Class PharmacophoreQueryBond
java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.ElectronContainer
org.openscience.cdk.Bond
org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
- All Implemented Interfaces:
Serializable
,Cloneable
,IBond
,ICDKObject
,IChemObject
,IElectronContainer
,IQueryBond
Represents a pharmacophore query distance constraint.
- Author:
- Rajarshi Guha
- See Also:
- Source code:
- main
- Belongs to CDK module:
- pcore
- Keywords:
- pharmacophore, 3D isomorphism
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond
IBond.Display, IBond.Order, IBond.Stereo
-
Field Summary
Fields inherited from class org.openscience.cdk.ElectronContainer
electronCount
-
Constructor Summary
ConstructorsConstructorDescriptionPharmacophoreQueryBond
(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double distance) Create a query distance constraint between two query groups.PharmacophoreQueryBond
(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double lower, double upper) Create a query distance constraint between two query groups. -
Method Summary
Methods inherited from class org.openscience.cdk.Bond
atoms, clone, compare, contains, equals, get2DCenter, get3DCenter, getAtom, getAtomCount, getBegin, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getEnd, getIndex, getOrder, getOther, getStereo, hashCode, isAromatic, isConnectedTo, isInRing, setAtom, setAtoms, setDisplay, setIsAromatic, setIsInRing, setOrder, setStereo
Methods inherited from class org.openscience.cdk.ElectronContainer
getElectronCount, setElectronCount
Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.openscience.cdk.interfaces.IBond
atoms, clone, compare, contains, get2DCenter, get3DCenter, getAtom, getAtomCount, getBegin, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getEnd, getIndex, getOrder, getOther, getStereo, isAromatic, isConnectedTo, isInRing, setAtom, setAtoms, setDisplay, setIsAromatic, setIsInRing, setOrder, setStereo
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
Methods inherited from interface org.openscience.cdk.interfaces.IElectronContainer
getElectronCount, setElectronCount
-
Constructor Details
-
PharmacophoreQueryBond
public PharmacophoreQueryBond() -
PharmacophoreQueryBond
public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double lower, double upper) Create a query distance constraint between two query groups. Note that the distance is only considered upto 2 decimal places.- Parameters:
atom1
- The first pharmacophore groupatom2
- The second pharmacophore grouplower
- The lower bound of the distance between the two groupsupper
- The upper bound of the distance between the two groups- See Also:
-
PharmacophoreQueryBond
public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double distance) Create a query distance constraint between two query groups. This constructor allows you to define a query distance constraint such that the distance between the two query groups is exact (i.e., not a range). Note that the distance is only considered upto 2 decimal places.- Parameters:
atom1
- The first pharmacophore groupatom2
- The second pharmacophore groupdistance
- The exact distance between the two groups- See Also:
-
-
Method Details
-
matches
Checks whether the query distance constraint matches a target distance. This method checks whether a query constraint is satisfied by an observed distance (represented by aPharmacophoreBond
in the target molecule. Note that distance are compared upto 2 decimal places.- Specified by:
matches
in interfaceIQueryBond
- Parameters:
bond
- The distance relationship in a target molecule- Returns:
- true if the target distance lies within the range of the query constraint
-
getUpper
public double getUpper() -
getLower
public double getLower() -
toString
String representation of a distance constraint.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classBond
- Returns:
- String representation of a distance constraint
-