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

Source code:

master

Belongs to CDK module:

builder3d

Created on:

2004-09-21

Method Summary

Methods

Modifier and Type	Method and 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 ringSystems, 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

Method Detail

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 ringSystems,
                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:

ringSystems - 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