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org::openscience::cdk::pharmacophore::PharmacophoreQueryAtom Class Reference

Inheritance diagram for org::openscience::cdk::pharmacophore::PharmacophoreQueryAtom:
Inheritance graph
Collaboration diagram for org::openscience::cdk::pharmacophore::PharmacophoreQueryAtom:
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List of all members.

Public Types

enum  Hybridization {
  S, SP1, SP2, SP3,
  PLANAR3, SP3D1, SP3D2, SP3D3,
  SP3D4, SP3D5

Public Member Functions

void addListener (IChemObjectListener col)
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
Integer getAtomicNumber ()
String getAtomTypeName ()
Double getBondOrderSum ()
IChemObjectBuilder getBuilder ()
Double getCharge ()
Double getCovalentRadius ()
Double getExactMass ()
boolean getFlag (int flag_type)
boolean[] getFlags ()
Integer getFormalCharge ()
Integer getFormalNeighbourCount ()
javax.vecmath.Point3d getFractionalPoint3d ()
IAtomType.Hybridization getHybridization ()
Integer getHydrogenCount ()
String getID ()
int getListenerCount ()
Integer getMassNumber ()
IBond.Order getMaxBondOrder ()
Double getNaturalAbundance ()
boolean getNotification ()
javax.vecmath.Point2d getPoint2d ()
javax.vecmath.Point3d getPoint3d ()
Map< Object, Object > getProperties ()
Object getProperty (Object description)
String getSmarts ()
Integer getStereoParity ()
String getSymbol ()
Integer getValency ()
boolean matches (IAtom atom)
void notifyChanged (IChemObjectChangeEvent evt)
void notifyChanged ()
 PharmacophoreQueryAtom (String symbol, String smarts)
void removeListener (IChemObjectListener col)
void removeProperty (Object description)
void setAtomicNumber (Integer atomicNumber)
void setAtomTypeName (String identifier)
void setBondOrderSum (Double bondOrderSum)
void setCharge (Double charge)
void setCovalentRadius (Double radius)
void setExactMass (Double exactMass)
void setFlag (int flag_type, boolean flag_value)
void setFlags (boolean[] flagsNew)
void setFormalCharge (Integer charge)
void setFormalNeighbourCount (Integer count)
void setFractionalPoint3d (javax.vecmath.Point3d point3d)
void setFractionalPoint3d (Point3d point3d)
void setHybridization (IAtomType.Hybridization hybridization)
void setHybridization (Hybridization hybridization)
void setHydrogenCount (Integer hydrogenCount)
void setID (String identifier)
void setMassNumber (Integer massNumber)
void setMaxBondOrder (IBond.Order maxBondOrder)
void setNaturalAbundance (Double naturalAbundance)
void setNotification (boolean bool)
void setOperator (String ID)
void setPoint2d (javax.vecmath.Point2d point2d)
void setPoint2d (Point2d point2d)
void setPoint3d (Point3d point3d)
void setPoint3d (javax.vecmath.Point3d point3d)
void setProperties (Map< Object, Object > properties)
void setProperty (Object description, Object property)
void setStereoParity (Integer stereoParity)
void setSymbol (String symbol)
void setValency (Integer valency)
Object shallowCopy ()
String toString ()

Public Attributes

Double exactMass
Double naturalAbundance

Protected Attributes

Integer atomicNumber = (Integer) CDKConstants.UNSET
Double charge = (Double) CDKConstants.UNSET
Integer electronValency = (Integer) CDKConstants.UNSET
Integer formalCharge = (Integer) CDKConstants.UNSET
Integer formalNeighbourCount = (Integer) CDKConstants.UNSET
javax.vecmath.Point3d fractionalPoint3d = (Point3d) CDKConstants.UNSET
IAtomType.Hybridization hybridization = (Hybridization) CDKConstants.UNSET
Integer hydrogenCount = (Integer) CDKConstants.UNSET
javax.vecmath.Point2d point2d = (Point2d) CDKConstants.UNSET
javax.vecmath.Point3d point3d = (Point3d) CDKConstants.UNSET
Integer stereoParity = (Integer) CDKConstants.UNSET
String symbol

Package Attributes

Double bondOrderSum = (Double) CDKConstants.UNSET
Double covalentRadius = (Double) CDKConstants.UNSET
IBond.Order maxBondOrder = null

Private Attributes

String smarts

Detailed Description

Represents a query pharmacophore group.

This class is meant to be used to construct pharmacophore queries in conjunction with org.openscience.cdk.pharmacophore.PharmacophoreQueryBond and an org.openscience.cdk.isomorphism.matchers.QueryAtomContainer.

Rajarshi Guha .module pcore .githash .keyword pharmacophore .keyword 3D isomorphism
See also:

Definition at line 49 of file PharmacophoreQueryAtom.java.

The documentation for this class was generated from the following file:

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