toxTree.tree.rules.smarts
Class Convertor

java.lang.Object
  extended by toxTree.tree.rules.smarts.Convertor

public class Convertor
extends java.lang.Object

Abstract class that provides convertor procedures to convert CDK classes to JOELib classes and visa versa. Fixed from CDK cConvertor class.

JOELib is a Java implementation of the OELib classes and can be found at: http://joelib.sourceforge.net/.

Author:
egonw, Joerg K. Wegner

Field Summary
static int COORDINATES_2D
           
static int COORDINATES_3D
           
 
Constructor Summary
Convertor()
           
 
Method Summary
static joelib.molecule.JOEAtom convert(org.openscience.cdk.interfaces.IAtom atom)
          Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom class.
static joelib.molecule.JOEAtom convert(org.openscience.cdk.interfaces.IAtom atom, int coordType)
          Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom class.
static joelib.molecule.JOEBond convert(org.openscience.cdk.interfaces.IBond bond)
          Converts an org.openscience.cdk.Bond class into a joelib.molecule.JOEBond class.
static joelib.molecule.JOEMol convert(org.openscience.cdk.interfaces.IMolecule mol)
          Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class.
static joelib.molecule.JOEMol convert(org.openscience.cdk.interfaces.IMolecule mol, int coordType)
          Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class.
static org.openscience.cdk.interfaces.IAtom convert(joelib.molecule.JOEAtom atom)
          Converts an joelib.molecule.JOEAtom class into a org.openscience.cdk.Atom class.
static org.openscience.cdk.interfaces.IBond convert(joelib.molecule.JOEBond bond)
          Converts an joelib.molecule.JOEBond class into a org.openscience.cdk.Bond class.
static org.openscience.cdk.interfaces.IMolecule convert(joelib.molecule.JOEMol mol)
          Converts an joelib.molecule.JOEMol class into a org.openscience.cdk.Molecule class.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

COORDINATES_3D

public static final int COORDINATES_3D
See Also:
Constant Field Values

COORDINATES_2D

public static final int COORDINATES_2D
See Also:
Constant Field Values
Constructor Detail

Convertor

public Convertor()
Method Detail

convert

public static joelib.molecule.JOEAtom convert(org.openscience.cdk.interfaces.IAtom atom)
Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom class. Conversion includes: - atomic number - coordinates

Parameters:
atom - class to be converted
Returns:
converted class in JOELib

convert

public static joelib.molecule.JOEAtom convert(org.openscience.cdk.interfaces.IAtom atom,
                                              int coordType)
Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom class. Conversion includes: - atomic number - coordinates

Parameters:
atom - CDK atom to be converted
coordType - coordinates to use. if -1 this converter uses the available coordinates. If 3D and 2D coordinates are available, the 3D coordinates are used
Returns:
converted JOELib atom
See Also:
COORDINATES_3D, COORDINATES_2D

convert

public static org.openscience.cdk.interfaces.IAtom convert(joelib.molecule.JOEAtom atom)
Converts an joelib.molecule.JOEAtom class into a org.openscience.cdk.Atom class. Conversion includes: - atomic number - coordinates

Parameters:
atom - class to be converted
Returns:
converted class in CDK

convert

public static joelib.molecule.JOEBond convert(org.openscience.cdk.interfaces.IBond bond)
Converts an org.openscience.cdk.Bond class into a joelib.molecule.JOEBond class. Conversion includes: - atoms which it conects - bond order

Parameters:
bond - class to be converted
Returns:
converted class in JOELib

convert

public static org.openscience.cdk.interfaces.IBond convert(joelib.molecule.JOEBond bond)
Converts an joelib.molecule.JOEBond class into a org.openscience.cdk.Bond class. Conversion includes: - atoms which it conects - bond order

Parameters:
bond - class to be converted
Returns:
converted class in CDK

convert

public static joelib.molecule.JOEMol convert(org.openscience.cdk.interfaces.IMolecule mol)
Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class. Conversion includes: - atoms - bonds

Parameters:
mol - molecule to be converted
Returns:
converted JOELib molecule
See Also:
COORDINATES_3D, COORDINATES_2D

convert

public static joelib.molecule.JOEMol convert(org.openscience.cdk.interfaces.IMolecule mol,
                                             int coordType)
Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class. Conversion includes: - atoms - bonds

Parameters:
mol - class to be converted
coordType - coordinates to use. if -1 this converter uses the available coordinates. If 3D and 2D coordinates are available, the 3D coordinates are used
Returns:
converted class in JOELib
See Also:
COORDINATES_3D, COORDINATES_2D

convert

public static org.openscience.cdk.interfaces.IMolecule convert(joelib.molecule.JOEMol mol)
Converts an joelib.molecule.JOEMol class into a org.openscience.cdk.Molecule class. Conversion includes: - atoms - bonds

Parameters:
mol - class to be converted
Returns:
converted class in CDK


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