StructureDiagramGenerator (cdk 2.2 API)

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();
 IAtomContainer 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)

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 double DEFAULT_BOND_LENGTH

static javax.vecmath.Vector2d DEFAULT_BOND_VECTOR

static double RAD_30

Fields
Modifier and Type	Field and Description
`static double`	`DEFAULT_BOND_LENGTH`
`static javax.vecmath.Vector2d`	`DEFAULT_BOND_VECTOR`
`static double`	`RAD_30`

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

All Methods Instance Methods Concrete Methods Deprecated Methods
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
  - RAD_30
```
public static final double RAD_30
```
  - DEFAULT_BOND_LENGTH
```
public static final double DEFAULT_BOND_LENGTH
```
    See Also:
    
    Constant Field Values
  - DEFAULT_BOND_VECTOR
```
public static javax.vecmath.Vector2d DEFAULT_BOND_VECTOR
```
- 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

Class StructureDiagramGenerator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

RAD_30

DEFAULT_BOND_LENGTH

DEFAULT_BOND_VECTOR

Constructor Detail

StructureDiagramGenerator

StructureDiagramGenerator

Method Detail

generateCoordinates

generateCoordinates

setMolecule

setMolecule

setUseTemplates

setUseIdentityTemplates

getUseTemplates

setTemplateHandler

getTemplateHandler

setMolecule

setAlignMappedReaction

getMolecule

generateExperimentalCoordinates

generateExperimentalCoordinates

generateCoordinates

generateCoordinates

setBondLength

getBondLength

getOtherBondAtom