org.openscience.cdk.pharmacophore
Class PharmacophoreQuery

java.lang.Object
  org.openscience.cdk.isomorphism.matchers.QueryChemObject
      org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
          org.openscience.cdk.pharmacophore.PharmacophoreQuery

All Implemented Interfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IQueryAtomContainer

@TestClass(value="org.openscience.cdk.pharmacophore.PharmacophoreQueryTest")
public class PharmacophoreQuery
extends QueryAtomContainer

Represents a colleciton of pharmacophore groups and constraints.

This extends QueryAtomContainer since we need to be able to support things such as exclusion volumes, which cannot (easily) be represented as atom or bond analogs.

Author:

Rajarshi Guha

Keywords:

pharmacophore, 3D isomorphism

Belongs to CDK module:

pcore

Source code:

cdk-1.4.x

Constructor Summary

PharmacophoreQuery()

Method Summary

String

toString() String representation of this query.

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, clone, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

addListener, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, matches, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Constructor Detail

PharmacophoreQuery

public PharmacophoreQuery()

Method Detail

toString

@TestMethod(value="testToString")
public String toString()

String representation of this query.

Specified by:

toString in interface IChemObject

Overrides:

toString in class QueryAtomContainer

Returns:

string representation of this query