atomradiitable.py

#!/usr/bin/env python
##############################################################################
#
# diffpy.srreal     by DANSE Diffraction group
#                   Simon J. L. Billinge
#                   (c) 2011 The Trustees of Columbia University
#                   in the City of New York.  All rights reserved.
#
# File coded by:    Pavol Juhas
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE_DANSE.txt for license information.
#
##############################################################################
"""Class AtomRadiiTable -- storage of empirical atom radii."""


# exported items, these also makes them show in pydoc.
__all__ = ["AtomRadiiTable", "ConstantRadiiTable", "CovalentRadiiTable"]

from diffpy.srreal.srreal_ext import AtomRadiiTable, ConstantRadiiTable

# class CovalentRadiiTable ---------------------------------------------------


class CovalentRadiiTable(AtomRadiiTable):
    """Covalent radii from Cordero et al., 2008, doi:10.1039/b801115j.

    Instantiation of this class requires the periodictable module.
    """

    # class variable that holds the periodictable.elements object
    _elements = None

    def _standardLookup(self, smbl):
        """Return covalent atom radius in Angstroms.

        smbl -- string symbol of an element

        Return float.  Raise ValueError for unknown element symbol.
        """
        if CovalentRadiiTable._elements is None:
            from periodictable import elements

            CovalentRadiiTable._elements = elements
        e = self._elements.isotope(smbl)
        rv = e.covalent_radius
        if rv is None:
            emsg = "Undefined covalent radius for %r." % smbl
            raise ValueError(emsg)
        return rv

    # HasClassRegistry overloads:

    def create(self):
        """Create new instance of the CovalentRadiiTable."""
        return CovalentRadiiTable()

    def clone(self):
        """Return a new duplicate instance of self."""
        import copy

        return copy.copy(self)

    def type(self):
        """Unique string identifier of the CovalentRadiiTable type. This
        is used for class registration and as an argument for the
        createByType function.

        Return string.
        """
        return "covalent"


# End of class CovalentRadiiTable
CovalentRadiiTable()._registerThisType()

# End of file