Package biotransformer.utils
Class ChemStructureManipulator
- java.lang.Object
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- biotransformer.utils.ChemStructureManipulator
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public class ChemStructureManipulator extends java.lang.Object
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Constructor Summary
Constructors Constructor Description ChemStructureManipulator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static org.openscience.cdk.interfaces.IAtomContainer
preprocessContainer(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function applies some preprocessing operations, such as setting the flag of atoms from aromatic rings to "ISAROMATIC", and kelulizing molecules.static org.openscience.cdk.interfaces.IAtomContainer
standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer molecule)
static org.openscience.cdk.interfaces.IAtomContainer
standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess)
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Method Detail
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preprocessContainer
public static org.openscience.cdk.interfaces.IAtomContainer preprocessContainer(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
This function applies some preprocessing operations, such as setting the flag of atoms from aromatic rings to "ISAROMATIC", and kelulizing molecules.- Parameters:
molecule
- : A molecule of interest- Returns:
- : A processed molecule (AtomContainer)
- Throws:
java.lang.Exception
org.openscience.cdk.exception.CDKException
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standardizeMoleculeWithCopy
public static org.openscience.cdk.interfaces.IAtomContainer standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer molecule) throws java.lang.Exception
- Throws:
java.lang.Exception
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standardizeMoleculeWithCopy
public static org.openscience.cdk.interfaces.IAtomContainer standardizeMoleculeWithCopy(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean preprocess) throws java.lang.Exception
- Throws:
java.lang.Exception
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