paths between two atoms. It also takes into account ring system, charges etc while generating a fingerprint.
The FingerPrinter assumes that hydrogens are explicitly given! Furthermore, if pseudo atoms or atoms with
malformed symbols are present, their atomic number is taken as one more than the last element currently supported in
Important! this fingerprint can not be used for substructure screening.
Field SummaryModifier and TypeFieldDescription
static final intThe default length of created fingerprints.
Method SummaryModifier and TypeMethodDescriptionGenerates a shortest path based BitSet fingerprint for the given AtomContainer.Returns the raw representation of the fingerprint for the given IAtomContainer.
getSize()Returns the size (or length) of the fingerprint.
Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter
getFingerprint, getParameters, getVersionDescription
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
DEFAULT_SIZEpublic static final int DEFAULT_SIZEThe default length of created fingerprints.
- See Also:
ShortestPathFingerprinterpublic ShortestPathFingerprinter()Creates a fingerprint generator of length
(int fingerprintLength)Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.
fingerprintLength- The desired fingerprintLength of the fingerprint
getBitFingerprintGenerates a shortest path based BitSet fingerprint for the given AtomContainer.
getRawFingerprintReturns the raw representation of the fingerprint for the given IAtomContainer. The raw representation contains counts as well as the key strings.
getSizepublic int getSize()Description copied from interface:
IFingerprinterReturns the size (or length) of the fingerprint.
getCountFingerprintDescription copied from interface:
- Specified by:
IAtomContainerfor which the fingerprint should be calculated.
- the count fingerprint
CDKException- if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.