Package org.openscience.cdk.modeling.builder3d

Class TemplateHandler3D

java.lang.Object

org.openscience.cdk.modeling.builder3d.TemplateHandler3D

public class TemplateHandler3D
extends Object

Helper class for ModelBuilder3D. Handles templates. This is our layout solution for 3D ring systems

Author:

cho, steinbeck, John Mayfield

Source code:

main

Belongs to CDK module:

builder3d

Created on:

2004-09-21

Field Summary

Fields

Modifier and Type	Field	Description
static final String	TEMPLATE_PATH

Method Summary

Modifier and Type	Method	Description
static BitSet	getBitSetFromFile(StringTokenizer st)
static TemplateHandler3D	getInstance()
IRingSet	getLargestRingSet(List<IRingSet> ringSystems)	Returns the largest (number of atoms) ring set in a molecule.
IAtomContainer	getTemplateAt(int position)	Gets the templateAt attribute of the TemplateHandler object.
int	getTemplateCount()	Gets the templateCount attribute of the TemplateHandler object.
void	mapTemplates(IAtomContainer ringSystems, double numberOfRingAtoms)	Deprecated. Use mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)
void	mapTemplates(IAtomContainer mol, int numberOfRingAtoms)	Checks if one of the loaded templates is a substructure in the given Molecule.

Methods inherited from class java.lang.Object

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

Field Details

TEMPLATE_PATH

public static final String TEMPLATE_PATH

See Also:

• Constant Field Values

Method Details

getInstance

public static TemplateHandler3D getInstance()
                                     throws CDKException

Throws:

CDKException

getBitSetFromFile

public static BitSet getBitSetFromFile(StringTokenizer st)
                                throws Exception

Throws:

Exception

getLargestRingSet

public IRingSet getLargestRingSet(List<IRingSet> ringSystems)

Returns the largest (number of atoms) ring set in a molecule.

Parameters:

ringSystems - RingSystems of a molecule

Returns:

The largestRingSet

mapTemplates

@Deprecated
public void mapTemplates(IAtomContainer ringSystems,
 double numberOfRingAtoms)
                  throws CDKException,
CloneNotSupportedException

Deprecated.

Use mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)

Throws:

CDKException

CloneNotSupportedException

mapTemplates

public void mapTemplates(IAtomContainer mol,
 int numberOfRingAtoms)
                  throws CDKException,
CloneNotSupportedException

Checks if one of the loaded templates is a substructure in the given Molecule. If so, it assigns the coordinates from the template to the respective atoms in the Molecule.

Parameters:

mol - AtomContainer from the ring systems.

numberOfRingAtoms - Number of atoms in the specified ring

Throws:

CloneNotSupportedException - The atomcontainer cannot be cloned.

CDKException

getTemplateCount

public int getTemplateCount()

Gets the templateCount attribute of the TemplateHandler object.

Returns:

The templateCount value

getTemplateAt

public IAtomContainer getTemplateAt(int position)

Gets the templateAt attribute of the TemplateHandler object.

Parameters:

position - Description of the Parameter

Returns:

The templateAt value