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92 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
87786c08b5 Merge branch 'master' into modern_cxx 
# Conflicts:
#	.travis.yml
#	Code/GraphMol/FileParsers/MolFileParser.cpp
#	Code/GraphMol/FileParsers/MolFileStereochem.cpp
#	Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
#	Code/GraphMol/MolAlign/testMolAlign.cpp
#	Code/GraphMol/MolDraw2D/MolDraw2D.cpp
#	Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
#	Code/GraphMol/QueryOps.cpp
#	Code/GraphMol/ROMol.cpp
#	Code/GraphMol/SmilesParse/test.cpp
#	Code/GraphMol/Trajectory/Trajectory.cpp
#	Code/GraphMol/Wrap/Atom.cpp
#	Code/GraphMol/Wrap/Bond.cpp
#	Code/GraphMol/new_canon.cpp
#	Code/RDGeneral/testDict.cpp
#	Code/SimDivPickers/Wrap/MaxMinPicker.cpp
 2017-10-05 05:58:38 +02:00
Brian Kelley
7488840ac4 Fix/urange check (#1506) 
* Fixes atom documentation

* Fixes #1461

This is a complicated one.  Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0.  The standard operations is
to check

URANGE(num, size-1)

Which (for unsigned integers) obviously rolls over.

This fixes all usage cases to be

URANGE(num+1, size)

And fixes the bugs found.  (addBond and the mmff tests)

* Fixes #1461 - Updates URANGE_CHECK to be 0<=x<hi
 2017-09-11 21:17:33 +02:00
Greg Landrum
12342c5643 merge to master 2017-07-21 04:50:35 +02:00
Alain Vaucher
af91db37ce Update two further targets 2017-07-01 14:21:12 +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
779ec747ac - put SnapshotVect in the RDKit namespace 2016-05-11 23:41:31 +01:00
Paolo Tosco
2b3a818f84 - removed the dependency on Trajectory from ROMol and ForceField 2016-05-11 19:37:09 +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
3f4c6ec9ff - switch to boost::shared_array 2016-04-25 21:53:04 +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
9316a15b38 - fixed docs 2016-04-14 23:59:48 +01:00
Paolo Tosco
584b77ea18 - work in progress on the Trajectory branch 2016-04-14 20:04:58 +01:00
Paolo Tosco
406ea052f5 - work in progress 2016-04-12 23:03:57 +01:00
Paolo Tosco
0c0b0a30be - started adding trajectory storage to minimizer 2016-04-12 21:30:55 +01:00
Greg Landrum
07fb36de44 A bit of minor optimization 2015-12-07 04:25:56 +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
Brian Kelley
fb84c9f0b7 Switches to URANGE_CHECK when appropriate 2015-10-18 21:14:02 -04:00
Brian Kelley
b31c2870ce Adds a symbol to fix no-symbol warning. 
The real fix is to add rdkit_headeronly_library macro
 2015-10-18 16:40:44 -04:00
Brian Kelley
66b1c81a61 Fixes more unused parameters 2015-10-18 16:38:50 -04:00
Brian Kelley
5f59333a56 Silences unused parameters 2015-10-18 14:02:29 -04:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
a146c3826a Remove unused variables/functions and register keyword 2015-10-18 10:01:00 -04:00
Greg Landrum
4f9e8cf730 dot product should be const 
add tanimoto similarity
 2015-09-11 11:22:45 +02:00
Greg Landrum
7e5c37e685 update some tests to ensure success on 32bit systems 2015-05-01 16:04:17 +02:00
Paolo Tosco
b7ca51d98c - modified BFGSOpt.h to remove a while(1) {} loop which might result 
into an infinite loop in linearSearch() with poor initial geometries
- added a relevant unit test in Code/ForceField/Wrap/testConstraints.py
 2015-04-20 23:46:23 +01:00
Paolo Tosco
7fe0024c48 - removed the possibility of an indefinite loop in linearSearch(); now an 
exception is thrown in such cases
- added a relevant unit test in testConstraints.py
 2015-04-20 23:31:55 +01:00
Greg Landrum
f33f5bf92d changes to better support numpy 1.9; 
from Peter Gedeck
 2015-01-06 08:24:11 +01:00
Riccardo Vianello
fb5c53b45f remove dependency from numpy's oldnumeric 2014-09-15 23:29:42 +02:00
Greg Landrum
d16438e009 Merge remote-tracking branch 'origin/master' into python3-support 2014-07-13 05:38:52 +02:00
Greg Landrum
9bf13137cf add explicit import of <algorithm> to resolve build problem on VS2013 2014-06-28 15:11:14 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
9f4471f872 more on #204 
A few other cleanups
 2014-02-06 06:43:28 +01:00
Greg Landrum
6736192f7e a couple of small vector modifications 2013-10-08 13:38:47 +02:00
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
Sereina Riniker
e535e97d06 c++ implementation of USR descriptor added 2013-08-20 17:33:28 +02:00
Greg Landrum
a3242e5c24 get the code building with boost 1.53: remove bogus initializer for a boost::shared_array 2013-02-06 04:25:54 +00:00
Greg Landrum
c48045c909 efficiency 2013-01-11 04:01:21 +00:00
Greg Landrum
80667746d3 suggestion from David Cosgrove to remove some compiler warnings 2012-08-14 03:40:58 +00:00
Greg Landrum
d00ee0825d another update 2012-02-25 16:27:54 +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
ec192d981e changes to robustify (and somewhat speed up) the optimizer. These will change results 2010-02-28 13:11:34 +00:00
Greg Landrum
9727cffa61 make python wrappers and tests optional 2010-01-22 11:22:58 +00:00
Greg Landrum
c346a41951 get the tests working on windows. 2010-01-19 06:34:58 +00:00