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36 Commits

Author SHA1 Message Date
Greg Landrum
d41752d558 run clang-tidy with readability-braces-around-statements (#2899) 
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows
 2020-01-25 14:19:32 +01:00
Greg Landrum
a75018fe38 Cleanups and additional tests to improve test coverage (#2852) 
* disable builds of the StructChecker code by default

* operator"" _smarts() doesn't need to catch sanitization errors

* remove unused function

* turn back on some tests that shouldn't have been disabled

* Remove unused code from SMARTS parser and simplify a bit

SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API

* Removes obsolete special case code for SMARTS

This was relevant when organic atoms in SMARTS queries were stored as two-part queries.

* improve SMARTS testing

make sure we can generate SMARTS from all the examples and then parse that again.

* Fixes #2814

* Fixes #2815

* some additional smarts tests to improve coverage

* test copy ctor and getPos

* remove obsolete test_list files

* include tests for the morgan invariant generators

* more cleanups and coverage improvements

* remove files that were mistakenly added
 2020-01-09 16:07:55 -05:00
Eisuke Kawashima
dc7cc84a0c Fix typo [ci skip] 2019-10-17 17:45:50 +09:00
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
Paolo Tosco
f77a0794a4 - implemented Python wrappers for computePrincipalAxesAndMoments() and computePrincipalAxesAndMomentsFromGyrationMatrix() (#1700) 2018-01-03 17:06:42 +00:00
Paolo Tosco
c8deb705e7 There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral (#1673) 
* - there is no need to enforce that (i, j) and (k, l) be bonded
  when setting a i, j, k, l dihedral

* - added unit tests for PR #1673
 2017-12-21 05:45:24 +01:00
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
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
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +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
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
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
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
e8f3536845 remove a bunch of compiler warnings 2008-05-26 20:05:57 +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
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
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