Package org.openscience.cdk.smsd.tools

Class ExtAtomContainerManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.AtomContainerManipulator

org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator

@Deprecated
public class ExtAtomContainerManipulator
extends AtomContainerManipulator

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Class that handles some customised features for SMSD atom containers.

This is an extension of CDK AtomContainer. Some part of this code was taken from CDK source code and modified.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

main

Belongs to CDK module:

smsd

Field Summary

Fields inherited from class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

MolWeight, MolWeightIgnoreSpecified, MonoIsotopic, MostAbundant, NAT_ABUN_COMP

Constructor Summary

Constructors

Constructor	Description
ExtAtomContainerManipulator()	Deprecated.

Method Summary

Modifier and Type	Method	Description
static void	aromatizeMolecule(IAtomContainer mol)	Deprecated. This function finds rings and uses aromaticity detection code to aromatize the molecule.
static IAtomContainer	convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)	Deprecated. Returns IAtomContainer without Hydrogen.
static int	getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)	Deprecated. Returns The number of explicit hydrogens for a given IAtom.
static int	getHydrogenCount(IAtomContainer atomContainer, IAtom atom)	Deprecated. The summed implicit + explicit hydrogens of the given IAtom.
static int	getImplicitHydrogenCount(IAtom atom)	Deprecated. Returns The number of Implicit Hydrogen Count for a given IAtom.
static IAtomContainer	makeDeepCopy(IAtomContainer container)	Deprecated. Retrurns deep copy of the molecule
static void	percieveAtomTypesAndConfigureAtoms(IAtomContainer container)	Deprecated. Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
static IAtomContainer	removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)	Deprecated. Returns IAtomContainer without Hydrogen.

Methods inherited from class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

anonymise, clearAtomConfigurations, convertImplicitToExplicitHydrogens, copy, copy, copy, copyAndSuppressedHydrogens, countExplicitHydrogens, countHydrogens, createAllCarbonAllSingleNonAromaticBondAtomContainer, extractSubstructure, extractSubstructure, getAllIDs, getAtomArray, getAtomArray, getAtomById, getBondArray, getBondArray, getBondOrderSum, getElectronContainerArray, getElectronContainerArray, getHeavyAtoms, getImplicitHydrogenCount, getIntersection, getMass, getMass, getMaximumBondOrder, getMolecularWeight, getNaturalExactMass, getSingleBondEquivalentSum, getTotalCharge, getTotalExactMass, getTotalFormalCharge, getTotalHydrogenCount, getTotalNaturalAbundance, getTotalNegativeFormalCharge, getTotalPositiveFormalCharge, percieveAtomTypesAndConfigureUnsetProperties, removeHydrogens, removeHydrogensPreserveMultiplyBonded, removeNonChiralHydrogens, replaceAtomByAtom, setAtomProperties, setSingleOrDoubleFlags, skeleton, suppressHydrogens, unregisterAtomListeners, unregisterElectronContainerListeners

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExtAtomContainerManipulator

public ExtAtomContainerManipulator()

Deprecated.

Method Detail

makeDeepCopy

public static IAtomContainer makeDeepCopy(IAtomContainer container)

Deprecated.

Retrurns deep copy of the molecule

Parameters:

container -

Returns:

deep copy of the mol

aromatizeMolecule

public static void aromatizeMolecule(IAtomContainer mol)

Deprecated.

This function finds rings and uses aromaticity detection code to aromatize the molecule.

Parameters:

mol - input molecule

getExplicitHydrogenCount

public static int getExplicitHydrogenCount(IAtomContainer atomContainer,
                                           IAtom atom)

Deprecated.

Returns The number of explicit hydrogens for a given IAtom.

Parameters:

atomContainer -

atom -

Returns:

The number of explicit hydrogens on the given IAtom.

getImplicitHydrogenCount

public static int getImplicitHydrogenCount(IAtom atom)

Deprecated.

Returns The number of Implicit Hydrogen Count for a given IAtom.

Parameters:

atom -

Returns:

Implicit Hydrogen Count

getHydrogenCount

public static int getHydrogenCount(IAtomContainer atomContainer,
                                   IAtom atom)

Deprecated.

The summed implicit + explicit hydrogens of the given IAtom.

Parameters:

atomContainer -

atom -

Returns:

The summed implicit + explicit hydrogens of the given IAtom.

removeHydrogensExceptSingleAndPreserveAtomID

public static IAtomContainer removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)

Deprecated.

Returns IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.

Parameters:

atomContainer -

Returns:

IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.

convertExplicitToImplicitHydrogens

public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)

Deprecated.

Returns IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.

Parameters:

atomContainer -

Returns:

IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.

percieveAtomTypesAndConfigureAtoms

public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
                                               throws CDKException

Deprecated.

Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher. If the matcher finds atom matching atom type, the IAtom will be configured to have the same properties as the IAtomType. If no matching atom type is found, no configuration is performed.

Parameters:

container -

Throws:

CDKException