Package org.openscience.cdk.config

Class 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:
    main
    Belongs to CDK module:
    core
    Keywords:
    atom, type
    Created on:
    2001-08-29

    • 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​(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