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. 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:

master

Belongs to CDK module:

sdg

Keywords:

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

Created on:

2004-02-02

Field Summary

Fields

Modifier and Type	Field and Description
static Comparator<IAtomContainer>	LARGEST_FIRST_COMPARATOR

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

Modifier and Type	Method and Description
void	generateCoordinates() The main method of this StructurDiagramGenerator.
void	generateCoordinates(IAtomContainer mol) Convenience method for generating 2D coordinates.
void	generateCoordinates(IReaction reaction) Convenience method to generate 2D coordinates for a reaction.
void	generateCoordinates(javax.vecmath.Vector2d firstBondVector) The main method of this StructurDiagramGenerator.
void	generateExperimentalCoordinates() Deprecated. use generateCoordinates()
void	generateExperimentalCoordinates(javax.vecmath.Vector2d firstBondVector) Deprecated. use generateCoordinates()
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() Deprecated. always null, substructure templates are not used anymore
boolean	getUseTemplates() Deprecated. always false, substructure templates are not used anymore
void	setAlignMappedReaction(boolean align) Set whether reaction reactants should be allignned to their product.
void	setBondLength(double bondLength) Deprecated. use GeometryUtil.scaleMolecule(IAtomContainer, double)
void	setMolecule(IAtomContainer molecule) Assings a molecule to be layed out.
void	setMolecule(IAtomContainer mol, boolean clone)
void	setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix) Assigns a molecule to be laid out.
void	setTemplateHandler(TemplateHandler templateHandler) Deprecated. substructure templates are no longer used for layout but those provided here will be converted to identity templates
void	setUseIdentityTemplates(boolean use) Set whether identity templates are used.
void	setUseTemplates(boolean useTemplates) Deprecated. always false, substructure templates are not used anymore

Methods inherited from class java.lang.Object

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

Field Detail

LARGEST_FIRST_COMPARATOR

public static final Comparator<IAtomContainer> LARGEST_FIRST_COMPARATOR

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

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()
                                                 throws CDKException

Deprecated. use generateCoordinates()

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

Throws:

CDKException - if an error occurs

See Also:

generateCoordinates(org.openscience.cdk.interfaces.IAtomContainer)

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

setBondLength

@Deprecated
public void setBondLength(double bondLength)

Deprecated. use GeometryUtil.scaleMolecule(IAtomContainer, double)

This method used to set the bond length used for laying out the molecule. Since bond lengths in 2D are are arbitrary, the preferred way to do this is with GeometryUtil.scaleMolecule(IAtomContainer, double).

 IAtomContainer mol = ...;
 sdg.generateCoordinates(mol);
 int targetBondLength = 28;
 double factor = targetBondLength/GeometryUtil.getMedianBondLength(mol);
 GeometryUtil.scaleMolecule(mol, factor);
 

Parameters:

bondLength - The new bondLength value

Throws:

UnsupportedOperationException - not supported

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