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Author SHA1 Message Date
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
Nathan Baker
45aa08a79c Merge pull request #109 from jensengroup/nathan/logging 
Remove logging abstraction to facilitate debugging and reduce bloat.
 2020-12-01 11:55:26 -08:00
Nathan Baker
e081bd53b3 Add line breaks to error message. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r533131022
 2020-12-01 06:40:44 -08:00
Nathan Baker
de020599d3 Raise error for ligand pKa errors. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r532735233 per @orbeckst.
 2020-11-30 15:21:47 -08:00
Nathan Baker
c281623078 Change logging message to error. 
Fixes https://github.com/jensengroup/propka/pull/109#discussion_r532735233 based on suggestion from @orbeckst.
 2020-11-30 15:17:18 -08:00
Nathan Baker
fda4fe577b Merge branch 'master' into nathan/logging 2020-11-29 16:14:43 -08:00
Nathan Baker
9350799be1 Remove logging abstraction to facilitate debugging and reduce bloat. 
Also performed minor delinting.

Fixes #108
 2020-11-29 16:09:45 -08:00
Nathan Baker
f3bbd807ae Merge pull request #100 from IAlibay/rm-propkainput 
Removal of PROPKA input
 2020-11-29 15:41:28 -08:00
IAlibay
3ca674776f Remove unused attributes 2020-11-18 18:15:42 +00:00
Nathan Baker
67039aabc0 Merge pull request #102 from IAlibay/python3.9 
Adds python 3.9 to CI
 2020-11-18 09:32:51 -08:00
IAlibay
b164c1db1a Adds python3.9 to CI 2020-11-18 01:27:41 +00:00
IAlibay
196a2c6a1f remove unused command 2020-11-18 01:13:59 +00:00
IAlibay
012865e9e9 fix argparse typo 2020-11-18 00:53:07 +00:00
IAlibay
da7999832d Remove unused initialized_atom_group 2020-11-18 00:51:46 +00:00
IAlibay
d6ebd48473 missed conf container code 2020-11-18 00:31:15 +00:00
IAlibay
239c8183c9 Initial removal of PROPKA input 2020-11-17 23:31:24 +00:00
Thomas Holder
9dfd87a0eb Fix handling of multi-model PDB without MODEL 1 
Fixes https://github.com/jensengroup/propka/issues/95
 2020-11-11 10:57:15 +01:00
Thomas Holder
810750cdd7 Fix pI reporting in last line of .pka file 2020-07-22 07:50:10 +02:00
Thomas Holder
552dd133e6 Report correct version in .pka file header 2020-07-21 17:31:59 -07:00
Oliver Beckstein
cb65c644c6 use versioneer for version management (#88) 
- fix #87
- user versioneer for version management
   - use tag "vMAJOR.MINOR.PATCH" to indicate release number
   - exclude generated files from coverage;
      also exclude tests from coverage reporting;
      allow use of "# pragma: no cover" to exclude lines of code
      from coverage
   - configure coverage with entries in setup.cfg (removed
      commandline config from workflows/python-package.yml)
- related doc updates
   - make docs automatically use current version
      (docs use versioneer-based propka.__version__)
   - also added @IAlibay to authors (forgotten in previous
      PRs #84 and #85)
   - generate a sitemap (add sphinx_sitemap to requirements.txt)
- add test_version
   Note: Versioneer-generated version is “0-untagged” on the branch where
   it is tested so need to add it to a valid result.
 2020-07-18 12:32:25 -07:00
Irfan Alibay
7563a706cf fixes run's single method (#85) 
* Fixes #82
* Changes:
    * input arguments now reflects the changes made to read_molecule_file in #84
    * Writing of pKa file is now optional (default behaviour has been kept). This will be particularly 
       useful downstream where we would just want to have access to the MoleculeContainer object.
     * new test_run file specific for testing run.
* add tests
* add docs
 2020-07-17 11:18:07 -07:00
Nathan Baker
d16257af9a Merge pull request #84 from IAlibay/streams 
Allows for file-like objects to be passed to read_molecule_file
 2020-07-15 18:27:29 -07:00