Greg Landrum
636a0f6e69
Cleanup a bunch of compiler warnings ( #1697 )
...
* remove a bunch of compiler warnings
* remove some more warnings on windows (there are still plenty to go...)
2017-12-22 12:59:52 +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
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
Greg Landrum
5f7e04fe5d
Fix github1240 ( #1396 )
...
* add a test (currently fails, of course)
* backup, not really working
* Fixes #1240
* a bit more parameter tweaking to get some more structures to embed
2017-04-18 02:33:23 -04:00
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
sriniker
7943b8c79d
Improved planarity for ETKDG ( #967 )
...
* enforce planarity
* increase the force constant for the impropers
* force constant adapted
* reduced tolerance for planarity and force constants changed for some torsions
* tolerance for planarity increased a bit again
* cerr outputs removed
* planarity tolerance increased
* boost log added in planarity check
2016-06-29 05:00:30 +02:00
Greg Landrum
b9ba12f8f9
Remove extra calls to python::register_exception_translator
2016-03-01 06:36:54 +01:00
Greg Landrum
e5311fa7aa
Fixes #696
2015-12-11 05:58:28 +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
2a75463959
get rid of some more warnings
2015-11-14 09:21:05 +01:00
Greg Landrum
5618819c64
merge #641
2015-11-14 05:03:24 +01:00
Paolo Tosco
517de5b5d8
- Fixed a few glitches which caused the build to fail on Windows
...
- added a few tests for ResonanceMolSupplier
2015-10-24 01:18:10 +01:00
Sereina
26ab552232
fixes based on code review
2015-10-21 14:51:53 +02:00
Sereina
ac7ef34f05
ETKDG implementation
2015-10-20 13:51:43 +02:00
Brian Kelley
fb84c9f0b7
Switches to URANGE_CHECK when appropriate
2015-10-18 21:14:02 -04:00
Brian Kelley
403a3d6b7c
Suppresses Boost warnings
2015-10-18 13:41:03 -04:00
Greg Landrum
79518c9a6f
Fixes #568
2015-08-17 04:24:58 +02:00
Greg Landrum
07078af4ca
support copying ForceField objects
2015-03-11 03:06:32 +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
Riccardo Vianello
3358ec5925
initial set of changes introducing python3 support
2014-06-17 18:26:41 +02:00
Greg Landrum
e71c0a2d2d
Fixes #167
...
I am not completely comfortable with the fact that one reference energy in testDistGeom.py
had to be changed. This is worth looking into some more
2013-11-27 07:26:05 +01:00
Greg Landrum
4adb4d9889
Fixes #55
2013-07-02 05:23:56 +02:00
Greg Landrum
43dc95bfea
fix issue 3528136
2012-05-20 08:54:08 +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
ea910aab19
minor cleanup action
2010-04-19 07:47:48 +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
Greg Landrum
53485592ca
builds on windows with visual studio; need to pass back to linux now
2009-10-01 13:35:48 +00:00
Greg Landrum
76297b0fff
builds and passes tests on linux
2009-09-28 11:02:18 +00:00
Greg Landrum
1449a7657c
get the embedding more robust in crowded chiral molecules
2009-04-20 16:37:59 +00:00
Greg Landrum
f0b288cfed
big changes again (repeat the 979, 980 disaster on the correct branch)
2009-02-04 20:13:44 +00:00
Greg Landrum
8bf7a4c187
now all tests pass here as well
2009-02-03 05:26:10 +00:00
Greg Landrum
8f5f6184fb
merge revs 877:893 from mingw branch back onto trunk. This builds and passes tests on mingw
2008-11-24 16:43:37 +00:00
Greg Landrum
8b321cc5b4
fix 2318431: deprecation warnings from numpy
2008-11-21 05:55:08 +00:00
Greg Landrum
2580fbaaa2
this is probably a ways from done, but now at least we can run bjam under mingw without it immediately erroring out
2008-11-15 17:14:13 +00:00
Greg Landrum
21bb475b61
further jamfile mods for macosx
2008-10-19 05:36:09 +00:00
Greg Landrum
89a34d1a39
get this building on Darwin; NOTE: this may not work on win or linux yet
2008-09-03 19:24:35 +00:00
Greg Landrum
ac5a7d72c7
these are no longer needed
2008-07-07 06:36:34 +00:00
Greg Landrum
c9eb4e91e1
merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008
...
This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
2008-07-05 07:42:38 +00:00
Greg Landrum
c1c356fa30
reflect changes in eigenvects code
2008-06-26 05:50:02 +00:00
Greg Landrum
05f390fe6d
rename EmbedObject.h -> ChiralSet.h and clean it up a bit
2008-05-18 05:14:40 +00:00
Greg Landrum
a643a9913a
dos2unix and untabify... sigh
2008-05-18 05:06:57 +00:00
Greg Landrum
8424d36830
get things building on windows.
2008-04-08 18:24:56 +00:00
