Greg Landrum
24f1737839
Remove a bunch of Python2-related warts ( #2315 )
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* 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 )
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* 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
2018-05-01 15:25:24 +01:00
Brian Kelley
e54601c456
Updates python test runner to always use sys.executable ( #1721 )
2018-01-27 08:14:21 +01:00
gedeck
e9af48ffd7
Issue1071/yapf ( #1078 )
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* 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
Greg Landrum
1cde397acb
merge commit
2015-10-30 02:58:46 +01:00
Greg Landrum
14558020c2
get the DbCLI tests working on windows
2015-10-26 07:25:11 +01:00
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
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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
5710e90943
really fix the python2 problems this time?
2014-06-25 05:04:30 +02:00
Greg Landrum
32991b6608
should fix python2 compatibility problem
2014-06-25 04:34:19 +02:00
Greg Landrum
91f3076f3a
clean up another batch of missed ResourceWarnings
2014-06-25 04:33:52 +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
158c9b9e45
Fixes #136
2013-10-21 05:55:42 +02:00
Greg Landrum
80f1454bd7
Fixes #134
2013-10-21 05:44:50 +02:00
Greg Landrum
a41a5dfcd0
Fixes #130
2013-10-13 07:49:44 +02:00
Greg Landrum
59bbc60378
fix a bug with negation of the queries
2010-11-16 05:26:27 +00:00
Greg Landrum
7819cf84cb
robustify
2009-07-29 06:25:00 +00:00
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
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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
f977cbb9e3
redundant, so it was removed
2009-07-09 04:20:10 +00:00
Greg Landrum
f9c716684b
robustify w.r.t. sqlalchemy
2009-06-27 15:40:10 +00:00
Greg Landrum
eb20435924
robustify when no error file is being used
2009-05-07 08:51:55 +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
494e98d009
make tests easier to run
2008-07-18 04:54:58 +00:00
Greg Landrum
93414b25ca
update test
2008-06-11 09:09:51 +00:00
Greg Landrum
d0f518ec56
make the old fingerprints optional (and better supported) in the DbCLI stuff
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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
0112549e51
robustify the handling of torsions and atom pairs pickles
2008-05-15 03:40:19 +00:00
Greg Landrum
ee66221de4
DbCLI updates:
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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
554a58fa7a
windows-proofing
2008-02-13 18:09:47 +00:00
Greg Landrum
f2ce922bd0
add --noSmiles option to speed things up (optionally, of course)
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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
afcc4c602d
add smilesOut option
2007-11-23 15:29:50 +00:00
Greg Landrum
522bdada01
move most of the SDSearch functionality into SearchDb.py.
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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
f889ab80d7
grn, fix another typo
2007-10-06 03:42:59 +00:00
Greg Landrum
a5d3b11f04
this should not have been checked in like that
2007-10-06 03:42:37 +00:00
Greg Landrum
2ddc1aaa77
rename fingerprint column (again);
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support bounds on dice metric
2007-10-05 15:36:09 +00:00
