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Author SHA1 Message Date
Nathan Baker
c7c626791a Remove duplicate propka.cfg. 2020-05-25 09:55:09 -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
d8ed3262b9 Ignore Visual Studio Code files. 2020-05-24 18:32:47 -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
6cbcac3be9 Make de-linting easier. 2020-05-24 11:12:47 -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
c2de394cb8 Merge pull request #41 from jensengroup/update-readme-with-doi 
Add DOIs to references
 2020-05-23 13:05:38 -07:00
Nathan Baker
a00617e7a5 Convert "DOI" to lower case 2020-05-23 13:04:41 -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
a647b80ae3 Add DOIs to references 
Make life easier for people.
 2020-05-23 11:47:00 -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
3cfcc8f6d3 Merge pull request #33 from Electrostatics/nathan/delint 
De-lint atoms.py and part of bonds.py
 2020-05-23 09:39:02 -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
62f7dfce1a Merge pull request #36 from Electrostatics/nathan/tests 
Add pytest-based testing to PROPKA
 2020-05-23 08:44:00 -07:00
Nathan Baker
73f0ce47af Replace pandas with numpy.testing 
Addresses https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429104797
 2020-05-23 08:40:17 -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
ebddfa1f9f Add tests_require argument to setup.py. 
Addresses https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429100526

Since the tests_require argument is deprecated, I'm also leaving the
requirements.txt file to make sure the dependencies are captured in the
future.
 2020-05-23 08:19:19 -07:00
Nathan Baker
1b0ad999b1 Remove unnecessary exception catching. 
Fixes https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429063049
 2020-05-23 08:06:54 -07:00
Nathan Baker
6f603ab17c Merge pull request #37 from Electrostatics/nathan/argpase 
Fix error when using PROPKA with PDB2PQR
 2020-05-23 08:04:30 -07:00
Nathan Baker
6288711209 Update requirements with pandas. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429106093
 2020-05-22 21:04:09 -07:00
Nathan Baker
2266e0a102 Consistent test naming. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429099054
 2020-05-22 20:55:58 -07:00
Nathan Baker
48f69eb544 Support Python 3.5 and higher. 
See https://github.com/jensengroup/propka-3.1/pull/36#discussion_r429094884
 2020-05-22 20:41:59 -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