org.openscience.cdk.atomtype.mapper

Class AtomTypeMapper

java.lang.Object

org.openscience.cdk.atomtype.mapper.AtomTypeMapper

public class AtomTypeMapper
extends Object

An AtomTypeMapper allows the mapping of atom types between atom type schemes. For example, it allows to convert atom types from the CDK scheme to the Sybyl scheme; using this approach it is possible to use the CDK atom type perception algorithm and write the resulting atom types using the Sybyl atom type scheme.

Source code:

master

Belongs to CDK module:

atomtype

Method Summary

Methods

Modifier and Type	Method and Description
static AtomTypeMapper	getInstance(String mappingFile) Instantiates an atom type to atom type mapping, based on the given mapping file.
static AtomTypeMapper	getInstance(String mappingFile, InputStream stream) Instantiates an atom type to atom type mapping, based on the given InputStream.
String	getMapping() Returns the name of this mapping.
String	mapAtomType(String type) Maps an atom type from one scheme to another, as specified in the input used when creating this AtomTypeMapper instance.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static AtomTypeMapper getInstance(String mappingFile)

Instantiates an atom type to atom type mapping, based on the given mapping file. For example, the mapping file org.openscience.cdk.config.data.cdk-sybyl-mappings.owl which defines how CDK atom types are mapped to Sybyl atom types.

Parameters:

mappingFile - File name of the OWL file defining the atom type to atom type mappings.

Returns:

An instance of AtomTypeMapper for the given mapping file.

getInstance

public static AtomTypeMapper getInstance(String mappingFile,
                         InputStream stream)

Instantiates an atom type to atom type mapping, based on the given InputStream.

Parameters:

mappingFile - Name of the InputStream defining the atom type to atom type mappings.

stream - the InputStream from which the mappings as read

Returns:

An instance of AtomTypeMapper for the given mapping file.

mapAtomType

public String mapAtomType(String type)

Maps an atom type from one scheme to another, as specified in the input used when creating this AtomTypeMapper instance.

Parameters:

type - atom type to map to the target schema

Returns:

atom type name in the target schema

getMapping

public String getMapping()

Returns the name of this mapping. In case of file inputs, it returns the filename, but when the input was an InputStream then the name is less well defined.

Returns:

the name of the mapping represented by this AtomTypeMapper.