Class ExtAtomContainerManipulator

java.lang.Object
org.openscience.cdk.tools.manipulator.AtomContainerManipulator
org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator

@Deprecated public class ExtAtomContainerManipulator extends AtomContainerManipulator
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Class that handles some customised features for SMSD atom containers.

This is an extension of CDK AtomContainer. Some part of this code was taken from CDK source code and modified.

Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • ExtAtomContainerManipulator

      public ExtAtomContainerManipulator()
      Deprecated.
  • Method Details

    • makeDeepCopy

      public static IAtomContainer makeDeepCopy(IAtomContainer container)
      Deprecated.
      Retrurns deep copy of the molecule
      Parameters:
      container -
      Returns:
      deep copy of the mol
    • aromatizeMolecule

      public static void aromatizeMolecule(IAtomContainer mol)
      Deprecated.
      This function finds rings and uses aromaticity detection code to aromatize the molecule.
      Parameters:
      mol - input molecule
    • getExplicitHydrogenCount

      public static int getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)
      Deprecated.
      Returns The number of explicit hydrogens for a given IAtom.
      Parameters:
      atomContainer -
      atom -
      Returns:
      The number of explicit hydrogens on the given IAtom.
    • getImplicitHydrogenCount

      public static int getImplicitHydrogenCount(IAtom atom)
      Deprecated.
      Returns The number of Implicit Hydrogen Count for a given IAtom.
      Parameters:
      atom -
      Returns:
      Implicit Hydrogen Count
    • getHydrogenCount

      public static int getHydrogenCount(IAtomContainer atomContainer, IAtom atom)
      Deprecated.
      The summed implicit + explicit hydrogens of the given IAtom.
      Parameters:
      atomContainer -
      atom -
      Returns:
      The summed implicit + explicit hydrogens of the given IAtom.
    • removeHydrogensExceptSingleAndPreserveAtomID

      public static IAtomContainer removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
      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.
    • convertExplicitToImplicitHydrogens

      public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
      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.
    • percieveAtomTypesAndConfigureAtoms

      public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException
      Deprecated.
      Convenience method to perceive atom types for all IAtoms 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.
      Parameters:
      container -
      Throws:
      CDKException