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98263516bc828f89f3fb0be4b9295b9d970cdf20
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15 Commits

Author SHA1 Message Date
Nathan Baker
98263516bc De-lint version.py 2020-05-25 14:35:02 -07:00
Nathan Baker
2fef500307 Restore 3.0 compatibility functions. 2020-05-25 14:31:17 -07:00
Nathan Baker
a534d97016 De-lint groups.py 
I did my best (via Google) to make sure that renamed public members and
methods had minimal impact on others' code.
 2020-05-24 11:13:06 -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
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
1611e9d6ea Partial de-lint of calculations.py. 
Pausing here since I just deleted contactDesolvation().  However, there
was no way that anyone was using this function since it was very badly
broken and could not run.
 2020-05-23 13:24:05 -07:00
Nathan Baker
f444d138ee Partial de-lint of calculations.py. 
This really should be 3 separate files.  The initial de-lint focused on
the distance and hydrogen addition functions.
 2020-05-23 12:34:31 -07:00
Nathan Baker
80c8cca420 Nuke some backwards-compatible PROPKA 3.0 support. 2020-05-21 20:50:39 -07:00
Nathan Baker
76418a1a15 De-lint calculations.py up to difficult decision. 
Do we drop 3.0 support?  I vote "yes" but will leave that for the next
commit.
 2020-05-21 20:45:47 -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
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
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