org.openscience.cdk.layout

Class TemplateHandler

java.lang.Object

org.openscience.cdk.layout.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:

master

Belongs to CDK module:

sdg

Keywords:

layout, 2D-coordinates, structure diagram generation

Created on:

2003-09-04

Requires:

java1.4+

Constructor Summary

Constructors

Constructor and Description
TemplateHandler() Creates a new TemplateHandler without any default templates.
TemplateHandler(IChemObjectBuilder builder) Creates a new TemplateHandler with default templates loaded.

Method Summary

Methods

Modifier and Type	Method and Description
void	addMolecule(IAtomContainer molecule) Adds a Molecule to the list of templates use by this TemplateHandler.
static TemplateHandler	createFromSubstructure(Pattern ptrn, IAtomContainer mol) Create a template from a substructure pattern.
static TemplateHandler	createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols) Create a template from a substructure pattern.
static TemplateHandler	createSingleton(IAtomContainer template) Singleton template instance, mainly useful for aligning molecules.
IAtomContainerSet	getMappedSubstructures(IAtomContainer molecule) Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.
IAtomContainer	getTemplateAt(int position) Gets the templateAt attribute of the TemplateHandler object
int	getTemplateCount() Gets the templateCount attribute of the TemplateHandler object
void	loadTemplates(IChemObjectBuilder builder) Loads all existing templates into memory.
boolean	mapTemplateExact(IAtomContainer molecule) Checks if one of the loaded templates is isomorph to the given Molecule.
boolean	mapTemplates(IAtomContainer molecule) Checks if one of the loaded templates is a substructure in the given Molecule.
IAtomContainer	removeMolecule(IAtomContainer molecule)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

removeMolecule

public IAtomContainer removeMolecule(IAtomContainer molecule)
                              throws CDKException

Throws:

CDKException

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