Class PharmacophoreQueryAngleBond
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.ElectronContainer
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- org.openscience.cdk.Bond
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- org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
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- All Implemented Interfaces:
Serializable
,Cloneable
,IBond
,ICDKObject
,IChemObject
,IElectronContainer
,IQueryBond
public class PharmacophoreQueryAngleBond extends Bond implements IQueryBond
Represents a pharmacophore query angle constraint.- Author:
- Rajarshi Guha
- See Also:
PharmacophoreQueryAtom
,PharmacophoreMatcher
,QueryAtomContainer
, Serialized Form- Source code:
- main
- Belongs to CDK module:
- pcore
- Keywords:
- pharmacophore, 3D isomorphism
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond
IBond.Display, IBond.Order, IBond.Stereo
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Field Summary
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Fields inherited from class org.openscience.cdk.ElectronContainer
electronCount
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Constructor Summary
Constructors Constructor Description PharmacophoreQueryAngleBond()
PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double angle)
Create a query angle constraint between three query groups.PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double lower, double upper)
Create a query angle constraint between three query groups.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getLower()
double
getUpper()
boolean
matches(IBond bond)
Checks whether the query angle constraint matches a target distance.String
toString()
String representation of an angle constraint.-
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
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Methods inherited from class org.openscience.cdk.ElectronContainer
getElectronCount, setElectronCount
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Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, clear, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IBond
atoms, clone, compare, contains, get2DCenter, get3DCenter, getAtom, getAtomCount, getBegin, getConnectedAtom, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getEnd, getIndex, getOrder, getOther, getStereo, isAromatic, isConnectedTo, isInRing, setAtom, setAtoms, setDisplay, setIsAromatic, setIsInRing, setOrder, setStereo
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from interface org.openscience.cdk.interfaces.IElectronContainer
getElectronCount, setElectronCount
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Constructor Detail
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PharmacophoreQueryAngleBond
public PharmacophoreQueryAngleBond()
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PharmacophoreQueryAngleBond
public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double lower, double upper)
Create a query angle constraint between three query groups. Note that the angle is only considered upto 2 decimal places.- Parameters:
atom1
- The first pharmacophore groupatom2
- The second pharmacophore groupatom3
- The third pharmacophore grouplower
- The lower bound of the angle between the three groupsupper
- The upper bound of the angle between the three groups
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PharmacophoreQueryAngleBond
public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double angle)
Create a query angle constraint between three query groups. This constructor allows you to define a query angle constraint such that the angle between the three query groups is exact (i.e., not a range). Note that the angle is only considered upto 2 decimal places.- Parameters:
atom1
- The first pharmacophore groupatom2
- The second pharmacophore groupatom3
- The third pharmacophore groupangle
- The exact angle between the two groups
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Method Detail
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matches
public boolean matches(IBond bond)
Checks whether the query angle constraint matches a target distance. This method checks whether a query constraint is satisfied by an observed angle (represented by aPharmacophoreAngleBond
in the target molecule. Note that angles are compared upto 2 decimal places.- Specified by:
matches
in interfaceIQueryBond
- Parameters:
bond
- The angle relationship in a target molecule- Returns:
- true if the target angle lies within the range of the query constraint
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getUpper
public double getUpper()
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getLower
public double getLower()
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toString
public String toString()
String representation of an angle constraint.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classBond
- Returns:
- String representation of and angle constraint
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