Package org.openscience.cdk.atomtype
Class SybylAtomTypeMatcher
- java.lang.Object
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- org.openscience.cdk.atomtype.SybylAtomTypeMatcher
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- All Implemented Interfaces:
IAtomTypeMatcher
public class SybylAtomTypeMatcher extends Object implements IAtomTypeMatcher
Atom Type matcher for Sybyl atom types. It uses theCDKAtomTypeMatcher
for perception and then maps CDK to Sybyl atom types.- Author:
- egonw
- Source code:
- main
- Belongs to CDK module:
- atomtype
- Keywords:
- atom type, Sybyl
- Created on:
- 2008-07-13
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Method Detail
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getInstance
public static SybylAtomTypeMatcher getInstance(IChemObjectBuilder builder)
Returns an instance of this atom typer. It uses the givenbuilder
to create atom type objects.- Parameters:
builder
-IChemObjectBuilder
to use to createIAtomType
instances.- Returns:
- an instance of this atom type matcher.
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findMatchingAtomTypes
public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
Method that assigns atom types to atoms in the given atom container.- Specified by:
findMatchingAtomTypes
in interfaceIAtomTypeMatcher
- 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
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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 interfaceIAtomTypeMatcher
- Parameters:
atomContainer
- theIAtomContainer
in which the atom is foundatom
- theIAtom
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
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