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919305d8a3027ea15e5b6d7424fa59b8fb4524e1
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78 Commits

Author SHA1 Message Date
Nathan Baker
919305d8a3 Clean up line breaks in group.py and hybrid36.py 
https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 18:49:51 -07:00
Nathan Baker
891fecaab3 Clean up line breaks in determinants.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 18:15:46 -07:00
Nathan Baker
ba8362f514 Clean up line breaks in coupled_groups.py 
See https://github.com/jensengroup/propka-3.1/issues/43.
 2020-05-25 18:09:59 -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
1ce44b77bf Clean up line breaks in calculations.py 
See https://github.com/jensengroup/propka-3.1/issues/43.
 2020-05-25 17:33:16 -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
4408b23448 Clean up line breaks. 
For https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 16:42:09 -07:00
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
6702f96730 De-lint vector_algebra.py 2020-05-25 13:53:04 -07:00
Nathan Baker
2321a4df8a De-lint run.py. 2020-05-25 13:10:55 -07:00
Nathan Baker
cd0e9e5c3d De-lint protonate.py. 2020-05-25 13:05:16 -07:00
Nathan Baker
b3e2685e94 De-lint propka.py. 2020-05-25 11:54:41 -07:00
Nathan Baker
47226bb4b0 Fix deprecated string syntax. 2020-05-25 11:29:11 -07:00
Nathan Baker
32fbb30464 De-lint parameters.py. 2020-05-25 09:58:51 -07:00
Nathan Baker
f38faaed97 De-lint output.py. 
Public methods/members changed; dependencies checked via Google.
 2020-05-25 08:24:54 -07:00
Nathan Baker
3342d3418c Document need to change Molecular_container name. 2020-05-25 07:59:55 -07:00
Nathan Baker
6190f6d5f5 De-lint molecular_container.py. 2020-05-24 19:47:10 -07:00
Nathan Baker
786a4c9292 De-lint ligand.py. 2020-05-24 18:29:38 -07:00
Nathan Baker
3a5bae5b41 De-lint ligand_pka_values.py 2020-05-24 16:39:59 -07:00
Nathan Baker
59a8717664 De-lint lib.py. 2020-05-24 15:30:35 -07:00
Nathan Baker
04b52d458c De-lint iterative.py. 2020-05-24 12:05:48 -07:00
Nathan Baker
95e132e520 De-lint hybrid36.py 2020-05-24 11:21:55 -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
25648327ce De-lint determinant.py. 2020-05-24 08:21:05 -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
5afc5d511a Removed missed comment. 2020-05-23 15:51:47 -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
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
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
f2aef4ce4f De-lint bonds.py 2020-05-23 09:57:53 -07:00
Nathan Baker
e1656a4911 Remove exec() from atom.py 2020-05-23 09:44:50 -07:00
Nathan Baker
120718fbd8 Remove property method suggestion. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429113755
 2020-05-23 09:33:47 -07:00
Nathan Baker
df6d8492da Simplify bonded atom counting 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-05-23 09:31:23 -07:00
Nathan Baker
69a369c17f Remove suggestion for @property method. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429112013
 2020-05-23 09:29:24 -07:00
Nathan Baker
4b3dee54f7 Simplify bonded atom counting. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429110880
and https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429111421
 2020-05-23 09:26:03 -07:00
Nathan Baker
66e3e552c9 Add description of hybrid36. 
Addresses https://github.com/jensengroup/propka-3.1/pull/33#discussion_r429108127
 2020-05-23 09:20:49 -07:00
Nathan Baker
98ad8702d6 Merge branch 'master' into nathan/delint 2020-05-23 09:20:01 -07:00
Nathan Baker
5114442610 Merge branch 'master' into nathan/delint 2020-05-23 08:57:50 -07:00
Nathan Baker
0b4241cce6 Merge remote-tracking branch 'origin/nathan/argpase' into nathan/tests 2020-05-23 08:25:24 -07:00
Nathan Baker
03e12ae15c Update propka/lib.py 
I cannot spell.

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-05-22 20:22:30 -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
51a59f9979 Merge branch 'nathan/tests' into nathan/delint 2020-05-21 15:58:49 -07:00
Nathan Baker
a49015c297 Merge branch 'nathan/tests' into nathan/argpase 2020-05-21 15:58:03 -07:00