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Author SHA1 Message Date
Thomas Holder
a62e2a4dae Merge pull request #172 from speleo3/mypy 
Add type annotations and mypy CI job
 2023-11-03 12:46:28 +01:00
Thomas Holder
57d7c6721b Add type annotations and mypy CI job 2023-10-26 11:46:54 +02:00
Thomas Holder
ee89e36f58 Merge pull request #171 from speleo3/versioneer-0.29 
Update versioneer to version 0.29
 2023-10-21 09:57:05 +02:00
Thomas Holder
a03d903acc Add Python 3.12 to CI 2023-10-21 09:32:06 +02:00
Thomas Holder
1c8885d400 Update versioneer to version 0.29 
Installed versioneer 0.29 with Python 3.12 and ran

```
versioneer install
```
 2023-10-21 09:20:54 +02:00
Nathan Baker
8ba1692e42 Merge pull request #170 from speleo3/test-issue-140 
Add test for issue #140
 2023-10-20 19:13:17 -07:00
Thomas Holder
54d76ec145 Add test for issue #140 2023-10-20 23:22:17 +02:00
Maohua Yang
33158d1172 Add more element valence (#169) 
* Add valence electrons for all elements
* fix: add unknown element valence to 4
* fix: group None bug
 2023-10-20 23:20:51 +02:00
Nathan Baker
d1d3b37b82 Merge pull request #167 from speleo3/top_up_from_atoms 
Improve MolecularContainer.top_up_conformations
 2023-09-17 08:18:26 -07:00
Thomas Holder
7d78acac6e Improve MolecularContainer.top_up_conformations 
Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147
 2023-09-17 15:30:29 +02:00
Nathan Baker
fd7b155171 Merge pull request #159 from jensengroup/nathan/153 
Release candidate for 3.5.0.
 2023-02-13 19:53:08 -08:00
Nathan Baker
af1b08dcbb Release candidate for 3.5.0. 
Fixes #153.

Once tagged as v3.5.0 (after commit to master), the version should
automatically update via versioneer.
 2023-02-12 20:49:59 -08:00
Nathan Baker
3155badf33 Merge pull request #158 from jensengroup/nathan/155 
Add past changes to ChangeLog.
 2023-02-05 14:16:26 -08:00
Nathan Baker
c74e7cda66 Clarify change in log. 
Fixes a863426e63 (r1096640761)
 2023-02-05 14:13:28 -08:00
Nathan Baker
0de6387b69 Clarify change in log. 
Fixes a863426e63 (r1096641709)
 2023-02-05 14:12:16 -08:00
Nathan Baker
a863426e63 Add past changes to ChangeLog. 
Fixes #155.
 2023-02-04 19:21:08 -08:00
Nathan Baker
430b631c9d Merge pull request #156 from jensengroup/nathan/154 
Update Python support.
 2023-02-04 18:47:55 -08:00
Nathan Baker
72c4950683 Remove Python 3.6 and 3.7 from more files. 2023-01-29 15:07:51 -08:00
Nathan Baker
74b8425234 Remove Python 3.7 support. 
Make corresponding changes to other files (including a few that I
missed before).
 2023-01-29 14:58:57 -08:00
Nathan Baker
967e8e7912 Convert Python version numbers to strings. 2023-01-29 14:53:12 -08:00
Nathan Baker
0a0602761b Update Python support. 
Remove 3.6 and change Change Log.
 2023-01-29 14:45:54 -08:00
Nathan Baker
01bf46ce74 Merge pull request #150 from IAlibay/py311 
Update CI and docs for Python up to py311
 2022-11-09 18:58:07 -08:00
Irfan Alibay
3e897b792f Update python-package.yml 2022-11-09 18:34:23 +00:00
IAlibay
f6f3c51c1c Update CI and docs for Python up to py311 2022-11-09 14:16:59 +00:00
Nathan Baker
8acfb4fe1b Merge pull request #148 from speleo3/fix-get_pi 
Refactor and fix MolecularContainer.get_pi()
 2022-08-08 19:52:36 -07:00
Thomas Holder
80c7bf07cd Refactor MolecularContainer.get_pi 
Use bisection instead of grid search. This is ~10x faster and also fixes
pI computation for one of my files which only got single digit precision
with the old code.
 2022-08-08 21:29:28 +02:00
Thomas Holder
6388e0c4ee Test pI (isoelectric point) result 2022-08-08 21:29:10 +02:00
Nathan Baker
ab80128c45 Merge pull request #141 from latrocinia/master 
protonate.py: Rename Vanadium element from Va to V
 2022-03-02 20:16:20 -08:00
Gydo van Zundert
b920f5aeec Add unit test for protonate.py 2022-03-02 15:45:11 -05:00
Gydo van Zundert
f49eaedefb protonate.py: Rename Vanadium element from Va to V 2022-02-24 15:49:36 -05:00
Nathan Baker
beddb0ac87 Merge pull request #124 from danny305/master 
CLI parameters for the -g and -w options did not output to .pka out file
 2021-11-22 15:09:47 -08:00
Darren Curtis
17197831de Merge pull request #133 from speleo3/open_file_for_reading_context_manager 
Return context manager from open_file_for_reading
 2021-11-01 11:19:34 -07:00
Thomas Holder
ed087b02c7 Return context manager from open_file_for_reading 2021-10-31 18:36:38 +01:00
Danny Diaz
c37f54b93c refactored Decimal/round order of operation. 2021-03-06 11:02:41 -06:00
Danny Diaz
38aab010dc Addressed bug CLI parameters for the -g and -w options did not output to .pka file 2021-02-17 20:39:29 -08:00
Nathan Baker
68007f065c Merge pull request #121 from jensengroup/nathan/docs 
Remove numbering from Sphinx documentation.
 2020-12-18 19:24:20 -08:00
Nathan Baker
a22fd506be Remove numbering from Sphinx documentation. 
Fixes #119.
 2020-12-17 16:00:00 -08:00
Nathan Baker
c443b218a8 Merge pull request #120 from jensengroup/nathan/changelog 
Address comments on change log.
 2020-12-16 19:35:32 -08:00
Nathan Baker
52e3649e27 Address comments on change log. 
See d87afb3df5 (commitcomment-45090556)
 2020-12-15 20:10:40 -08:00
Nathan Baker
d87afb3df5 Document changes associated with older releases. 
Fixes #117.
 2020-12-13 16:49:26 -08:00
Nathan Baker
d1df3844fe Fix incorrect restructured text. 2020-12-13 16:46:27 -08:00
Nathan Baker
2f10ecdd1f Merge pull request #114 from jensengroup/issue-17 
Missing N or O in AMD Group: Keep going
 2020-12-13 10:45:27 -08:00
Thomas Holder
82879cdda5 Add a changelog 2020-12-09 20:05:14 +01:00
Thomas Holder
578b57694f propka3 --version prints version 
Closes https://github.com/jensengroup/propka/issues/89
 2020-12-09 10:19:54 -07:00
Thomas Holder
f028562026 Missing N or O in AMD Group: Keep going 
Print a warning but don't fail if the N or O atoms are missing in an
amide group. This is consistent with how other groups handle missing
atoms.

Closes https://github.com/jensengroup/propka/issues/17
 2020-12-07 09:26:53 +01:00
Thomas Holder
3937cb1467 Merge pull request #112 from jensengroup/fix-105 
Fix `propka --display-coupled-residues`
 2020-12-06 17:40:49 +01:00
Thomas Holder
8f8aa29be4 Fix propka --display-coupled-residues 
Fixes https://github.com/jensengroup/propka/issues/105
 2020-12-06 17:22:30 +01:00
Thomas Holder
31b41c32df Merge pull request #110 from jensengroup/fix-97-speedup-box-bonding 
Fix and speedup box bonding
 2020-12-03 10:19:01 +01:00
Thomas Holder
c78345c75c Refactor box bonding 
5x speedup of `find_bonds_for_molecules_using_boxes`
 2020-12-02 08:52:59 +01:00
Thomas Holder
cc8514e3dc Fix BondMaker.put_atom_in_box 
Was only populating 8 out of 14 necessary boxes.

Fixes https://github.com/jensengroup/propka/issues/97
 2020-12-02 08:15:59 +01:00