Package org.openscience.cdk.tools

Class AtomTypeAwareSaturationChecker

  • All Implemented Interfaces:
    IDeduceBondOrderTool, IValencyChecker
    public class AtomTypeAwareSaturationChecker
extends Object
implements IValencyChecker, IDeduceBondOrderTool
    This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e. set to true).
    The code is written with the assumption that the properties of the atoms in the molecule has configured with the help of AtomContainerManipulator. This class uses the SaturationChecker internally.
    If it can't find a solution where all atoms in the molecule are saturated, it gives a "best guess", i.e. the solution with most saturated atoms. If not all atoms are saturated then it will be noticed as a warning in the log.
    Author:
    Klas Jönsson, Egon Willighagen
    Source code:
    main
    Belongs to CDK module:
    valencycheck
    Keywords:
    bond order
    Created on:
    2012-04-13

    • Method Detail

      • decideBondOrder

        public void decideBondOrder​(IAtomContainer atomContainer,
                            boolean atomsSaturated)
                     throws CDKException
        This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
        Parameters:
        atomContainer - The molecule to investigate
        atomsSaturated - Set to true if you want to make sure that all atoms are saturated.
        Throws:
        CDKException

      • decideBondOrder

        public void decideBondOrder​(IAtomContainer atomContainer)
                     throws CDKException
        This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
        Parameters:
        atomContainer - The molecule to investigate.
        Throws:
        CDKException

      • bondOrderCanBeIncreased

        public boolean bondOrderCanBeIncreased​(IBond bond,
                                       IAtomContainer atomContainer)
                                throws CDKException
        Check if the bond order can be increased. This method assumes that the bond is between only two atoms.
        Parameters:
        bond - The bond to check
        atomContainer - The IAtomContainer that the bond belongs to
        Returns:
        True if it is possibly to increase the bond order
        Throws:
        CDKException

      • getMaxNoOfBonds

        public double getMaxNoOfBonds​(IAtom atom)
                       throws CDKException
        This method calculates the number of bonds that an IAtom can have.
        Parameters:
        atom - The IAtom to be investigated
        Returns:
        The max number of bonds the IAtom can have
        Throws:
        CDKException - when the atom's valency is not set