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pkienzle/periodictable: v1.5.3

Paul Kienzle; Björn Pedersen; Kurt Forrester; Stuart Prescott; Pavol Juhas; Petr Čermák; Mark Dickinson

Documentation: http://periodictable.readthedocs.org

1.5.3 2020-11-04

Known issues:

  • Incoherent scattering computed for contrast matched mixture in D2O_sld(), differs from the value that would be computed for a compound with the same isotope proportions and density computed in neutron_sld(). This may change in a future release.

Breaking changes:

  • Fix calculation of contrast match points for biomolecules. The old formula used the density of H2O for the D2O sld calculation.
  • Modify biomolecule support to use H[1] rather than T for labile hydrogen. This will result in less error when the labile formula is used in lieu of the natural formula or the contrast-matched formula, and make it more obvious from glancing at the formula that labile hydrogen is present.
  • Modify fasta.Molecule attributes, dropping Hmass and Hsld. Hnatural has been moved to natural_formula. The formula with labile hydrogen is stored in labile_formula, as well as formula as before.

New:

  • Add replace() method to formula to allow isotope substitution.
  • Add nsf.D2O_match() and nsf.D2O_sld() functions.

Modified:

  • Neutron wavelength now defaults to 1.798 A when wavelength and energy are both None in neutron_sld() and neutron_scattering() rather than throwing an assertion error.
  • table can be passed to neutron sld calculators as the source of isotope information when parsing the chemical formula.
  • Switch unit test framework from nose to pytest.
  • Update docs.

See README.rst for complete history.

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