@Deprecated public class SMSDNormalizer extends AtomContainerManipulator
Constructor and Description |
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SMSDNormalizer()
Deprecated.
|
Modifier and Type | Method and Description |
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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(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 molecule
|
static void |
percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IAtomContainer |
removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
anonymise, clearAtomConfigurations, convertImplicitToExplicitHydrogens, copyAndSuppressedHydrogens, countExplicitHydrogens, countHydrogens, createAllCarbonAllSingleNonAromaticBondAtomContainer, extractSubstructure, getAllIDs, getAtomArray, getAtomArray, getAtomById, getBondArray, getBondArray, getBondOrderSum, getElectronContainerArray, getElectronContainerArray, getHeavyAtoms, getImplicitHydrogenCount, getIntersection, getMaximumBondOrder, getNaturalExactMass, getSingleBondEquivalentSum, getTotalCharge, getTotalExactMass, getTotalFormalCharge, getTotalHydrogenCount, getTotalNaturalAbundance, getTotalNegativeFormalCharge, getTotalPositiveFormalCharge, percieveAtomTypesAndConfigureUnsetProperties, removeHydrogens, removeHydrogensPreserveMultiplyBonded, removeNonChiralHydrogens, replaceAtomByAtom, setAtomProperties, setSingleOrDoubleFlags, skeleton, suppressHydrogens, unregisterAtomListeners, unregisterElectronContainerListeners
public static IAtomContainer makeDeepCopy(IAtomContainer container)
container
- public static void aromatizeMolecule(IAtomContainer mol)
mol
- input moleculepublic static int getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)
atomContainer
- atom
- public static int getImplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)
atomContainer
- atom
- public static int getHydrogenCount(IAtomContainer atomContainer, IAtom atom)
atomContainer
- atom
- public static IAtomContainer removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
atomContainer
- public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
atomContainer
- public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException
IAtom
s 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.container
- CDKException
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