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cc8514e3dc43d93d1fbfa5c545692451d8014806
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18 Commits

Author SHA1 Message Date
Thomas Holder
cc8514e3dc Fix BondMaker.put_atom_in_box 
Was only populating 8 out of 14 necessary boxes.

Fixes https://github.com/jensengroup/propka/issues/97
 2020-12-02 08:15:59 +01:00
Nathan Baker
9350799be1 Remove logging abstraction to facilitate debugging and reduce bloat. 
Also performed minor delinting.

Fixes #108
 2020-11-29 16:09:45 -08:00
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
3266521d31 Replace old formatting with new str.format() 2020-05-27 20:55:44 -07:00
Nathan Baker
142fa5a004 Clean up line breaks in bonds.py. 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 17:18:57 -07:00
Nathan Baker
5afc5d511a Removed missed comment. 2020-05-23 15:51:47 -07:00
Nathan Baker
02ca72d91d Remove self.h_dist attribute. 
Only used in __init__ function.

Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r429570945
 2020-05-23 13:16:18 -07:00
Nathan Baker
db8571414e Convert classmethod to staticmethod. 
Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r429570235
and https://github.com/jensengroup/propka-3.1/pull/40#discussion_r429570322
 2020-05-23 13:11:38 -07:00
Nathan Baker
f2aef4ce4f De-lint bonds.py 2020-05-23 09:57:53 -07:00
Nathan Baker
013167026f De-lint bonds.py 2020-05-21 19:29:54 -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
Nathan Baker
303aaae25a Partial pylint de-linting of bonds.py. 2020-05-16 21:11:09 -07:00
Nathan Baker
2bd7e70249 Load data from JSON rather than pickle. 
Increases platform independence.
 2020-05-05 11:55:45 -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
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
Mike Beachy
edd25afad3 add a reference to the math.ceil note 2014-02-22 17:48:16 -05:00
Oliver Beckstein
7008ed9f24 use pkg_resources to access bundled files 
* egg file can remain zipped
* see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources
  for details
 2013-07-25 11:40:50 -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