Package org.openscience.cdk.smsd.tools
Class ExtAtomContainerManipulator
java.lang.Object
org.openscience.cdk.tools.manipulator.AtomContainerManipulator
org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
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
Fields inherited from class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
MolWeight, MolWeightIgnoreSpecified, MonoIsotopic, MostAbundant, NAT_ABUN_COMP
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic void
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
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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Constructor Details
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ExtAtomContainerManipulator
public ExtAtomContainerManipulator()Deprecated.
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Method Details
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makeDeepCopy
Deprecated.Retrurns deep copy of the molecule- Parameters:
container
-- Returns:
- deep copy of the mol
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aromatizeMolecule
Deprecated.This function finds rings and uses aromaticity detection code to aromatize the molecule.- Parameters:
mol
- input molecule
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getExplicitHydrogenCount
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
Deprecated.Returns The number of Implicit Hydrogen Count for a given IAtom.- Parameters:
atom
-- Returns:
- Implicit Hydrogen Count
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getHydrogenCount
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
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
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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