Class ModelBuilder3D
- java.lang.Object
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- org.openscience.cdk.modeling.builder3d.ModelBuilder3D
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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:
- main
- Belongs to CDK module:
- builder3d
- Keywords:
- 3D coordinates, coordinate generation, 3D
- Created on:
- 2004-09-07
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Method Detail
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getInstance
public static ModelBuilder3D getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder) throws CDKException
- Throws:
CDKException
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getInstance
public static ModelBuilder3D getInstance(IChemObjectBuilder builder) throws CDKException
- Throws:
CDKException
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getFfTypes
public String[] getFfTypes()
Gives a list of possible force field types.- Returns:
- the list
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generate3DCoordinates
public IAtomContainer generate3DCoordinates(IAtomContainer molecule, boolean clone) throws CDKException, CloneNotSupportedException, IOException
Generate 3D coordinates with force field information.
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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
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