Nathan Baker
a27f054ac7
Clean up line breaks in molecular_container.py.
2020-05-25 19:43:32 -07:00
Nathan Baker
2658f80906
Clean up line breaks in ligand.py
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See https://github.com/jensengroup/propka-3.1/issues/43
2020-05-25 19:33:07 -07:00
Nathan Baker
72851b5498
Clean line breaks.
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See https://github.com/jensengroup/propka-3.1/issues/43
2020-05-25 19:21:56 -07:00
Nathan Baker
5242366006
Clean up line breaks in lib.py
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See https://github.com/jensengroup/propka-3.1/issues/43
2020-05-25 19:09:11 -07:00
Nathan Baker
e5dedc1786
De-lint iterative.py
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See https://github.com/jensengroup/propka-3.1/issues/43 .
2020-05-25 18:55:02 -07:00
Nathan Baker
919305d8a3
Clean up line breaks in group.py and hybrid36.py
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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
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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
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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.
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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
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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.
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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.
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For https://github.com/jensengroup/propka-3.1/issues/43
2020-05-25 16:42:09 -07:00
Nathan Baker
75cdf0ea04
De-lint tests.
2020-05-25 14:44:53 -07:00
Nathan Baker
d30705d490
De-lint propka31.py.
2020-05-25 14:38:20 -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
0de12f0f3a
Merge branch 'master' into nathan/delint
2020-05-25 10:00:29 -07:00
Nathan Baker
a88774c136
Have Git ignore Visual Studio code files.
2020-05-25 09:59:52 -07:00
Nathan Baker
0164630e2f
Remove duplicate propka.cfg file.
2020-05-25 09:59:20 -07:00
Nathan Baker
32fbb30464
De-lint parameters.py.
2020-05-25 09:58:51 -07:00
Nathan Baker
c7c626791a
Remove duplicate propka.cfg.
2020-05-25 09:55:09 -07:00
Nathan Baker
f38faaed97
De-lint output.py.
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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
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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
3cfcc8f6d3
Merge pull request #33 from Electrostatics/nathan/delint
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De-lint atoms.py and part of bonds.py
2020-05-23 09:39:02 -07:00
