org.openscience.cdk.modeling.builder3d

Class ModelBuilder3D

java.lang.Object

org.openscience.cdk.modeling.builder3d.ModelBuilder3D

public class ModelBuilder3D
extends Object

The main class to generate the 3D coordinates of a molecule ModelBuilder3D. Its use looks like:

  ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
  IAtomContainer molecule = mb3d.generate3DCoordinates(molecule, false);
  

Standing problems:

• condensed ring systems which are unknown for the template class
• vdWaals clashes
• stereochemistry
• chains running through ring systems

Author:

cho, steinbeck

Source code:

master

Belongs to CDK module:

builder3d

Keywords:

3D coordinates, coordinate generation, 3D

Created on:

2004-09-07

Method Summary

Modifier and Type	Method and Description
IAtomContainer	generate3DCoordinates(IAtomContainer molecule, boolean clone) Generate 3D coordinates with force field information.
String[]	getFfTypes() Gives a list of possible force field types.
static ModelBuilder3D	getInstance(IChemObjectBuilder builder)
static ModelBuilder3D	getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder)
int	getTemplateCount() Returns the number of loaded templates.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static ModelBuilder3D getInstance(TemplateHandler3D templateHandler,
                                         String ffname,
                                         IChemObjectBuilder chemObjectBuilder)
                                  throws CDKException

Throws:

CDKException

getInstance

public static ModelBuilder3D getInstance(IChemObjectBuilder builder)
                                  throws CDKException

Throws:

CDKException

getFfTypes

public String[] getFfTypes()

Gives a list of possible force field types.

Returns:

the list

generate3DCoordinates

public IAtomContainer generate3DCoordinates(IAtomContainer molecule,
                                            boolean clone)
                                     throws CDKException,
                                            NoSuchAtomTypeException,
                                            CloneNotSupportedException,
                                            IOException

Generate 3D coordinates with force field information.

Throws:

CDKException

NoSuchAtomTypeException

CloneNotSupportedException

IOException

getTemplateCount

public int getTemplateCount()

Returns the number of loaded templates. Note that it may return 0 because templates are lazy loaded, that is upon the first ring being laid out.

Returns:

0, if not templates are loaded