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Author SHA1 Message Date
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
Nathan Baker
f13d3d8121 PROPKA testing working with pytest. 2020-05-21 15:50:23 -07:00
Nathan Baker
fc27d8bfc3 Fix bugs in invocation and options. 
Add non-command-arguments.
Restore --quiet option.
 2020-05-21 11:53:03 -07:00
Nathan Baker
393f5cee50 Rename "Tests" directory for consistency. 2020-05-21 10:39:08 -07:00
Nathan Baker
fa4a547f1f Enforce Python 3.*. 2020-05-21 10:29:45 -07:00
Nathan Baker
17bad90dc4 Start fixing tests. 2020-05-18 20:37:56 -07:00
Nathan Baker
d0e80b810b Handle multiple additions of same argument. 
APBS and PROPKA add the same arguments.
 2020-05-18 16:29:39 -07:00
Nathan Baker
747333d4ac Merge branch 'master' into nathan/delint 2020-05-18 16:27:58 -07:00
Nathan Baker
e9a88bee4b Restore Tests/runtest.py. 
Also update README.md to document the existence of multiple tests.
 2020-05-18 16:23:39 -07:00
Nathan Baker
10efc3c7f9 De-lint propka/atom.py 
Other changes are a result of Atom use in other files.
 2020-05-17 17:08:38 -07:00
Nathan Baker
303aaae25a Partial pylint de-linting of bonds.py. 2020-05-16 21:11:09 -07:00
Nathan Baker
22d83ae29e Fix some pylint issues for propka.atom. 
Only implemented fixes that do not change functonality.
Avoided changing numbers of arguments, numbers of attribute,
variable/function names, etc.
 2020-05-16 21:10:55 -07:00
Nathan Baker
61c200c3f4 Remove duplicate tests. 2020-05-16 18:18:15 -07:00
Nathan Baker
6ae2908c4b Merge pull request #29 from Electrostatics/master 
* Replace PROPKA pickle with JSON.
* Replace optionparser with argparse.
* Fix tests for Ubuntu WSL.
* Fix verbosity/logging.
 2020-05-16 17:09:52 -07:00
Nathan Baker
0fbaa6711f Update minor version number. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424575807
 2020-05-16 17:06:28 -07:00
Nathan Baker
6c67ef152c Remove unnecessary OptionParser statements. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424418158.
 2020-05-16 16:58:19 -07:00
Nathan Baker
9cafb41e06 Document acceptable error in PROPKA tests. 
Addresses
https://github.com/jensengroup/propka-3.1/pull/29#discussion_r424572620
 2020-05-16 16:49:47 -07:00
Nathan Baker
cddda2f515 Fix verbosity/logging in PROPKA. 2020-05-14 19:02:11 -07:00
Nathan Baker
387d0a5664 Move argparse sub-command to group. 2020-05-12 14:27:46 -07:00
Nathan Baker
847004a2d6 Fix subparser syntax for argparse. 2020-05-12 13:51:44 -07:00
Nathan Baker
6ddc32c101 Add newline to end of __init__.py. 2020-05-12 13:51:24 -07:00
Nathan Baker
ae7e8b6430 Replace optparse with argparse. 
Optparse is deprecated.  Argparse will allow tighter integration with
PDB2PQR/APBS.
 2020-05-12 13:13:28 -07:00
Nathan Baker
aeb1663d7b Add code to clean up files after test. 2020-05-10 19:19:37 -07:00
Nathan Baker
997298f1f0 Loosen error tolerance in test. 
The PROPKA31 tests fail on Windows 10 Ubuntu 18.04 Windows Subsystem
Linux without any changes.  The relative error is less than 1e-3.  This
commit chnages the behavior to a test of absolute agreement to a test of
relative error less than 1e-3.
 2020-05-10 18:29:51 -07:00
Nathan Baker
4fa015a54e Fix typo in PROPKA test. 
Fail() -> fail().
 2020-05-10 18:18:36 -07:00
Nathan Baker
2bd7e70249 Load data from JSON rather than pickle. 
Increases platform independence.
 2020-05-05 11:55:45 -07:00
Nathan Baker
726d6aa412 Update __init__.py. 
Fix __all__ list and add docstring to point users to PROPKA website when
used as module.
 2020-05-05 11:38:36 -07:00
Oliver Beckstein
91925bb920 test for stream-ness in Py 3/Py 2 compatible manner 2018-03-19 22:34:22 -07:00
Oliver Beckstein
9ebc76bcdc modernized installation procedure 
- set VERSION to 3.1.0 (introduce a patch level 0 so that it becomes
  easier to publish packages with small fixes, eg for installation)
- got rid of ancient ez_install: just use pip
- updated README and INSTALL
- updated classifiers in setup.py (license: LGPL v2.1 and other meta data);
  updated URL to point to http://propka.org because unlike http://propka.ki.ku.dk
  it is not completely dead and has a link to the pdb2pqr propka server as well
  as the GitHub page
 2018-03-19 22:34:22 -07:00
Toni G
5fbbdd4868 Output performed with loggers. Adds options --no-print. (#12) 
Output performed with loggers.  Adds --quiet and --verbose options.
 2016-04-28 23:21:35 -07:00
Jimmy Charnley Kromann
ca6224433a Merge pull request #8 from orbeckst/ASU 
improved integration of PROPKA into Python scripts
 2014-11-22 03:58:40 +01:00
Oliver Beckstein
ddaf27dea8 run.single() to run a propka calculation without script 
- can pass a single pdffile (or stream(!))
- added options lib.loadOptions() to pass opt string
 2014-11-20 17:30:27 -07:00
Oliver Beckstein
f17fc9acfe file open/close functions can process any stream *filename* 2014-11-20 17:30:27 -07:00
Jimmy Charnley Kromann
6e1b0365e0 Merge pull request #6 from schrodinger/titrate_only 
Titrate only option
 2014-08-27 14:53:54 +02:00
Jimmy Charnley Kromann
b617175f77 Merge pull request #5 from schrodinger/lgpl 
change LICENSE from GPL to LGPL
 2014-08-27 14:53:38 +02:00
Mike Beachy
bc50c7a3a4 change LICENSE from GPL to LGPL 2014-08-25 11:52:21 -04:00
Matvey Adzhigirey
8084b31393 Added --titrate_only option and tests for it. 
This option makes it possible for PROPKA to treat only a subset of protein
residues as titratable.
 2014-08-20 20:14:38 -04:00
Matvey Adzhigirey
c420b4c2a5 Use get_titratable_groups() instead of manually building up this list 
in find_covalently_coupled_groups().
 2014-08-13 11:12:21 -07:00
Matvey Adzhigirey
5fe2ac0279 Fix the help message for -c option (regarding chains w/o ID) 2014-08-11 16:37:29 -07:00
Jimmy Charnley Kromann
2b6c20e9a6 added license 2014-06-07 10:43:48 +02:00
Jimmy Charnley Kromann
54ebb22fb4 Merge pull request #3 from schrodinger/master 
merge from schrodinger
 2014-04-04 17:08:52 +02:00
Matvey Adzhigirey
ae462842c1 replace empty chains with "_" instead "A" 2014-02-27 18:15:18 -05:00
Matvey Adzhigirey
4566cd67f9 Fix a number of crashes and special conditions 
- Fix an issue where non-existing interactions were analyzed.

  Bug fix in setIonDeterminants(): skip interactions if either
  titratable_group_interaction_atoms or the backbone_interaction_atoms
  is empty.

- Set center of COO_group to self.atom if no oxygens present in residue.

  COO_group: If self.atom.get_bonded_elements('O') returns an emtpy list
  (the residue has missing side-chain), simply set the center of the
  group to the <self.atom> atom, instead of the center of the
  (non-existing) oxygens.

- Raise more friendly exception in Group.set_center() if an empty atom
  set is passed in.

- Cterm_group: Fix crash if residue is missing a carbon.

  The previous code would crash if the C-termini residue group was
  missing the carbon atom.

- Fix a failure when a HIS residue has missing side-chain atoms.

- Added an entry for Iodine (I) to the valence electrons table.
 2014-02-27 18:15:18 -05:00
Matvey Adzhigirey
73c7a2a4be optimize a number of functions 
- Major optimization of the put_atom_in_box() function.
- Major optimization of the protein_precheck() function.
- Minor optimization in radial_volume_desolvation()
- Optimization in top_up() to scale for large structures.
 2014-02-27 18:15:18 -05:00
Mike Beachy
e0ed5da44b handle structures with 100,000 or more atoms 
- the pdb format requires a 5-character field for the atom number; the
  hybrid-36 format allows up to a ridiculous number of atoms
 2014-02-27 18:15:18 -05:00