Class ChemStructureManipulator


  • public class ChemStructureManipulator
    extends java.lang.Object
    • 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)  
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • ChemStructureManipulator

        public ChemStructureManipulator()
    • Method Detail

      • 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
      • standardizeMoleculeWithCopy

        public static org.openscience.cdk.interfaces.IAtomContainer standardizeMoleculeWithCopy​(org.openscience.cdk.interfaces.IAtomContainer molecule)
                                                                                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • 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