Package org.openscience.cdk.layout

Class StructureDiagramGenerator

  • public class StructureDiagramGenerator
extends Object
    Generates 2D coordinates for a molecule. Basic Usage: If you just want to generate coordinate for a molecule (or reaction) you can use the following one-liner: 
     new StructureDiagramGenerator().generateCoordinates(molecule);
    The older versions of the API suggested using the following a set/generate/get idiom but this performs an unnecessary (in most cases) copy. 
     StructureDiagramGenerator sdg = new StructureDiagramGenerator();
 sdg.setMolecule(molecule); // cloned!
 sdg.generateCoordinates();
 molecule = sdg.getMolecule();
    This idiom only needs to be used when 'fixing' parts of an existing layout with setMolecule(IAtomContainer, boolean, Set, Set)
    Author:
    steinbeck
    This class is affected by these bug(s):
    1536561 1788686
    Dictionary pointer(s):
    layoutMolecule in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:layoutMolecule]
    Source code:
    main
    Belongs to CDK module:
    sdg
    Keywords:
    Layout, Structure Diagram Generation (SDG), 2D-coordinates, Coordinate generation, 2D
    Created on:
    2004-02-02

    • Constructor Detail

      • StructureDiagramGenerator

        public StructureDiagramGenerator()
        The empty constructor.

      • StructureDiagramGenerator

        public StructureDiagramGenerator​(IAtomContainer molecule)
        Creates an instance of this class while assigning a molecule to be layed out.
        Parameters:
        molecule - The molecule to be layed out.

    • Method Detail

      • generateCoordinates

        public final void generateCoordinates​(IAtomContainer mol)
                               throws CDKException

        Convenience method for generating 2D coordinates.

        The method is short-hand for calling:

         sdg.setMolecule(mol, false);
 sdg.generateCoordinates();
        Parameters:
        mol - molecule to layout
        Throws:
        CDKException - problem with layout

      • generateAlignedCoordinates

        public final void generateAlignedCoordinates​(IAtomContainer mol,
                                             IAtomContainer ref,
                                             Pattern pattern)
                                      throws CDKException
        Generate coordinates aligned to a reference based on the provided pattern. The pattern is matched against both the input and reference molecules. The reference coordinates are generated and scaled accordingly if needed. The part of the pattern which can be aligned (consistent ring flags) is then copied and fixed in place before laying out the rest of the molecule.
        Note: An internal read/write lock is used to ensure consistency in threaded environments.
        Parameters:
        mol - molecule
        ref - reference molecule (may be null)
        pattern - the substructure pattern to match
        Throws:
        CDKException - there was a problem generating the layout

      • generateAlignedCoordinates

        public final void generateAlignedCoordinates​(IAtomContainer mol,
                                             Pattern pattern)
                                      throws CDKException
        Generate coordinates aligned, the atoms in substructure pattern is used to cache/provide the coordinates. If no coordinates are present the substructure from the molecule is generated first and its coordinates cached. If an atom in the
        Parameters:
        mol - molecule
        pattern - the substructure pattern to match (will be modified)
        Throws:
        CDKException - there was a problem generating the layout

      • generateCoordinates

        public final void generateCoordinates​(IReaction reaction)
                               throws CDKException

        Convenience method to generate 2D coordinates for a reaction. If atom-atom maps are present on a reaction, the substructures are automatically aligned.

        This feature can be disabled by changing the setAlignMappedReaction(boolean)

        Parameters:
        reaction - reaction to layout
        Throws:
        CDKException - problem with layout

      • setMolecule

        public void setMolecule​(IAtomContainer mol,
                        boolean clone)

      • setMolecule

        public void setMolecule​(IAtomContainer mol,
                        boolean clone,
                        Set<IAtom> afix,
                        Set<IBond> bfix)
        Assigns a molecule to be laid out. After, setting the molecule call generateCoordinates() to assign 2D coordinates. An optional set of atoms/bonds can be parsed in to allow partial layout, these will be 'fixed' in place. This only applies to non-cloned molecules, and only atoms with coordinates can be fixed.
        Parameters:
        mol - the molecule for which coordinates are to be generated.
        clone - Should the whole process be performed with a cloned copy?
        afix - Atoms that should be fixed in place, coordinates are not changed.
        bfix - Bonds that should be fixed in place, they will not be flipped, bent, or streched.

      • setUseTemplates

        @Deprecated
public void setUseTemplates​(boolean useTemplates)
        Deprecated.
        always false, substructure templates are not used anymore
        Sets whether to use templates or not. Some complicated ring systems like adamantane are only nicely layouted when using templates. This option is by default set true.
        Parameters:
        useTemplates - set true to use templates, false otherwise

      • setUseIdentityTemplates

        public void setUseIdentityTemplates​(boolean use)
        Set whether identity templates are used. Identity templates use an exact match are are very fast. They are used for layout of the 'primary' ring system in de facto orientation.
        Parameters:
        use - whether to use identity templates

      • getUseTemplates

        @Deprecated
public boolean getUseTemplates()
        Deprecated.
        always false, substructure templates are not used anymore
        Returns whether the use of templates is enabled or disabled.
        Returns:
        true, when the use of templates is enables, false otherwise

      • setTemplateHandler

        @Deprecated
public void setTemplateHandler​(TemplateHandler templateHandler)
        Deprecated.
        substructure templates are no longer used for layout but those provided here will be converted to identity templates
        Sets the templateHandler attribute of the StructureDiagramGenerator object
        Parameters:
        templateHandler - The new templateHandler value

      • getTemplateHandler

        @Deprecated
public TemplateHandler getTemplateHandler()
        Deprecated.
        always null, substructure templates are not used anymore
        Gets the templateHandler attribute of the StructureDiagramGenerator object
        Returns:
        The templateHandler value

      • setMolecule

        public void setMolecule​(IAtomContainer molecule)
        Assings a molecule to be layed out. Call generateCoordinates() to do the actual layout.
        Parameters:
        molecule - the molecule for which coordinates are to be generated.

      • setAlignMappedReaction

        public void setAlignMappedReaction​(boolean align)
        Set whether reaction reactants should be allignned to their product.
        Parameters:
        align - align setting

      • getMolecule

        public IAtomContainer getMolecule()
        Returns the molecule, usually used after a call of generateCoordinates()
        Returns:
        The molecule with new coordinates (if generateCoordinates() had been called)

      • generateExperimentalCoordinates

        @Deprecated
public void generateExperimentalCoordinates​(javax.vecmath.Vector2d firstBondVector)
                                     throws CDKException
        Deprecated.
        use generateCoordinates()
        Generates 2D coordinates on the non-hydrogen skeleton, after which coordinates for the hydrogens are calculated.
        Parameters:
        firstBondVector - the vector of the first bond to lay out
        Throws:
        CDKException - if an error occurs

      • generateCoordinates

        public void generateCoordinates​(javax.vecmath.Vector2d firstBondVector)
                         throws CDKException
        The main method of this StructurDiagramGenerator. Assign a molecule to the StructurDiagramGenerator, call the generateCoordinates() method and get your molecule back.
        Parameters:
        firstBondVector - The vector of the first bond to lay out
        Throws:
        CDKException - if an error occurs

      • generateCoordinates

        public void generateCoordinates()
                         throws CDKException
        The main method of this StructurDiagramGenerator. Assign a molecule to the StructurDiagramGenerator, call the generateCoordinates() method and get your molecule back.
        Throws:
        CDKException - if an error occurs

      • getBondLength

        public double getBondLength()
        Returns the bond length used for laying out the molecule.
        Returns:
        The current bond length

      • getOtherBondAtom

        public IAtom getOtherBondAtom​(IAtom atom,
                              IBond bond)
        Returns the other atom of the bond. Expects bond to have only two atoms. Returns null if the given atom is not part of the given bond.
        Parameters:
        atom - the atom we already have
        bond - the bond
        Returns:
        the other atom of the bond