org.openscience.cdk.atomtype

Class SybylAtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.SybylAtomTypeMatcher

All Implemented Interfaces:

IAtomTypeMatcher

public class SybylAtomTypeMatcher
extends Object
implements IAtomTypeMatcher

Atom Type matcher for Sybyl atom types. It uses the CDKAtomTypeMatcher for perception and then maps CDK to Sybyl atom types.

Author:

egonw

Source code:

master

Belongs to CDK module:

atomtype

Keywords:

atom type, Sybyl

Created on:

2008-07-13

Method Summary

Modifier and Type	Method and Description
IAtomType	findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) Sybyl atom type perception for a single atom.
IAtomType[]	findMatchingAtomTypes(IAtomContainer atomContainer) Method that assigns atom types to atoms in the given atom container.
static SybylAtomTypeMatcher	getInstance(IChemObjectBuilder builder) Returns an instance of this atom typer.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static SybylAtomTypeMatcher getInstance(IChemObjectBuilder builder)

Returns an instance of this atom typer. It uses the given builder to create atom type objects.

Parameters:

builder - IChemObjectBuilder to use to create IAtomType instances.

Returns:

an instance of this atom type matcher.

findMatchingAtomTypes

public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer)
                                  throws CDKException

Method that assigns atom types to atoms in the given atom container.

Specified by:

findMatchingAtomTypes in interface IAtomTypeMatcher

Parameters:

atomContainer - AtomContainer for which atom types are perceived

Returns:

The matching AtomType

Throws:

CDKException - when something went wrong with going through the AtomType's

findMatchingAtomType

public IAtomType findMatchingAtomType(IAtomContainer atomContainer,
                                      IAtom atom)
                               throws CDKException

Sybyl atom type perception for a single atom. The molecular property aromaticity is not perceived; Aromatic carbons will, therefore, be perceived as C.2 and not C.ar. If the latter is required, please use findMatchingAtomType(IAtomContainer) instead.

Specified by:

findMatchingAtomType in interface IAtomTypeMatcher

Parameters:

atomContainer - the IAtomContainer in which the atom is found

atom - the IAtom to find the atom type of

Returns:

the atom type perceived from the given atom

Throws:

CDKException - when something went wrong with going through the AtomType's