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98 Commits

Author SHA1 Message Date
Greg Landrum
7e6600f3be Fixes #2516 (#2519) 
* RDStreams now installed properly

* skip Wrap directories if RDK_BUILD_PYTHON_WRAPPERS is not set

Fixes #2516
 2019-06-28 09:57:00 -04:00
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
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
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
Ric
91008ff11d Address compile warnings & trivial improvements (#2097) 
* Address compile warnings & trivial improvements

* revert unwanted initializers; use RDUNUSED_PARAM for unused params

* revert fix in testRDFcustom; marked with 'TO DO' comment
 2018-10-12 06:39:32 -04:00
Paolo Tosco
f7c888844d moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074) 2018-10-11 17:35:23 -04:00
Greg Landrum
2738c35178 Fixes #1903 (#1971) 
* Fixes #1903

* update SWIG bindings too
 2018-07-25 09:14:17 +02:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861) 
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
 2018-05-16 08:42:41 +02:00
susanhleung
1743ced5a5 add Tversky index calculation for shapes (#1777) 
* trying to add shape tversky

* alpha and beta no defaults, added more tverskyIndex tests to testGrid

* corrections to GridUtils.h and ShapeUtils.cpp

* corrections to GridUtils.h
 2018-03-24 08:33:30 +01:00
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
Paolo Tosco
2b3a818f84 - removed the dependency on Trajectory from ROMol and ForceField 2016-05-11 19:37:09 +01:00
Paolo Tosco
8b5176f8c9 - initial work to put the Trajectory code into a separate object 2016-05-09 19:05:15 +01:00
Paolo Tosco
3bfe792653 Updated copyright notices and docs for Trajectory 2016-05-07 22:03:53 +01:00
Paolo Tosco
a2eca41365 - the Trajectory object now holds a vector of Snapshots rather than 
a vector of shared_ptr to Snapshots
- The PySnapshot class was removed
- the Trajectory::readAmber and Trajectory::readGromos member functions
  were converted into non-member functions
- tests were modified accordingly
 2016-05-04 18:42:23 +01:00
Paolo Tosco
5538cef587 No change 2016-04-26 21:58:22 +01:00
Paolo Tosco
fdd9b7b38f No change 2016-04-26 21:57:06 +01:00
Paolo Tosco
a47cf48624 - added a test to check adding Snapshots to a Trajectory from Python 
- removed a spurious NOGIL residuated from a copy/paste
 2016-04-26 19:36:36 +01:00
Paolo Tosco
9ffd1670f0 - added a few tests 
- changed a few PRECONDITION into URANGE_CHECK
 2016-04-26 09:00:22 +01:00
Paolo Tosco
96d585957e - switched from a vector of Snapshot* to a vector of boost::shared_ptr<Snapshot> 
- added a test case for Snapshot to C++ and Python
 2016-04-25 22:39:27 +01:00
Paolo Tosco
3f4c6ec9ff - switch to boost::shared_array 2016-04-25 21:53:04 +01:00
Paolo Tosco
605ff9264c - fixed a typo in the headers 2016-04-25 07:16:22 +01:00
Paolo Tosco
d16b312ee6 - Completely revised coordinate ownership 
- Implemented Python wrappers
- prepared relevant test cases
 2016-04-24 23:30:25 +01:00
Paolo Tosco
6f8071f7a5 - Progress on Python wrappers 
- Some adjustments to the C++ API
 2016-04-19 20:53:39 +01:00
Paolo Tosco
249ae83694 - Implemented Trajectory::readGromos() and added relevant tests 2016-04-16 22:27:37 +01:00
Paolo Tosco
b35538599f - Added AMBER trajectory reader and relevant tests 2016-04-16 20:28:45 +01:00
Paolo Tosco
9d5e56fcd2 - added a test for testAddConformersFromTrajectory() 
- added some documentation
 2016-04-14 23:45:24 +01:00
Paolo Tosco
584b77ea18 - work in progress on the Trajectory branch 2016-04-14 20:04:58 +01:00
Greg Landrum
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
2a75463959 get rid of some more warnings 2015-11-14 09:21:05 +01:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Greg Landrum
b9045e6573 add a copy() method to points 2015-03-09 05:41:52 +01:00
Greg Landrum
077eec1be1 more pickle cleanups 2014-06-20 06:59:11 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
9f4471f872 more on #204 
A few other cleanups
 2014-02-06 06:43:28 +01:00
Greg Landrum
54dc305600 add GetGridIndices to python wrapper 2013-12-20 12:11:56 +01:00
Greg Landrum
a117c643ac Add UniformGrid3D::getGridIndices() 2013-12-20 11:56:37 +01:00
Greg Landrum
4f9f25d73d remove clang warning 2013-12-02 04:31:26 +01:00
ptosco
ec8eb5a1bf - Changed all occurrences of RDKit::PI into M_PI 
- added #ifdef M_PI (...) #endif in all relevant places
- made length() and sqLength() method consistent
  with respect to usage of pow(x, 2) vs x*x in
  Code/Geometry/point.h
- removed gzip-related boost.iostreams dependency and
  replaced with portable "cmake -E tar xzf" command
  in Code/ForceField/MMFF/CMakeLists.txt
 2013-09-20 17:45:41 +02:00
Greg Landrum
9a0425b4ee remove some compiler warnings 2013-07-04 09:16:18 +02:00
Greg Landrum
5b5bb4b15c add signed dihedral calculation. Add dihedral calculation to python interface 2012-03-11 05:21:09 +00:00
Greg Landrum
5f85129f22 initial support for clang 
this is minor build-system variations and some code cleanup
the python wrapper still needs cleanup and 
the sln stuff doesn't work at all under clang due to weirdness with boost::regex
 2011-05-25 19:40:31 +00:00
Greg Landrum
b993f89afe remove the bjam-based build system 2010-09-27 03:54:07 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
cb6cdb99b3 merge in a set of changes from Riccardo V. to install .h files as well; 
this needs more testing.
 2010-09-04 14:07:22 +00:00
Greg Landrum
bfeac1c52d fix and test sf.net issue2948402 2010-02-13 05:53:22 +00:00