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jbarnoud avatar mnmelo avatar

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jbarnoud diogovv ggerogiokas farshadsm muntereiner

mdreader's Issues

fork under MDAnalysis org?

@mnmelo what do you think about forking mdreader into the MDAnalysis org? In this way it gains visibility and MDAnalysis users can discover it?

Ideally, you'd push changes to the fork, too, so that the MDAnalysis/mdreader repo is also current.

Nicer error message when a file is missing

If a program that relies on MDreader is called without -f, -s, or -n, then the program fails during do_parse whith a python traceback.

The message for a missing -f looks like:

Traceback (most recent call last):
  File "./count_between.py", line 22, in <module>
    md = user_cli()
  File "./count_between.py", line 18, in user_cli
    md.do_parse()
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 483, in do_parse
    map(check_file,(self.opts.topol,)+tuple(self.opts.infile))
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 63, in check_file
    raise IOError('Can\'t find file %s' % (fname))
IOError: Can't find file t

The message for a missing -s looks like:

Traceback (most recent call last):
  File "./count_between.py", line 22, in <module>
    md = user_cli()
  File "./count_between.py", line 18, in user_cli
    md.do_parse()
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 483, in do_parse
    map(check_file,(self.opts.topol,)+tuple(self.opts.infile))
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 63, in check_file
    raise IOError('Can\'t find file %s' % (fname))
IOError: Can't find file topol.tpr

And the message for a missing -n looks like:

Traceback (most recent call last):
  File "./count_between.py", line 22, in <module>
    md = user_cli()
  File "./count_between.py", line 18, in user_cli
    md.do_parse()
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 500, in do_parse
    self._parse_ndx()
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 512, in _parse_ndx
    self._get__ndx_atgroups()
  File "/home/jon/Envs/dev2/local/lib/python2.7/site-packages/MDreader/mdreader.py", line 923, in _get__ndx_atgroups
    resnames = numpy.unique(self.atoms.resnames())
TypeError: 'numpy.ndarray' object is not callable

MDreader could display a more human friendly error message.

Optionnally prevent automatic index group selection

If an index file is read with the add_ndx method, and that index file contains the number of groups that is expected, then the interactive selection process is skipped and all the groups are read. This is extremely convenient when the order of the groups does not matter. When the order of the groups does matter, though, it can be surprising and lead to mistakes.

Maybe there could be a flag (in the command line or in the API, I do not know at what level it should be), to prevent MDreader to automatically select the groups.

Allow to select TPR default group when no index file is provided

When it expects an index file but that none is provided by the user, Gromacs allows to select groups among the default one read in the TPR. MDreader could do it too. This would require MDAnalysis to be able to read these default groups from the TPR, though.

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