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20 Commits

Author SHA1 Message Date
Ricardo Rodriguez
c63ddaffa2 Minor refactor of the python wrappers (#8847) 
* refactor python wrappers

* fix FilterHierarchyMatcher converted already registered warning
 2025-10-31 13:41:18 +01:00
Paolo Tosco
2b4202867e Add Python modules to generate stubs and automatically patch docstrings (#6919) 
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)

* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest

* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods

* patched sources

* address residual few remarks

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2023-11-30 04:54:18 +01:00
Paolo Tosco
261fd7812e fixes #4302 (#4303) 
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
 2021-07-10 05:06:25 +02:00
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
Eisuke Kawashima
dc7cc84a0c Fix typo [ci skip] 2019-10-17 17:45:50 +09:00
Paolo Tosco
f77a0794a4 - implemented Python wrappers for computePrincipalAxesAndMoments() and computePrincipalAxesAndMomentsFromGyrationMatrix() (#1700) 2018-01-03 17:06:42 +00:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +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
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
8b321cc5b4 fix 2318431: deprecation warnings from numpy 2008-11-21 05:55:08 +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
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
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