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Release_2016_09
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48 Commits

Author SHA1 Message Date
Greg Landrum
b9e8ab4a53 Fix/github1262 (#1265) 
* fix for calculation of prinicipal moments of inertia

* fix a typo
update expected values

* PMI and NPR tests working

* cleanup some of the other descriptors and tests

* Test against Moments.py descriptors

* add new tests from Brian

* remove some warnings
 2017-02-05 08:35:34 +01:00
Greg Landrum
4f2ec84e7b Add some 3D molecular descriptors (#1084) 
* update .gitignore

* foundation for 3D descriptors
move PBF into core

* cleanup work

* a bit more cleanup

* move the principal moments calc to MolTransforms

* cleanup

* cleanups

* add caching of the principal moments and values

* do not include the 3D descriptors in MolDescriptors.h

* the properties are computed

* add PMI descriptors and tests

* add tests for NPR descriptors

* return 0 when the largest PMI is zero

* PMI edge case tests

* NPR edge case tests

* PBF edge case tests

* PBF edge case tests

* more edge cases

* add a few more 3d descriptors

* add defns to docs

* tests for the new descriptors

* add versions to new descriptors

* add 3d descriptors to python wrapper

* add eigen support to the travis build

* try to get non-windows builds working

* remove computeCovarianceMatrix() from java wrapper

* make pmi property names "private"
 2016-10-10 08:34:08 -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
Paolo Tosco
dbaff21056 - fixed a few missing "const" declarations on "get" functions 2016-02-21 21:24:56 +00:00
Greg Landrum
581d852c99 clean up a couple of missed files 2015-12-03 06:01:09 +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
210f2951e0 Silences warnings in tests 2015-10-18 21:20:11 -04:00
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
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
60a68669da remove more clang warnings 2013-12-02 04:46:46 +01:00
Greg Landrum
9c7369b8a4 some cleanup 2013-10-16 03:40:34 +02:00
ptosco
865175104b - added getters/setters for bond lengths, angles, dihedrals 
in the MolTransforms namespace:

  * getBondLength(conf, iAtomId, jAtomId)
                 (only in this case, atoms need not be covalently bonded)
  * setBondLength(conf, iAtomId, jAtomId, value)
  * getAngleRad(conf, iAtomId, jAtomId, kAtomId)
  * setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
  * getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
  * setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
  * getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
  * getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)

- added the corresponding Python wrappers in rdMolTransforms
  (same prototype as C++; as usual all Python methods
  have an uppercase initial)

- added relevant C++/Python tests
 2013-10-15 11:59:08 +02:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +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
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +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
0e9dc3f8c7 improvements to query writing to mol files 2010-06-05 13:44:08 +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
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
76297b0fff builds and passes tests on linux 2009-09-28 11:02:18 +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
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
a3e6cb057e this is a mass of cleanup stuff; mostly line endings 2008-07-07 13:21:24 +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
84bcc0813c reflect changes in eigenvects code 2008-06-26 05:50:24 +00:00
Greg Landrum
e8f3536845 remove a bunch of compiler warnings 2008-05-26 20:05:57 +00:00
Greg Landrum
8424d36830 get things building on windows. 2008-04-08 18:24:56 +00:00
Greg Landrum
d3aea154ef switch everything over to dynamic linking in order to try and solve 
the horrible cross-library exception handling mess on linux. This may well break things on windows, which
might want these things static. Regardless, even as it is, this should be considered experimental
 2008-04-08 10:24:57 +00:00
Greg Landrum
26a4124ad9 remove files for old build system 2008-02-20 17:06:59 +00:00
Greg Landrum
430a83bd96 merge in the jamfiles from the bjam branch; 
various and sundry minor code cleanups;
this probably does not yet build on windows... that is next
 2007-11-23 15:55:30 +00:00
Greg Landrum
47d47a49d3 remove vestiges of old windows build system 2007-07-31 17:09:53 +00:00
Greg Landrum
cf728dbc7c primarily project file changes to make things work 
with python 2.5
Also includes a slackening of the tolerance for a distgeomhelpers test.
 2007-01-15 20:30:01 +00:00
Santosh Putta
3061511f68 All typedefs based on points move to point.h - dependancies updated here 2006-10-19 23:37:59 +00:00
Greg Landrum
8a19c38e21 - Get windows debug builds working 
- Remove requirement that boost be in $RDBASE/External on windows (the BOOSTHOME environment variable is now required)
- fix dependencies

This builds on windows in debug mode now and most tests pass. There's a problem with PySVD in debug mode and for some reason the rdAlignments wrapper test fails; but these don't seem super important.

https://sourceforge.net/tracker/index.php?func=detail&aid=1485703&group_id=160139&atid=814650
 2006-05-11 00:42:39 +00:00
Greg Landrum
b87de75d56 get g++ out of the makefiles... use CXX instead 2006-05-09 23:20:26 +00:00
Greg Landrum
5d03333c22 setup svn keywords (should have done this before import... grn) 2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00