Package org.openscience.cdk.normalize
Class SMSDNormalizer
java.lang.Object
org.openscience.cdk.tools.manipulator.AtomContainerManipulator
org.openscience.cdk.normalize.SMSDNormalizer
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public
access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent
version of SMSD is available at http://github.com/asad/smsd.
This class containes set of modules required to clean a molecule
before subjecting it for MCS search. eg. aromatizeMolecule
- 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
getImplicitHydrogenCount
(IAtomContainer atomContainer, IAtom atom) Deprecated.Returns The number of Implicit Hydrogen Count for a given IAtom.static IAtomContainer
makeDeepCopy
(IAtomContainer container) Deprecated.Returns 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
removeHydrogensAndPreserveAtomID
(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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SMSDNormalizer
public SMSDNormalizer()Deprecated.
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Method Details
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makeDeepCopy
Deprecated.Returns 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:
atomContainer
-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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removeHydrogensAndPreserveAtomID
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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