Package org.openscience.cdk.fingerprint

Class FingerprinterTool

java.lang.Object

org.openscience.cdk.fingerprint.FingerprinterTool

public class FingerprinterTool
extends Object

Tool with helper methods for IFingerprint.

Author:

steinbeck

Source code:

main

Belongs to CDK module:

standard

Keywords:

fingerprint

Created on:

2002-02-24

Constructor Summary

Constructors

Constructor	Description
FingerprinterTool()

Method Summary

Modifier and Type	Method	Description
static Set<Integer>	differences(BitSet s, BitSet t)	List all differences between the two bit vectors.
static boolean	isSubset(BitSet bs1, BitSet bs2)	Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
static List<Integer>	listDifferences(BitSet bs1, BitSet bs2)	This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger.
static IBitFingerprint	makeBitFingerprint(Map<String,Integer> features)	Convert a mapping of features and their counts to a 1024-bit binary fingerprint.
static IBitFingerprint	makeBitFingerprint(Map<String,Integer> features, int len)	Convert a mapping of features and their counts to a binary fingerprint.
static IBitFingerprint	makeBitFingerprint(Map<String,Integer> features, int len, int bits)	Convert a mapping of features and their counts to a binary fingerprint.
static ICountFingerprint	makeCountFingerprint(Map<String,Integer> features)	Wrap a mapping of features and their counts to a continuous (count based) fingerprint.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FingerprinterTool

public FingerprinterTool()

Method Detail

isSubset

public static boolean isSubset(BitSet bs1,
                               BitSet bs2)

Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1. If so, the molecular structure from which bs2 was generated is a possible substructure of bs1.

Example:

  Molecule mol = MoleculeFactory.makeIndole();
  BitSet bs = Fingerprinter.getBitFingerprint(mol);
  Molecule frag1 = MoleculeFactory.makePyrrole();
  BitSet bs1 = Fingerprinter.getBitFingerprint(frag1);
  if (Fingerprinter.isSubset(bs, bs1)) {
      System.out.println("Pyrrole is subset of Indole.");
  }
  

Parameters:

bs1 - The reference BitSet

bs2 - The BitSet which is compared with bs1

Returns:

True, if bs2 is a subset of bs1

Keywords:

substructure search

listDifferences

public static List<Integer> listDifferences(BitSet bs1,
                                            BitSet bs2)

This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger. See. differences(java.util.BitSet, java.util.BitSet) for a method to list all differences, including those missing present in bs2 but not bs1.

Parameters:

bs1 - First bitset

bs2 - Second bitset

Returns:

An arrayList of Integers

See Also:

differences(java.util.BitSet, java.util.BitSet)

differences

public static Set<Integer> differences(BitSet s,
                                       BitSet t)

List all differences between the two bit vectors. Unlike listDifferences(java.util.BitSet, java.util.BitSet) which only list those which are set in s but not in t.

Parameters:

s - a bit vector

t - another bit vector

Returns:

all differences between s and t

makeBitFingerprint

public static IBitFingerprint makeBitFingerprint(Map<String,Integer> features)

Convert a mapping of features and their counts to a 1024-bit binary fingerprint. A single bit is set for each pattern.

Parameters:

features - features to include

Returns:

the continuous fingerprint

See Also:

makeBitFingerprint(java.util.Map, int, int)

makeBitFingerprint

public static IBitFingerprint makeBitFingerprint(Map<String,Integer> features,
                                                 int len)

Convert a mapping of features and their counts to a binary fingerprint. A single bit is set for each pattern.

Parameters:

features - features to include

len - fingerprint length

Returns:

the continuous fingerprint

See Also:

makeBitFingerprint(java.util.Map, int, int)

makeBitFingerprint

public static IBitFingerprint makeBitFingerprint(Map<String,Integer> features,
                                                 int len,
                                                 int bits)

Convert a mapping of features and their counts to a binary fingerprint. Each feature can set 1-n hashes, the amount is modified by the bits operand.

Parameters:

features - features to include

len - fingerprint length

bits - number of bits to set for each pattern

Returns:

the continuous fingerprint

makeCountFingerprint

public static ICountFingerprint makeCountFingerprint(Map<String,Integer> features)

Wrap a mapping of features and their counts to a continuous (count based) fingerprint.

Parameters:

features - features to include

Returns:

the continuous fingerprint