org.openscience.cdk.layout

Class StructureDiagramGenerator

java.lang.Object

org.openscience.cdk.layout.StructureDiagramGenerator

public class StructureDiagramGenerator
extends Object

Generates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason. Usage: Create an instance of this class, thereby assigning a molecule, call generateCoordinates() and get your molecule back:

 StructureDiagramGenerator sdg = new StructureDiagramGenerator();
 sdg.setMolecule(someMolecule);
 sdg.generateCoordinates();
 Molecule layedOutMol = sdg.getMolecule();
 

The method will fail if the molecule is disconnected. The partitionIntoMolecules(AtomContainer) can help here.

Author:

steinbeck

See Also:

ConnectivityChecker.partitionIntoMolecules(IAtomContainer)

Keywords:

Layout, Structure Diagram Generation (SDG), 2D-coordinates, Coordinate generation, 2D

Created on:

2004-02-02

Belongs to CDK module:

sdg

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:

master

Constructor Summary

Constructors

Constructor and Description
StructureDiagramGenerator() The empty constructor.
StructureDiagramGenerator(IAtomContainer molecule) Creates an instance of this class while assigning a molecule to be layed out.

Method Summary

Methods

Modifier and Type	Method and Description
void	generateCoordinates() The main method of this StructurDiagramGenerator.
void	generateCoordinates(javax.vecmath.Vector2d firstBondVector) The main method of this StructurDiagramGenerator.
void	generateExperimentalCoordinates() This method uses generateCoordinates, but it removes the hydrogens first, lays out the structuren and then adds them again.
void	generateExperimentalCoordinates(javax.vecmath.Vector2d firstBondVector) Generates 2D coordinates on the non-hydrogen skeleton, after which coordinates for the hydrogens are calculated.
double	getBondLength() Returns the bond length used for laying out the molecule.
IAtomContainer	getMolecule() Returns the molecule, usually used after a call of generateCoordinates()
IAtom	getOtherBondAtom(IAtom atom, IBond bond) Returns the other atom of the bond.
TemplateHandler	getTemplateHandler() Gets the templateHandler attribute of the StructureDiagramGenerator object
boolean	getUseTemplates() Returns whether the use of templates is enabled or disabled.
void	setBondLength(double bondLength) Set the bond length used for laying out the molecule.
void	setMolecule(IAtomContainer molecule) Assings a molecule to be layed out.
void	setMolecule(IAtomContainer mol, boolean clone) Assings a molecule to be layed out.
void	setTemplateHandler(TemplateHandler templateHandler) Sets the templateHandler attribute of the StructureDiagramGenerator object
void	setUseTemplates(boolean useTemplates) Sets whether to use templates or not.

Methods inherited from class java.lang.Object

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

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

setMolecule

public void setMolecule(IAtomContainer mol,
               boolean clone)

Assings a molecule to be layed out. Call generateCoordinates() to do the actual layout.

Parameters:

mol - the molecule for which coordinates are to be generated.

clone - Should the whole process be performed with a cloned copy?

setUseTemplates

public void setUseTemplates(boolean useTemplates)

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

getUseTemplates

public boolean getUseTemplates()

Returns whether the use of templates is enabled or disabled.

Returns:

true, when the use of templates is enables, false otherwise

setTemplateHandler

public void setTemplateHandler(TemplateHandler templateHandler)

Sets the templateHandler attribute of the StructureDiagramGenerator object

Parameters:

templateHandler - The new templateHandler value

getTemplateHandler

public TemplateHandler getTemplateHandler()

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.

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

public void generateExperimentalCoordinates()
                                     throws CDKException

This method uses generateCoordinates, but it removes the hydrogens first, lays out the structuren and then adds them again.

Throws:

CDKException - if an error occurs

See Also:

generateCoordinates(javax.vecmath.Vector2d)

generateExperimentalCoordinates

public void generateExperimentalCoordinates(javax.vecmath.Vector2d firstBondVector)
                                     throws CDKException

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

setBondLength

public void setBondLength(double bondLength)

Set the bond length used for laying out the molecule. The default value is 1.5.

Parameters:

bondLength - The new bondLength value

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