Package 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

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

Source code:

main

Belongs to CDK module:

pcore

Keywords:

pharmacophore, 3D isomorphism

Field Summary

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

atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors

Constructor	Description
PharmacophoreQuery()

Method Summary

Modifier and Type	Method	Description
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, create, create, 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, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements

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

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

Methods inherited from class java.lang.Object

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

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

getBuilder

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

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

Constructor Detail

PharmacophoreQuery

public PharmacophoreQuery()

Method Detail

toString

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