org.openscience.cdk.fingerprint

Class FingerprinterTool

java.lang.Object

org.openscience.cdk.fingerprint.FingerprinterTool

@TestClass(value="org.openscience.cdk.fingerprint.FingerprinterToolTest")
public class FingerprinterTool
extends Object

Tool with helper methods for IFingerprint.

Author:

steinbeck

Keywords:

fingerprint

Created on:

2002-02-24

Belongs to CDK module:

standard

Source code:

master

Constructor Summary

Constructors

Constructor and Description
FingerprinterTool()

Method Summary

Methods

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

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

Constructor Detail

FingerprinterTool

public FingerprinterTool()

Method Detail

isSubset

@TestMethod(value="testIsSubset_BitSet_BitSet")
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

@TestMethod(value="testListDifferences_BitSet_BitSet")
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

@TestMethod(value="testDifferences,testDifferences_Scenario")
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