public class ExtAtomContainerManipulator
extends org.openscience.cdk.tools.manipulator.AtomContainerManipulator
implements java.io.Serializable
This is an extension of CDK GraphAtomContainer. Some part of this code was taken from CDK source code and modified.
Constructor and Description |
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ExtAtomContainerManipulator() |
Modifier and Type | Method and Description |
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static org.openscience.cdk.interfaces.IAtomContainer |
addExplicitH(org.openscience.cdk.interfaces.IAtomContainer gMol) |
static void |
aromatizeCDK(org.openscience.cdk.interfaces.IAtomContainer molecule) |
static void |
aromatizeDayLight(org.openscience.cdk.interfaces.IAtomContainer molecule) |
static void |
aromatizeMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static org.openscience.cdk.interfaces.IAtomContainer |
checkAndCleanMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule_orignal)
Modules for cleaning a molecule
|
static org.openscience.cdk.interfaces.IAtomContainer |
cloneWithIDs(org.openscience.cdk.interfaces.IAtomContainer container)
Returns deep copy of the molecule
|
static org.openscience.cdk.interfaces.IAtomContainer |
convertExplicitToImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
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static org.openscience.cdk.interfaces.IAtomContainer |
copyAndSuppressedHydrogens(org.openscience.cdk.interfaces.IAtomContainer org)
Copy the input container and suppress any explicit hydrogens.
|
static void |
fixDativeBonds(org.openscience.cdk.interfaces.IAtomContainer mol)
This method is a workaround by assigning dative bonds to single
|
static int |
getExplicitHydrogenCount(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
org.openscience.cdk.interfaces.IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
getHydrogenCount(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
org.openscience.cdk.interfaces.IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
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static int |
getImplicitHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)
Returns The number of Implicit Hydrogen Count for a given IAtom.
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static org.openscience.cdk.interfaces.IAtomContainer |
newInstanceWithIDs(org.openscience.cdk.interfaces.IAtomContainer container)
Returns deep copy of the molecule
|
static void |
percieveAtomTypesAndConfigureAtoms(org.openscience.cdk.interfaces.IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in
the IAtomContainer , using the
CDKAtomTypeMatcher . |
static org.openscience.cdk.interfaces.IAtomContainer |
removeHydrogensExceptSingleAndPreserveAtomID(org.openscience.cdk.interfaces.IAtomContainer org)
Create an copy of the
org structure with explicit hydrogens
removed. |
anonymise, clearAtomConfigurations, convertImplicitToExplicitHydrogens, 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 org.openscience.cdk.interfaces.IAtomContainer removeHydrogensExceptSingleAndPreserveAtomID(org.openscience.cdk.interfaces.IAtomContainer org)
org
structure with explicit hydrogens
removed. Stereochemistry is updated but up and down bonds in a depiction
may need to be recalculated (see. StructureDiagramGenerator).org
- The AtomContainer from which to remove the hydrogenscopyAndSuppressedHydrogens(org.openscience.cdk.interfaces.IAtomContainer)
public static org.openscience.cdk.interfaces.IAtomContainer copyAndSuppressedHydrogens(org.openscience.cdk.interfaces.IAtomContainer org)
AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)
.org
- the container from which to remove hydrogensAtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)
public static org.openscience.cdk.interfaces.IAtomContainer checkAndCleanMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule_orignal)
molecule_orignal
- public static void aromatizeMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
mol
- input moleculepublic static org.openscience.cdk.interfaces.IAtomContainer cloneWithIDs(org.openscience.cdk.interfaces.IAtomContainer container) throws java.lang.CloneNotSupportedException
container
- java.lang.CloneNotSupportedException
public static org.openscience.cdk.interfaces.IAtomContainer newInstanceWithIDs(org.openscience.cdk.interfaces.IAtomContainer container) throws java.lang.CloneNotSupportedException
container
- java.lang.CloneNotSupportedException
public static int getExplicitHydrogenCount(org.openscience.cdk.interfaces.IAtomContainer atomContainer, org.openscience.cdk.interfaces.IAtom atom)
atomContainer
- atom
- public static int getImplicitHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)
atom
- public static int getHydrogenCount(org.openscience.cdk.interfaces.IAtomContainer atomContainer, org.openscience.cdk.interfaces.IAtom atom)
atomContainer
- atom
- public static org.openscience.cdk.interfaces.IAtomContainer convertExplicitToImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- public static void percieveAtomTypesAndConfigureAtoms(org.openscience.cdk.interfaces.IAtomContainer container) throws org.openscience.cdk.exception.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
- org.openscience.cdk.exception.CDKException
public static org.openscience.cdk.interfaces.IAtomContainer addExplicitH(org.openscience.cdk.interfaces.IAtomContainer gMol) throws java.lang.CloneNotSupportedException
gMol
- java.lang.CloneNotSupportedException
public static void aromatizeDayLight(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
molecule
- org.openscience.cdk.exception.CDKException
public static void aromatizeCDK(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
molecule
- org.openscience.cdk.exception.CDKException
public static void fixDativeBonds(org.openscience.cdk.interfaces.IAtomContainer mol)
mol
-