openbabel/openbabel — pull request #26 by kartlee (2013-09-12 15:09:29+00:00)
Title: Improve space group support in .car files

- Support Hermann-Mauguin notation space groups with spaces and also
the unspecified default space group.

- HM space group is enclosed within parentheses and can contain space
between them as per the given format details in -
http://hincklab.uthscsa.edu/html/soft_packs/msi_docs/insight980/formats980/ClassicFiles.html.

The previous code didn't recognize such a spacegroup as it strictly
looked for 8 fields after tokenizing them using default delimiters as
space, tab, newline.

- It is legal to have .car files with PBC=ON and no space group defined
in the fifth line and just have PBC and a,b,c,alpha,beta,gamma
parameters. Such structure is considered to have lowest symmetry
space-group as P1. This means there are no symmetry operations in play
and all atoms are explicit within the unit cell. The .car files for
H2O and polymers fall under this category since they are amorphous but
are periodic.

- Added tests in new format to ensure this is working.

- I found following tests in openbabel:master already fail. So this has nothing to do with this change when you address my request.

11 - test_builder_1 (Failed)
12 - test_builder_2 (Failed)
96 - test_charge_mmff94_1 (Failed)
100 - test_ffgaff_1 (Failed)
101 - test_ffghemical_1 (Failed)
104 - test_ffuff_1 (Failed)
112 - test_logp_psa_1 (Failed)
126 - inchiSamples.sdf_Test (Failed)
127 - inchiSamplesTechMan.sdf_Test (Failed)