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Author SHA1 Message Date
Nathan Baker
7a25ec6598 Update executable script name. 
Changed script name to propka3 based on https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442326049

Updated additional information in setup.py
 2020-06-18 08:57:12 -07:00
Nathan Baker
573b38db38 Fix stray propka31 to propka32. 2020-06-18 08:24:51 -07:00
Nathan Baker
a2196cdc6f Consolidate documentation. 
Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442016279.
 2020-06-18 08:19:22 -07:00
Nathan Baker
2909173caf Add missing *.json to package data list. 2020-06-17 15:31:16 -07:00
Nathan Baker
0c4979560d Change propka31 to propka32. 2020-06-17 15:25:50 -07:00
Nathan Baker
4e7a41730d Change module version number. 2020-06-17 15:25:23 -07:00
Nathan Baker
0e4f565c90 Remove version number from tests. 
Tests aren't version-dependent.
 2020-06-17 15:24:20 -07:00
Nathan Baker
d52620d4e9 Update PROPKA header banner. 2020-06-17 15:24:00 -07:00
Nathan Baker
54294684b0 Remove broken links from README.md. 2020-06-17 13:22:17 -07:00
Nathan Baker
89a9eb15d4 Update INSTALL with better instructions. 
Remove explicit references to version 3.1 except for name of `propka31`
script which will be changed in subsequent commit.
 2020-06-17 13:17:33 -07:00
Nathan Baker
e8576fb4f3 Remove specific 3.1 version information. 
Except for name of script `propka31`; will handle that in another commit.
 2020-06-17 13:12:09 -07:00
Nathan Baker
1d8fa2bbbe Update setup.py with 3.2.0 information. 2020-06-17 12:33:52 -07:00
Nathan Baker
616540ebd6 Merge branch 'nathan/tempfile' 2020-06-03 18:36:47 -07:00
Nathan Baker
9126e3059f Fix PROPKA output naming. 
Addresses https://github.com/jensengroup/propka-3.1/pull/59#discussion_r434360267
 2020-06-03 18:34:12 -07:00
Nathan Baker
5d8e271420 Merge branch 'nathan/import' into nathan/tempfile 2020-06-03 17:51:16 -07:00
Nathan Baker
879c48a3d8 Merge branch 'nathan/import' 2020-06-03 17:50:56 -07:00
Nathan Baker
7085271ad5 Simplify with .writable() method. 
Addresses https://github.com/jensengroup/propka-3.1/pull/50#discussion_r434349737
 2020-06-03 17:49:19 -07:00
Nathan Baker
9b59d924b2 Make PROPKA input file generation optional. 
Fixes https://github.com/jensengroup/propka-3.1/issues/51.
 2020-05-31 10:26:56 -07:00
Nathan Baker
1d17cb05ed Remove TODO for refactoring. 
Done already.
 2020-05-30 13:15:45 -07:00
Nathan Baker
52554d905a Remove TODO statements for refactoring. 
Already done.
 2020-05-30 13:12:44 -07:00
Nathan Baker
84846aad8c Resolve cyclic import problem. 
Fixes https://github.com/jensengroup/propka-3.1/issues/49

Moved I/O into higher level of of code; should make
issue https://github.com/jensengroup/propka-3.1/issues/51
easier to resolve
 2020-05-30 12:01:30 -07:00
Nathan Baker
b597a6f257 Remove cyclic import based on I/O in pdb.py. 
Partially addresses https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 10:00:31 -07:00
Nathan Baker
397d5e10aa Remove cyclic import based on atom.py 
Partially addresses https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 09:26:13 -07:00
Nathan Baker
461edda3b2 Break propka.calculations into parts. 
Broken into three files to simplify import analysis:

* `calculations.py` - distance calculations and simple math
* `energy.py` - energy calculations
* `hydrogens.py` - hydrogen geometry calculations

Working towards addressing https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 08:45:39 -07:00
Nathan Baker
dde0d67ea5 Merge pull request #40 from Electrostatics/nathan/delint 
De-lint PROPKA
 2020-05-30 08:14:45 -07:00
Nathan Baker
d7147799d8 Python formatting is annoying. 
I sometimes miss C -- but only with output formatting.  C++ cout marks
some decline of civilization, I think...

Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r432313434
 2020-05-29 20:55:32 -07:00
Nathan Baker
a716c89a36 Remove unused argument from Atom() constructor. 2020-05-29 20:49:47 -07:00
Nathan Baker
5010d9fa14 Merge branch 'nathan/strings' into nathan/delint 2020-05-29 20:41:53 -07:00
Nathan Baker
83a7099d79 Fix my formatting mistakes. 
Python formatting makes me miss K&R C.
 2020-05-29 20:37:47 -07:00
Nathan Baker
b54190ef27 Fix complicated string formatting. 
PEP8 be damned!  https://www.python.org/dev/peps/pep-0008/#a-foolish-consistency-is-the-hobgoblin-of-little-minds

Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r432302025
 2020-05-29 20:08:41 -07:00
Nathan Baker
7bd12c725e Merge remote-tracking branch 'upstream/master' into nathan/strings 2020-05-29 20:06:57 -07:00
Nathan Baker
91570cbf68 Merge branch 'master' into nathan/delint 2020-05-28 20:35:27 -07:00
Nathan Baker
87347a7d60 Modernize print statements with str.format() 2020-05-28 20:31:03 -07:00
Nathan Baker
ba67f5149d Replace old-style printf with str.format 2020-05-28 16:10:48 -07:00
Nathan Baker
3266521d31 Replace old formatting with new str.format() 2020-05-27 20:55:44 -07:00
Nathan Baker
6e7c188dbd Update string formatting to modern version. 
Focuses only on complex formatting.
 2020-05-27 16:26:52 -07:00
Nathan Baker
5916a80d56 Merge pull request #47 from Electrostatics/nathan/fix-run 
Add missing option to lib.loadOptions()
 2020-05-27 08:38:58 -07:00
Nathan Baker
33493cc4d2 Remove unnecessary args testing. 
Addresses https://github.com/jensengroup/propka-3.1/pull/47#discussion_r431224753
 2020-05-27 08:25:46 -07:00
Nathan Baker
557ab19312 Replace complex old-style format with new format strings. 2020-05-27 08:19:36 -07:00
Nathan Baker
2305615fbe Add line breaks to format strings. 
Addresses https://github.com/jensengroup/propka-3.1/issues/44#issuecomment-634233970
 2020-05-27 08:01:30 -07:00
Nathan Baker
959f978abb Add default argument to loadOptions(). 
Fixes https://github.com/jensengroup/propka-3.1/issues/46
 2020-05-27 07:39:41 -07:00
Nathan Baker
46ae3d8251 Add __main__.py 
Makes it easier to run (and test) PROPKA as a module.
 2020-05-27 07:38:34 -07:00
Nathan Baker
bcccd89ca4 Add str.format() to atom.py. 
Addresses https://github.com/jensengroup/propka-3.1/issues/44
 2020-05-26 16:17:50 -07:00
Nathan Baker
36bea44a4d Clean up line breaks in tests. 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:35:54 -07:00
Nathan Baker
2bb6cf6293 Clean up line breaks in version.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:33:34 -07:00
Nathan Baker
c2f362a101 Clean up line endings for vector_algebra.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:30:58 -07:00
Nathan Baker
d965d95fba Clean up line breaks in run.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:26:18 -07:00
Nathan Baker
0ac800333d Clean up line breaks in protonate.py. 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:25:15 -07:00
Nathan Baker
a6016ed827 Clean up line breaks for pdb.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:22:28 -07:00
Nathan Baker
baed55e79a Clean up line breaks in parameters.py 
See https://github.com/jensengroup/propka-3.1/issues/43
 2020-05-25 20:12:47 -07:00