Package org.openscience.cdk.smsd.tools
Class ExtAtomContainerManipulator
- java.lang.Object
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- org.openscience.cdk.tools.manipulator.AtomContainerManipulator
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- org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
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@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
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Field Summary
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Fields inherited from class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
MolWeight, MolWeightIgnoreSpecified, MonoIsotopic, MostAbundant, NAT_ABUN_COMP
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Constructor Summary
Constructors Constructor Description ExtAtomContainerManipulator()
Deprecated.
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Method Summary
All Methods Static Methods Concrete Methods Deprecated Methods 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 moleculestatic void
percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.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
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Method Detail
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makeDeepCopy
public static IAtomContainer makeDeepCopy(IAtomContainer container)
Deprecated.Retrurns deep copy of the molecule- Parameters:
container
-- Returns:
- deep copy of the mol
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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
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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.
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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
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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.
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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.
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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.
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percieveAtomTypesAndConfigureAtoms
public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
. If the matcher finds atom matching atom type, theIAtom
will be configured to have the same properties as theIAtomType
. If no matching atom type is found, no configuration is performed.- Parameters:
container
-- Throws:
CDKException
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