Package org.openscience.cdk.layout

Class TemplateHandler

  • public final class TemplateHandler
extends Object
    Helper class for Structure Diagram Generation. Handles templates. This is our layout solution for ring systems which are notoriously difficult to layout, like cubane, adamantane, porphyrin, etc.
    Author:
    steinbeck
    Source code:
    main
    Belongs to CDK module:
    sdg
    Keywords:
    layout, 2D-coordinates, structure diagram generation
    Created on:
    2003-09-04
    Requires:
    java1.4+

    • Constructor Detail

      • TemplateHandler

        public TemplateHandler​(IChemObjectBuilder builder)
        Creates a new TemplateHandler with default templates loaded.

      • TemplateHandler

        public TemplateHandler()
        Creates a new TemplateHandler without any default templates.

    • Method Detail

      • loadTemplates

        public void loadTemplates​(IChemObjectBuilder builder)
        Loads all existing templates into memory. To add templates to be used in SDG, place a drawing with the new template in org/openscience/cdk/layout/templates and add the template filename to org/openscience/cdk/layout/templates/template.list

      • addMolecule

        public void addMolecule​(IAtomContainer molecule)
        Adds a Molecule to the list of templates use by this TemplateHandler.
        Parameters:
        molecule - The molecule to be added to the TemplateHandler

      • mapTemplateExact

        public boolean mapTemplateExact​(IAtomContainer molecule)
                         throws CDKException
        Checks if one of the loaded templates is isomorph to the given Molecule. If so, it assigns the coordinates from the template to the respective atoms in the Molecule, and marks the atoms as ISPLACED.
        Parameters:
        molecule - The molecule to be check for potential templates
        Returns:
        True if there was a possible mapping
        Throws:
        CDKException

      • mapTemplates

        public boolean mapTemplates​(IAtomContainer molecule)
                     throws CDKException
        Checks if one of the loaded templates is a substructure in the given Molecule. If so, it assigns the coordinates from the template to the respective atoms in the Molecule, and marks the atoms as ISPLACED.
        Parameters:
        molecule - The molecule to be check for potential templates
        Returns:
        True if there was a possible mapping
        Throws:
        CDKException

      • getTemplateCount

        public int getTemplateCount()
        Gets the templateCount attribute of the TemplateHandler object
        Returns:
        The templateCount value

      • getTemplateAt

        public IAtomContainer getTemplateAt​(int position)
        Gets the templateAt attribute of the TemplateHandler object
        Parameters:
        position - Description of the Parameter
        Returns:
        The templateAt value

      • getMappedSubstructures

        public IAtomContainerSet getMappedSubstructures​(IAtomContainer molecule)
                                         throws CDKException
        Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet. This method does not assign any coordinates.
        Parameters:
        molecule - The molecule to be check for potential templates
        Returns:
        an IAtomContainerSet of all matched substructures of the molecule
        Throws:
        CDKException - if an error occurs

      • createSingleton

        public static TemplateHandler createSingleton​(IAtomContainer template)
        Singleton template instance, mainly useful for aligning molecules. If the template does not have coordinates an error is thrown. For safety we clone the molecule.
        Parameters:
        template - the molecule
        Returns:
        new template handler

      • createFromSubstructure

        public static TemplateHandler createFromSubstructure​(Pattern ptrn,
                                                     Iterable<IAtomContainer> mols)
        Create a template from a substructure pattern. Using this template handler in the diagram generator then allows us to align to common reference.
        Parameters:
        ptrn - the structure pattern to match
        mols - list of molecules
        Returns:
        new template handler

      • createFromSubstructure

        public static TemplateHandler createFromSubstructure​(Pattern ptrn,
                                                     IAtomContainer mol)
        Create a template from a substructure pattern. Using this template handler in the diagram generator then allows us to align to common reference.
        Parameters:
        ptrn - the structure pattern to match
        mol - molecule
        Returns:
        new template handler