public class HybridizationFingerprinter extends Fingerprinter implements IFingerprinter
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 allow for a fast screening step to exclude candidates for a substructure search in a database. They are also a means for determining the similarity of chemical structures.
A fingerprint is generated for an AtomContainer with this code:
Molecule molecule = new Molecule(); IFingerprinter fingerprinter = new HybridizationFingerprinter(); BitSet fingerprint = fingerprinter.getFingerprint(molecule); fingerprint.size(); // returns 1024 by default fingerprint.length(); // returns the highest set bit
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
Fingerprinter, this fingerprinter does not take into
account aromaticity. Instead, it takes into account SP2
|Constructor and Description|
Creates a fingerprint generator of length
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|
Gets the bond Symbol attribute of the Fingerprinter class.
encodePaths, findPathes, getBitFingerprint, getBitFingerprint, getCountFingerprint, getParameters, getRawFingerprint, getSearchDepth, getSize, setHashPseudoAtoms, setPathLimit
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getBitFingerprint, getCountFingerprint, getFingerprint, getRawFingerprint, getSize, getVersionDescription
DEFAULT_SIZEand with a search depth of
public HybridizationFingerprinter(int size)
public HybridizationFingerprinter(int size, int searchDepth)
size- The desired size of the fingerprint
searchDepth- The desired depth of search
protected String getBondSymbol(IBond bond)
bond- Description of the Parameter
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