Package org.openscience.cdk.silent

Class AtomType

java.lang.Object
org.openscience.cdk.silent.ChemObject
org.openscience.cdk.silent.Element
org.openscience.cdk.silent.Isotope
org.openscience.cdk.silent.AtomType
All Implemented Interfaces:
Serializable, Cloneable, IAtomType, ICDKObject, IChemObject, IElement, IIsotope
Direct Known Subclasses:
Atom
public class AtomType extends Isotope implements IAtomType, Serializable, Cloneable
The base class for atom types. Atom types are typically used to describe the behaviour of an atom of a particular element in different environment like sp3 hybridized carbon C3, etc., in some molecular modelling applications.
Author:
steinbeck
See Also:
Keywords:
atom, type
Created on:
2001-08-08

  • Field Details

    • formalCharge

      protected Integer formalCharge
      The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0

    • hybridization

      protected IAtomType.Hybridization hybridization
      The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.

    • electronValency

      protected Integer electronValency
      The electron Valency of this atom with CDKConstants.UNSET as default.

    • formalNeighbourCount

      protected Integer formalNeighbourCount
      The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitely connected atoms, including implicit hydrogens.

  • Constructor Details

    • AtomType

      protected AtomType()

    • AtomType

      public AtomType(String elementSymbol)
      Constructor for the AtomType object. Defaults to a zero formal charge. All other fields are set to CDKConstants.UNSET.
      Parameters:
      elementSymbol - Symbol of the atom

    • AtomType

      public AtomType(String identifier, String elementSymbol)
      Constructor for the AtomType object. Defaults to a zero formal charge.
      Parameters:
      identifier - An id for this atom type, like C3 for sp3 carbon
      elementSymbol - The element symbol identifying the element to which this atom type applies

    • AtomType

      public AtomType(IElement element)
      Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope. It does not copy the listeners and properties. If the element is an instanceof IAtomType, then the maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name are copied too.
      Parameters:
      element - IIsotope to copy information from

  • Method Details