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26a5ab042e30a8eafbe47528fe5121dd223eab01
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16 Commits

Author SHA1 Message Date
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
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
3266521d31 Replace old formatting with new str.format() 2020-05-27 20:55:44 -07:00
Nathan Baker
6e7c188dbd Update string formatting to modern version. 
Focuses only on complex formatting.
 2020-05-27 16:26:52 -07:00
Nathan Baker
284a33dfe8 Clean up line breaks. 
See https://github.com/jensengroup/propka-3.1/issues/43.
 2020-05-25 17:49:52 -07:00
Nathan Baker
98263516bc De-lint version.py 2020-05-25 14:35:02 -07:00
Nathan Baker
476ab1f276 De-lint determinants.py. 
Public methods/members names were changed.  These were checked against
Google for potential impact on other packages.
 2020-05-24 08:53:51 -07:00
Nathan Baker
c985e02713 De-lint coupled_groups.py 
Some methods/attributes were changed but were checked in Google to make
sure other codes were not affected.
 2020-05-23 17:57:12 -07:00
Nathan Baker
83c54ec153 De-lint conformation_container.py. 
Some public methods/members were changed.  These were checked against
Google for obvious use in other packages.
 2020-05-23 17:22:18 -07:00
Nathan Baker
5ed77a7cf6 De-lint calculations.py. 
Changes were made to function names; impacted functions changed in other
files.  Google searches performed to look for impacts to other software.
 2020-05-23 15:02:23 -07:00
Nathan Baker
10efc3c7f9 De-lint propka/atom.py 
Other changes are a result of Atom use in other files.
 2020-05-17 17:08:38 -07:00
Toni G
5fbbdd4868 Output performed with loggers. Adds options --no-print. (#12) 
Output performed with loggers.  Adds --quiet and --verbose options.
 2016-04-28 23:21:35 -07:00
Matvey Adzhigirey
8084b31393 Added --titrate_only option and tests for it. 
This option makes it possible for PROPKA to treat only a subset of protein
residues as titratable.
 2014-08-20 20:14:38 -04:00
Matvey Adzhigirey
c420b4c2a5 Use get_titratable_groups() instead of manually building up this list 
in find_covalently_coupled_groups().
 2014-08-13 11:12:21 -07:00
Matvey Adzhigirey
73c7a2a4be optimize a number of functions 
- Major optimization of the put_atom_in_box() function.
- Major optimization of the protein_precheck() function.
- Minor optimization in radial_volume_desolvation()
- Optimization in top_up() to scale for large structures.
 2014-02-27 18:15:18 -05:00
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