Index (cdk-fingerprint 2.9 API)

A C D E F G H I K L M O P S T
All Classes All Packages

A

AtomPairs2DFingerprinter - Class in org.openscience.cdk.fingerprint: Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.
AtomPairs2DFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
atoms - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP

C

calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates the continuous Tanimoto coefficient for two real valued vectors.
calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two bit sets.
calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.LingoSimilarity: Evaluate the LINGO similarity between two key,value sty;e fingerprints.
calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
calculate(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two IBitFingerprint.
calculate(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
calculate(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the fingerprints for the given IAtomContainer, and stores them for subsequent retrieval.
calculate(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment: Evaluate the 3D similarity between two molecules.
canonicalizeAtoms(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
CircularFingerprinter - Class in org.openscience.cdk.fingerprint: Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6 fingerprints, which are partially described by Rogers et al.
CircularFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Default constructor: uses the ECFP6 type.
CircularFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
CircularFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
CircularFingerprinter.FP - Class in org.openscience.cdk.fingerprint
CLASS_ECFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
compare(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator

D

decode(String) - Static method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: The default length of created fingerprints.
DistanceMoment - Class in org.openscience.cdk.similarity: Fast similarity measure for 3D structures.
DistanceMoment() - Constructor for class org.openscience.cdk.similarity.DistanceMoment

E

EMPTY_FINGERPRINTS_PROVIDED - Static variable in class org.openscience.cdk.similarity.Tanimoto
EStateFingerprinter - Class in org.openscience.cdk.fingerprint: This fingerprinter generates 79 bit fingerprints using the E-State fragments.
EStateFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.EStateFingerprinter
EStateFragments - Class in org.openscience.cdk.config.fragments: A class representing the 79 E-state atom types in terms of SMARTS.
EStateFragments() - Constructor for class org.openscience.cdk.config.fragments.EStateFragments
ExtendedFingerprinter - Class in org.openscience.cdk.fingerprint: Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional (25) bits describing ring features and isotopic masses.
ExtendedFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
ExtendedFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter
ExtendedFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

F

FP(int, int, int[]) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
FP_SIZE - Static variable in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Number of bits in this fingerprint.

G

generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment: Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the circular fingerprint for the given IAtomContainer, and folds the result into a single bitset (see getSize()).
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Calculate 881 bit Pubchem fingerprint for a molecule.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Generates a shortest path based BitSet fingerprint for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
getBitFingerprint(IAtomContainer, IRingSet, List<IRingSet>) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getCountableMACCSSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets: Subset of the MACCS fingerprint definitions.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the circular fingerprint for the given IAtomContainer, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getFingerprintAsBytes() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns the fingerprint generated for a molecule as a byte[].
getFP(int) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the requested fingerprint.
getFPCount() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the number of fingerprints generated.
getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets: The functional groups.
getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments: Get the fragment names.
getParameters() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
getPatterns() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Invalid: it is not appropriate to convert the integer hash codes into strings.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the extent of the folded fingerprints.
getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Get the size of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments: Get the SMARTS patterns.
getSubstructure(int) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Retrieves the SMARTS representation of a substructure for a given bit in the fingerprint.
getVersionDescription() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

H

hashCode - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP

I

iteration - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP

K

KlekotaRothFingerprinter - Class in org.openscience.cdk.fingerprint: SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity [Klekota, Justin and Roth, Frederick P.. Bioinformatics. 2008. 24].
KlekotaRothFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.KlekotaRothFingerprinter

L

LingoSimilarity - Class in org.openscience.cdk.similarity: A class to evaluate the similarity between two LINGO's as described in [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].

M

MACCSFingerprinter - Class in org.openscience.cdk.fingerprint: This fingerprinter generates 166 bit MACCS keys.
MACCSFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
MACCSFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
method1(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Calculates Tanimoto distance for two count fingerprints using method 1.
method2(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Calculates Tanimoto distance for two count fingerprints using method 2 [J.A. Grant, J.A. Haigh, B.T. Pickup, A. Nicholls and R.A. Sayle. J. Chem. Inf. Model.. 2006. 46].

O

org.openscience.cdk.config.fragments - package org.openscience.cdk.config.fragments
org.openscience.cdk.fingerprint - package org.openscience.cdk.fingerprint
org.openscience.cdk.similarity - package org.openscience.cdk.similarity

P

paths() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker: Access a set of all shortest paths.
PubchemFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a Pubchem fingerprint for a molecule.
PubchemFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.PubchemFingerprinter
PubchemFingerprinter(IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.fingerprint.PubchemFingerprinter

S

setHashPseudoAtoms(boolean) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Set the hashPseudoAtoms for the base daylight/path fingerprint.
setPathLimit(int) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Set the pathLimit for the base daylight/path fingerprint.
setPerceiveStereo(boolean) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.
ShortestPathFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given IAtomContainer.
ShortestPathFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE
ShortestPathFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.
ShortestPathWalker - Class in org.openscience.cdk.fingerprint
ShortestPathWalker(IAtomContainer) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathWalker: Create a new shortest path walker for a given container.
SimpleAtomCanonicalizer - Class in org.openscience.cdk.fingerprint: This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomCanonicalizer() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
SimpleAtomComparator - Class in org.openscience.cdk.fingerprint: This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomComparator() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomComparator
StandardSubstructureSets - Class in org.openscience.cdk.fingerprint: Default sets of atom containers aimed for use with the substructure.
StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets
SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint: IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.
SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Set up the fingerprinter to use the fragments from StandardSubstructureSets.
SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Set up the fingerprinter to use a user-defined set of fragments.

T

Tanimoto - Class in org.openscience.cdk.similarity: Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors.
toString() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker

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