org.openscience.cdk.config

Class AtomTypeFactory

java.lang.Object

org.openscience.cdk.config.AtomTypeFactory

public class AtomTypeFactory
extends Object

General class for defining AtomTypes. This class itself does not define the items types; for this classes implementing the AtomTypeConfiguration interface are used.

To see which AtomTypeConfigurator's CDK provides, one should check the AtomTypeConfigurator API.

The AtomTypeFactory is a singleton class, which means that there exists only one instance of the class. Well, almost. For each atom type table, there is one AtomTypeFactory instance. An instance of this class is obtained with:

  AtomTypeFactory factory = AtomTypeFactory.getInstance(someChemObjectBuilder);
  

For each atom type list a separate AtomTypeFactory is instantiated.

To get all the atom types of an element from a specific list, this code can be used:

  AtomTypeFactory factory = AtomTypeFactory.getInstance(
    "org/openscience/cdk/config/data/jmol_atomtypes.txt",
      someChemObjectBuilder
  );
  AtomType[] types = factory.getAtomTypes("C");
  

Author:

steinbeck

See Also:

IAtomTypeConfigurator

Source code:

master

Belongs to CDK module:

core

Keywords:

atom, type

Created on:

2001-08-29

Field Summary

Fields

Modifier and Type	Field and Description
static String	ATOMTYPE_ID_JMOL Used as an ID to describe the atom type.
static String	ATOMTYPE_ID_MODELING Used as an ID to describe the atom type.
static String	ATOMTYPE_ID_STRUCTGEN Used as an ID to describe the atom type.

Method Summary

Methods

Modifier and Type	Method and Description
IAtom	configure(IAtom atom) Configures an atom.
IAtomType[]	getAllAtomTypes() Gets the allAtomTypes attribute of the AtomTypeFactory object.
IAtomType	getAtomType(String identifier) Get an AtomType with the given ID.
IAtomType[]	getAtomTypes(String symbol) Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.
static AtomTypeFactory	getInstance(IChemObjectBuilder builder) Method to create a default AtomTypeFactory, using the structgen atom type list.
static AtomTypeFactory	getInstance(InputStream ins, String format, IChemObjectBuilder builder) Method to create a default AtomTypeFactory, using the given InputStream.
static AtomTypeFactory	getInstance(String configFile, IChemObjectBuilder builder) Method to create a specialized AtomTypeFactory.
int	getSize() Returns the number of atom types in this list.

Methods inherited from class java.lang.Object

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

Field Detail

ATOMTYPE_ID_STRUCTGEN

public static final String ATOMTYPE_ID_STRUCTGEN

Used as an ID to describe the atom type.

See Also:

Constant Field Values

ATOMTYPE_ID_MODELING

public static final String ATOMTYPE_ID_MODELING

Used as an ID to describe the atom type.

See Also:

Constant Field Values

ATOMTYPE_ID_JMOL

public static final String ATOMTYPE_ID_JMOL

Used as an ID to describe the atom type.

See Also:

Constant Field Values

Method Detail

getInstance

public static AtomTypeFactory getInstance(InputStream ins,
                          String format,
                          IChemObjectBuilder builder)

Method to create a default AtomTypeFactory, using the given InputStream. An AtomType of this kind is not cached.

Parameters:

ins - InputStream containing the data

format - String representing the possible formats ('xml' and 'txt')

builder - IChemObjectBuilder used to make IChemObject instances

Returns:

The AtomTypeFactory for the given data file

See Also:

getInstance(String, IChemObjectBuilder)

getInstance

public static AtomTypeFactory getInstance(IChemObjectBuilder builder)

Method to create a default AtomTypeFactory, using the structgen atom type list.

Parameters:

builder - IChemObjectBuilder used to make IChemObject instances

Returns:

The AtomTypeFactory for the given data file

See Also:

getInstance(String, IChemObjectBuilder)

getInstance

public static AtomTypeFactory getInstance(String configFile,
                          IChemObjectBuilder builder)

Method to create a specialized AtomTypeFactory. Available lists in CDK are:

• org/openscience/cdk/config/data/jmol_atomtypes.txt
• org/openscience/cdk/config/data/mol2_atomtypes.xml
• org/openscience/cdk/config/data/structgen_atomtypes.xml
• org/openscience/cdk/config/data/mm2_atomtypes.xml
• org/openscience/cdk/config/data/mmff94_atomtypes.xml
• org/openscience/cdk/dict/data/cdk-atom-types.owl
• org/openscience/cdk/dict/data/sybyl-atom-types.owl

Parameters:

configFile - String the name of the data file

builder - INewChemObjectBuilder used to make IChemObject instances

Returns:

The AtomTypeFactory for the given data file

getSize

public int getSize()

Returns the number of atom types in this list.

Returns:

The number of atom types

getAtomType

public IAtomType getAtomType(String identifier)
                      throws NoSuchAtomTypeException

Get an AtomType with the given ID.

Parameters:

identifier - an ID for a particular atom type (like C$)

Returns:

The AtomType for this id

Throws:

NoSuchAtomTypeException - Thrown if the atom type does not exist.

getAtomTypes

public IAtomType[] getAtomTypes(String symbol)

Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.

Parameters:

symbol - An element symbol to search for

Returns:

An array of atomtypes that matches the given element symbol and atomtype class

getAllAtomTypes

public IAtomType[] getAllAtomTypes()

Gets the allAtomTypes attribute of the AtomTypeFactory object.

Returns:

The allAtomTypes value

configure

public IAtom configure(IAtom atom)
                throws CDKException

Configures an atom. Finds the correct element type by looking at the Atom's atom type name, and if that fails, picks the first atom type matching the Atom's element symbol..

Parameters:

atom - The atom to be configured

Returns:

The configured atom

Throws:

CDKException - when it could not recognize and configure the IAtom