public class AtomTypeMapper extends Object
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.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. |
public static AtomTypeMapper getInstance(String mappingFile)
org.openscience.cdk.config.data.cdk-sybyl-mappings.owl
which defines how CDK atom types are mapped to Sybyl atom types.mappingFile
- File name of the OWL file defining the atom type to atom type mappings.public static AtomTypeMapper getInstance(String mappingFile, InputStream stream)
InputStream
.mappingFile
- Name of the InputStream
defining the atom type to atom type mappings.stream
- the InputStream
from which the mappings as readpublic String mapAtomType(String type)
AtomTypeMapper
instance.type
- atom type to map to the target schemapublic String getMapping()
InputStream
then the name is less well defined.AtomTypeMapper
.Copyright © 2021. All rights reserved.