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Author SHA1 Message Date
Nathan Baker
f392969e33 Merge pull request #634 from Electrostatics/nathan/docs 
Remove stray documentation.
 2020-07-26 17:22:21 -07:00
Nathan Baker
6a8ba66c6e Remove stray documentation. 2020-07-26 17:19:18 -07:00
Nathan Baker
94937b894a Merge pull request #633 from Electrostatics/nathan/docs 
Move documentation
 2020-07-26 17:18:33 -07:00
Nathan Baker
deaa61778a Documentation has moved. 2020-07-26 17:15:15 -07:00
Nathan Baker
e8c9e92a14 Move docs over to new repo. 
Most things are moved except the VR docs.
 2020-07-25 20:34:04 -07:00
Nathan Baker
06c4457770 Move examples to new repo. 
Examples moved in 5637fc8647
 2020-07-25 19:07:06 -07:00
Nathan Baker
e5364f0f2c Move release history to apbs-specific repo. 
Release history moved in 333dd1e98e
 2020-07-25 15:58:58 -07:00
Nathan Baker
b041d33378 Move documentation to https://apbs.readthedocs.io/ 2020-07-23 20:02:33 -07:00
Nathan Baker
b5203db6ca Migrate docs to separate APBS/PDB2PQR repos. 
Partial checkin.  Deleting some content as its migrated to help track.
 2020-07-20 15:17:16 -07:00
Darren Curtis
b82cf42630 Merge pull request #632 from Electrostatics/nathan/docs 
Move PDB2PQR-specific docs to separate repo
 2020-07-18 22:33:09 -07:00
Nathan Baker
9e17ee7605 Move PDB2PQR-specific docs to separate repo. 2020-07-18 21:05:59 -07:00
Nathan Baker
3ea52707ef Fix typo. 2020-07-17 08:47:20 -07:00
Darren Curtis
a84b1c722b Merge pull request #630 from Electrostatics/nathan/rm-apbs 
Remove APBS code from this repo
 2020-07-05 08:36:16 -07:00
Nathan Baker
ecb3114981 Remove APBS-specific configuration files and documentation. 2020-07-04 17:26:34 -07:00
Nathan Baker
7971124699 Remove APBS files. 
Works towards resolving https://github.com/Electrostatics/apbs-pdb2pqr/issues/628
 2020-07-04 17:18:52 -07:00
Nathan Baker
001324e87b Remove PDB2PQR-specific content. 
Fixes #624.
 2020-07-04 17:05:19 -07:00
Nathan Baker
d5bf9e2e1d Remove redundant PDB2PQR files. 
PDB2PQR has moved to a separate repository; see https://github.com/Electrostatics/pdb2pqr

This commit works towards resolving https://github.com/Electrostatics/apbs-pdb2pqr/issues/624
 2020-07-04 16:45:03 -07:00
Darren Curtis
0b1bc01263 Merge pull request #622 from Electrostatics/nathan/pdb2pka 
Restore ligand functionality to PDB2PQR
 2020-06-29 10:01:29 -07:00
intendo
f472da5d22 Corrected comparison of strings 2020-06-29 09:47:03 -07:00
intendo
2913ae8f8b Fixed some pylint warnings. 2020-06-29 09:13:21 -07:00
Nathan Baker
4a59cf2a72 Restore ligand functionality to PDB2PQR. 2020-06-28 17:57:36 -07:00
Nathan Baker
d8a4bee4b6 Make ligand atom names consistent with PDB file. 2020-06-28 17:57:18 -07:00
Nathan Baker
50b1180ab4 Fix documentation. 
Missing argument in docstring.
 2020-06-28 17:56:27 -07:00
Nathan Baker
405a8596a1 Combine parameterization functions and tests. 2020-06-28 15:45:03 -07:00
Nathan Baker
4cb18b166f Remove bond-order guessing. 
Remove guess_bond_order function and associated tests.  Bond orders are
already specified in the MOL2 file and the existing code wasn't very
good at guessing them.
 2020-06-28 10:39:50 -07:00
Nathan Baker
3f8db56c3e Expand ring test set. 2020-06-28 10:36:09 -07:00
Nathan Baker
bc8a4158f1 Fix torsion testing. 
Expanded test set and removed torsions involving hydrogen.
 2020-06-28 10:15:38 -07:00
Nathan Baker
0de37548ef Working charge assignment with PEOE. 
Yay!!!
 2020-06-28 09:56:36 -07:00
Nathan Baker
d7c5569ac6 Add formal charge calculation. 
Add charge calculation and tests.  Breaks other tests.
 2020-06-27 18:42:18 -07:00
Nathan Baker
9955571448 Merge branch 'nathan/fix-readme' into nathan/pdb2pka 2020-06-27 12:44:55 -07:00
Nathan Baker
6e8133af73 Clean up README.md 
Most of these changes are to improve rendering on http://www.poissonboltzmann.org/ and include:

* Clean up spacing between badges and standardize -- @intendo do we still need all of the testing badges?
* Replace GitHub-specific symbols with unicode emoji
* Remove "Tests pass" column from datasheet table since it is covered by badges
* Add explanation to datasheet table
 2020-06-27 11:29:54 -07:00
Nathan Baker
0a86951fa7 Merge branch 'master' into nathan/pdb2pka 2020-06-27 10:17:03 -07:00
Nathan Baker
a4cc2c63c4 Merge pull request #605 from Electrostatics/find_dat 
Find dat folder.
 2020-06-27 10:14:41 -07:00
Nathan Baker
fd4aafc8d3 Clean up setup.py 
* De-lint file
* Fix typos in keyword list ("chemestry modelcular")
* Remove extra space in URL
* Correct BSD license classifier
* Add python version requirement
* Add additional classifiers
* Expand author list
* Change author email

Addresses https://github.com/Electrostatics/apbs-pdb2pqr/pull/605#discussion_r446542634 and https://github.com/Electrostatics/apbs-pdb2pqr/pull/605#discussion_r446544327
 2020-06-27 10:04:55 -07:00
Nathan Baker
0ee632b7c4 Remove commented-out code. 
Addresses https://github.com/Electrostatics/apbs-pdb2pqr/pull/605#discussion_r446542582

Also fix ugly non-PEP8 code to address https://github.com/Electrostatics/apbs-pdb2pqr/pull/605#discussion_r446543544
 2020-06-27 09:41:13 -07:00
kozlac
4197c14cac Basic propka restored. Passing tests/propka_test.py 2020-06-25 10:49:07 -04:00
kozlac
a642cc2704 Added dependency. 2020-06-24 12:48:34 -04:00
kozlac
36dd331270 Resolved local merge conflict. 2020-06-24 12:47:20 -04:00
kozlac
6281dc9868 Resolving merging conflict. 2020-06-24 10:09:27 -04:00
kozlac
f96367442d Added setup.py and pdb2pqr/__main__.py to be able to install pdb2pqr as a module. 2020-06-24 10:05:18 -04:00
kozlac
ee6190cb79 Made some modifications so that we can files the dat/ folder regardless of where pdb2pqr is being run. 2020-06-24 10:02:19 -04:00
Nathan Baker
1c6cbef3c3 Implement old bond-order detection methods. 
Note that the old bond-order detection approach fails for some bond types; see #614 for more information.

Also note that the new ring detection method fails for multiply fused rings; see #613 for more information.
 2020-06-21 16:48:12 -07:00
Darren Curtis
e7b467bf8c Merge pull request #612 from Electrostatics/issue611 
This resolves issue #611
 2020-06-16 11:01:55 -07:00
bran780
f8f67ad226 This resolves issue 611 2020-06-16 13:46:17 -04:00
bran780
55ddfb401c Revert "noci Modified root cmake file to increase stack size when building on windows." 
This reverts commit 0d7aba1b52.
Forgot to make pull request.
 2020-06-16 13:39:40 -04:00
bran780
97a0d9fb33 Merge branch 'master' of https://github.com/Electrostatics/apbs-pdb2pqr 2020-06-16 13:34:36 -04:00
bran780
0d7aba1b52 noci Modified root cmake file to increase stack size when building on windows. 2020-06-16 13:33:22 -04:00
Nathan Baker
0703103cc1 Add type checking for bond type. 2020-06-15 20:03:52 -07:00
Nathan Baker
3dbc8c5217 Add test that breaks current ring calculations. 2020-06-15 19:34:29 -07:00
Nathan Baker
2c155d56ec Identify rings in ligands. 2020-06-15 16:27:47 -07:00