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7563a706cf00dd70f3f3b5d1de635dd5a6f92e66
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10 Commits

Author SHA1 Message Date
Irfan Alibay
7563a706cf fixes run's single method (#85) 
* Fixes #82
* Changes:
    * input arguments now reflects the changes made to read_molecule_file in #84
    * Writing of pKa file is now optional (default behaviour has been kept). This will be particularly 
       useful downstream where we would just want to have access to the MoleculeContainer object.
     * new test_run file specific for testing run.
* add tests
* add docs
 2020-07-17 11:18:07 -07:00
Oliver Beckstein
26a5ab042e API docs for propka 
- use autosummary (with custom module template)
- updated module docs for all modules so that they are included
  with sphinx autodocs
 2020-06-19 16:25:24 -07:00
Nathan Baker
9b59d924b2 Make PROPKA input file generation optional. 
Fixes https://github.com/jensengroup/propka-3.1/issues/51.
 2020-05-31 10:26:56 -07:00
Nathan Baker
84846aad8c Resolve cyclic import problem. 
Fixes https://github.com/jensengroup/propka-3.1/issues/49

Moved I/O into higher level of of code; should make
issue https://github.com/jensengroup/propka-3.1/issues/51
easier to resolve
 2020-05-30 12:01:30 -07:00
Nathan Baker
87347a7d60 Modernize print statements with str.format() 2020-05-28 20:31:03 -07:00
Nathan Baker
d965d95fba Clean up line breaks in run.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:26:18 -07:00
Nathan Baker
2321a4df8a De-lint run.py. 2020-05-25 13:10:55 -07:00
Nathan Baker
ae7e8b6430 Replace optparse with argparse. 
Optparse is deprecated.  Argparse will allow tighter integration with
PDB2PQR/APBS.
 2020-05-12 13:13:28 -07:00
Oliver Beckstein
ddaf27dea8 run.single() to run a propka calculation without script 
- can pass a single pdffile (or stream(!))
- added options lib.loadOptions() to pass opt string
 2014-11-20 17:30:27 -07:00
Oliver Beckstein
b928c18bab Re-packaged with setuptools for standard installation 
* 'python setup.py install' will install
  - a package 'propka' (which contains everything that 'Source' contained
    in the original distribution)
  - an executable script 'propka31' (which is identical to the original
    'propka.py' script but it is automatically generated via the setuptools
    mechanism; it uses propka.run.main().
* 'pip install' will also work
* the README.md file was changed to reflect the alterations
* metadata in the setup.py file was added

NOTE: The licence is still unclear!
 2013-07-25 11:14:44 -07:00