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105 Commits

Author SHA1 Message Date
Matt Swain
e57b7a9bc8 Use numpy not numeric for boost 1.65+ - fixes #1581 (#1664) 
boost python numeric no longer exists in boost 1.65, so check boost version and conditionally use boost python numpy.
 2017-11-20 05:44:19 +01:00
Greg Landrum
67bc7a647c merge on master; modernization needs to be repeated 2017-09-05 17:09:50 +02:00
Greg Landrum
a7065dc36d fixes #1447 (#1529) 
* fixes #1447

* python2 compatibility
 2017-08-23 17:25:04 -04:00
Greg Landrum
f6ced134f0 a number of other small changes from manually reviewing the PR 2017-04-22 17:24:57 +02:00
Greg Landrum
142a1f4fed an observation from the review 2017-04-22 17:22:13 +02:00
Greg Landrum
915cf08faa run clang-format with c++-11 style over that 2017-04-22 17:19:10 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
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
Greg Landrum
2907166444 Add a MultiFPBReader class (#909) 
* first pass at a MultiFPBReader in c++
includes initial tests

* first pass at multi-threading; untested

* add multi-threaded test

* multi-threaded tversky

* add multi-threaded contains searches

* allow FPBReader::init() to be called multiple times

* add a cleanup() method to clear out whatever memory we are using

* allow the init() call to be pushed to search-time;
this allows calls to the contained init() methods to be run in separate threads

* make ownership of FPBReader pointers optional
add addReader() method

* Add MultiFPBReader python wrapper

* support multi-threaded initOnSearch

* add a couple of more tests
 2016-05-29 09:38:14 -04:00
Greg Landrum
2d78b7f710 FPB Reader documentation update 2016-04-12 06:21:18 +02:00
Greg Landrum
249146afaa Dev/containing nbrs in python 
* expose GetContainingNeighbors() to python

* add another contains test from python
 2016-04-11 13:09:18 -04:00
Greg Landrum
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +01:00
Greg Landrum
6e6c200bd3 add Tversky code to the python wrapper 2016-01-18 10:57:48 +01:00
Greg Landrum
6b06bccf3f clean up the uses of casts in the new code 2016-01-12 12:09:56 +01:00
Greg Landrum
606ae353ca stop reading in all Ids when in lazy mode 2016-01-12 12:09:56 +01:00
Greg Landrum
5af208a1e4 add a lazy mode that does not need to read in the whole database 2016-01-12 12:09:54 +01:00
Greg Landrum
9ae728ef5c remove the topN arg since it isn't being used and won't save time anyway 2016-01-12 12:09:54 +01:00
Greg Landrum
50e925a478 further lessening of memory management stupidity 2016-01-12 12:09:54 +01:00
Greg Landrum
8722043df8 add nBits() method 
add getTanimotoNeighbors() method
 2016-01-12 12:09:54 +01:00
Greg Landrum
08ce5a287d crude initial python wrapper 2016-01-12 12:09:54 +01:00
Greg Landrum
79e1f8b1fa compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10 2015-11-28 06:49:34 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7 post review 2015-11-14 08:08:14 +01:00
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Greg Landrum
1cde397acb merge commit 2015-10-30 02:58:46 +01:00
Brian Kelley
23ef7fae3b Fixes meaningless const qualifier for int 2015-10-18 15:13:41 -04:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
12d562399a Merge branch 'master' into fix/const-string-ref 2015-10-13 07:08:00 -04:00
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Greg Landrum
a743cff4d7 Fixes #573 2015-09-20 04:44:39 +02:00
Andrew Dalke
6d66534743 removed bare except statements 2015-09-07 13:27:14 +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
Schneider
3af5ba223c ExplicitBitVect: Add +operator to concatenate two ExplicitBitVects 2014-08-19 12:59:50 +02:00
Riccardo Vianello
609009b1ec additional changes related to pickling. 
- fixed dependency from ordering of dict keys in a doctest
- replaced import of cPickle from the python2 lib w/ rdkit.six.moves.cPickle
- fixed a few more tests
- support pickle load/loads kw arguments with a portable interface
 2014-07-06 09:13:38 +02:00
Greg Landrum
47931754da fix DbCLI tests; includes fixing the pickling of SparseIntVects 2014-06-24 07:17:12 +02:00
Greg Landrum
408b178b91 undo a couple un-necessary changes and, hopefully, get this working with python2 again 2014-06-21 04:48:48 +02:00
Greg Landrum
077eec1be1 more pickle cleanups 2014-06-20 06:59:11 +02:00
Greg Landrum
50332b599e get some of the pickle problems resolved; this probably only works with python3 and is not yet 100% functional 2014-06-19 06:05:42 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
8d651453b8 Fixes #281 2014-06-17 15:38:56 +02:00
Sereina Riniker
3ea1ad93e6 explicit bitvect with all ones updated 2014-04-08 11:11:35 +02:00
Sereina Riniker
52069683b9 function UnSetBitsFromList added 2014-04-08 10:38:52 +02:00
Greg Landrum
caae56b087 Changes to the various bulk similarity functions for #119; not closing yet since there may still be other places that need to be updated 2013-10-05 08:02:04 +02:00
Greg Landrum
879efa3be3 add support for integer arithmatic ops on SparseIntVects. operator+ et al. do not yet work from python 2013-08-26 06:51:13 +02:00
Greg Landrum
05840816cd Add Rogot Goldberg and AllBit similarity to C++ and the python wrapper. 
(contribution from Sereina Riniker)
 2013-01-08 15:10:51 +00:00
Greg Landrum
72efd4a58b support a somewhat more consistent API for size/value info across the data types; 
add DataStructs.ConvertToNumpyArray function;
 2012-12-03 08:41:53 +00:00
Greg Landrum
dc60eb0c47 add another test 2012-01-10 04:08:58 +00:00
Greg Landrum
0086f88100 additional consistency checking 2012-01-10 04:04:07 +00:00
Greg Landrum
b6300a86fe support bit vects <-> byte strings 2012-01-08 06:12:47 +00:00
Greg Landrum
29312e73e1 minor updates 2012-01-03 07:50:53 +00:00