toxTree.tree.rules.smarts

Class Convertor

java.lang.Object

toxTree.tree.rules.smarts.Convertor

public class Convertor
extends 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

Fields

Modifier and Type	Field and Description
static int	COORDINATES_2D
static int	COORDINATES_3D

Constructor Summary

Constructors

Constructor and Description
Convertor()

Method Summary

Modifier and Type	Method and Description
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.JOEMol	convert(org.openscience.cdk.interfaces.IAtomContainer mol) Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class.
static joelib.molecule.JOEMol	convert(org.openscience.cdk.interfaces.IAtomContainer mol, int coordType) Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol 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 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.IAtomContainer	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.IAtomContainer 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.IAtomContainer 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.IAtomContainer 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