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
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
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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
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- Implemented Python wrappers
- prepared relevant test cases
2016-04-24 23:30:25 +01:00
Paolo Tosco
6f8071f7a5
- Progress on Python wrappers
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- 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.
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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
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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
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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
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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;
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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
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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
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- 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;
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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
Greg Landrum
e1a55230d9
remove lapack stuff from cmake build system
2009-11-01 11:01:24 +00:00
Greg Landrum
7f0c2c05fc
remove lapack from the jamfiles
2009-10-31 06:09:20 +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
6caabd787e
move these changes over to the windows side and try again there
2009-10-01 08:24:43 +00:00
Greg Landrum
1ec5a0a039
builds on darwin; all tests except testGrid pass
2009-09-28 14:07:28 +00:00
Greg Landrum
76297b0fff
builds and passes tests on linux
2009-09-28 11:02:18 +00:00
