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35 Commits

Author SHA1 Message Date
Ric
880a8e5725 Reformat Python code for 2023.03 release (#6294) 
* run yapf

* run isort

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2023-04-28 06:53:56 +02:00
Greg Landrum
24f1737839 Remove a bunch of Python2-related warts (#2315) 
* remove all of the "from __future__" imports

* remove the first batch of rdkit.six imports/uses

* next step of rdkit.six removal

* removing xrange, range, and some maps

* next round of removals

* next round of cleanups

* fix inchi test

* last bits of "from rdkit.six" are gone

* and the last of the six stuff is gone

* strange importlib problem
 2019-03-06 20:43:49 -05:00
gedeck
0626136f66 Replace optparse with argparse (#1835) 
* 1194: Review assignments of range in Python code 

Task-Url: https://github.com/rdkit/rdkit/issues/1194
Either wrapped the range expression into a list or made sure that the
code is working with a range object.

* Refactored FeatFinderCLI script

* Revert "Refactored FeatFinderCLI script"

This reverts commit d9dcbce95d.

* Review rdkit.Chem.UnitTestSuppliers

* Replace optparse with argparse

* Change outDir default and fix variable name error
 2018-05-01 15:25:24 +01:00
gedeck
e9af48ffd7 Issue1071/yapf (#1078) 
* Issue #1071: add yapf configuration file

* yapf formatting of Code directory

* yapf formatting of Contrib directory

* yapf formatting of Data directory

* yapf formatting of Docs directory

* yapf formatting of External directory

* yapf formatting of Projects directory

* yapf formatting of Regress directory

* yapf formatting of Scripts directory

* yapf formatting of Web directory

* yapf formatting of rdkit directory
 2016-09-23 04:58:46 +02:00
Andrew Dalke
ff5ba623a5 remove bare excepts but was not able to test them 2015-09-07 13:12:07 +02:00
Paolo Tosco
4f7482139f - fixed tests failing on Windows when retrieving sources through the 
Windows git client, which converts line terminators to CR+LF
- added a conditional compilation clause to Code/RDBoost/import_array.h
  to avoid a compilation error on Windows with Python3
 2015-02-22 21:49:40 +00:00
Greg Landrum
32991b6608 should fix python2 compatibility problem 2014-06-25 04:34:19 +02:00
Greg Landrum
47931754da fix DbCLI tests; includes fixing the pickling of SparseIntVects 2014-06-24 07:17:12 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
2659c929b5 Fixes #197 2014-01-16 07:36:24 -05:00
Greg Landrum
a67853445d switch to using integer primary keys in the db 2009-07-29 05:08:23 +00:00
Greg Landrum
bb4a49fa3a moving closer and closer to having this useful in other scripts 2009-07-28 19:07:52 +00:00
Greg Landrum
64b7dea99f put the smiles extraction back in CreateDb.py just in case it is needed later 
otherwise minor cleanups
 2009-07-24 10:16:45 +00:00
Greg Landrum
23b6665f09 refactoring and cleanup 2009-07-24 06:00:11 +00:00
Greg Landrum
d648ffba08 rearrange fingerprint generation 2009-07-13 11:50:48 +00:00
Greg Landrum
0c745b2b60 try to be smarter about arguments 2009-07-13 10:18:10 +00:00
Greg Landrum
40e6d352dc ongoing improvements 2009-07-13 08:55:01 +00:00
Greg Landrum
4323696481 cleaning up the DbCLI code 2009-07-09 04:29:12 +00:00
Greg Landrum
33e7be513d we're going to call the package rdkit, not pyRDKit 2009-01-26 20:08:53 +00:00
Greg Landrum
d7e924456e update 2009-01-25 12:32:16 +00:00
Greg Landrum
d0f518ec56 make the old fingerprints optional (and better supported) in the DbCLI stuff 
continuing update of documentation
 2008-05-15 04:33:40 +00:00
Greg Landrum
3383664c45 add the new RDK topological fps as well 2008-05-15 03:41:39 +00:00
Greg Landrum
ee66221de4 DbCLI updates: 
1) make the fingerprint search stuff, at least with atom pairs, use the bulk similarity function
 2) fix some problems in the loader
 2008-04-18 16:36:12 +00:00
Greg Landrum
6e7b01a133 grab smiles from db when it is there 2008-02-19 07:44:02 +00:00
Greg Landrum
41a6493633 add better prop support, bug fixes 2008-02-19 06:29:21 +00:00
Greg Landrum
f2ce922bd0 add --noSmiles option to speed things up (optionally, of course) 
add --maxRowsCached option for dealing with larger data sets.
change default dbDir in search script.
 2007-12-03 21:18:12 +00:00
Greg Landrum
522bdada01 move most of the SDSearch functionality into SearchDb.py. 
This can now to property- and/or substructure-driven searches
 2007-10-27 08:10:54 +00:00
Greg Landrum
b79434b631 support noProps argument 2007-10-10 05:52:20 +00:00
Greg Landrum
a5ae3cee34 move more stuff into Chem.MolDb.Loader 2007-10-10 05:50:18 +00:00
Greg Landrum
8aa3437782 better error support using the new GetItemText() method of suppliers 2007-10-09 05:32:25 +00:00
Greg Landrum
2ddc1aaa77 rename fingerprint column (again); 
support bounds on dice metric
 2007-10-05 15:36:09 +00:00
Greg Landrum
ab67c1e1e0 set up testing, some cleanups 2007-10-05 05:21:53 +00:00
Greg Landrum
144a0a14dc backup update, getting ready to setup tests 2007-10-04 05:33:44 +00:00
Greg Landrum
c99a83febd add standard descriptor calculator; 
stop reading in the whole file before parsing sd files
 2007-10-04 03:45:24 +00:00
Greg Landrum
66011a49f7 this still needs testing code added, but it is time to get it checked in 2007-10-02 19:34:34 +00:00