Commit Graph

35 Commits

Author SHA1 Message Date
Greg Landrum
2e3f31990d Allow batch editing of molecules: removal only (#3875)
* backup

* simple first pass, passes all tests

* cleanup a bunch of existing uses

* ensure that we can safely add atoms/bonds while in edit mode

* add context manager on python side

* handle exceptions properly in those

* changes in response to review
2021-03-11 05:10:43 +01:00
Paolo Tosco
f04a9c9a42 - switched to using std::vector<unsigned int> for isotopichs property (#3878)
- switched to using std::vector<int> instead of std::list<int> for _ErGAtomTypes property
- added RegisterListConverter<std::vector<unsigned int>>

Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
2021-03-05 16:37:43 +01:00
Ric
703fe5a225 Remove boost::foreach from public headers (#3820)
* remove include from headers

* update implementation files

* completely remove BOOST_FOREACH (#7)

* convert those changes to use auto

* get rid of all usage of BOOST_FOREACH

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2021-02-17 14:15:48 +01:00
Greg Landrum
c0a62388a2 switch to using target_compile_definitions instead of add_definitions (#3350)
* switch to using target_compile_definitions instead of add_definitions

* missed one
2020-08-21 04:49:07 +02:00
Eisuke Kawashima
e86e2c1d5d Modernization: use nullptr (#3143) 2020-05-25 09:40:01 +02:00
Greg Landrum
45bf58754a Cleanup some cmake dependencies (#3077)
* change minimal cmake version to a consistent 3.5

* progress towards a cleanup

* get the basic python deps working

* two more libs

* another round of changes
all tests pass at this point

* next round of changes
all tests pass at this point

* close to done
all tests pass

* very close

* almost done

* shift the RDBoost dependencies around a bit

* remove an extraneous python linkage
this is trying to get the mac builds working again

* Only link to python if it was built shared (#3091)

* change in response to review

Co-Authored-By: Ric <ricrogz@users.noreply.github.com>

* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h

Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
2020-04-17 14:34:23 +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
Greg Landrum
7e6600f3be Fixes #2516 (#2519)
* RDStreams now installed properly

* skip Wrap directories if RDK_BUILD_PYTHON_WRAPPERS is not set

Fixes #2516
2019-06-28 09:57:00 -04:00
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
Paolo Tosco
f7c888844d moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074) 2018-10-11 17:35:23 -04:00
Greg Landrum
2738c35178 Fixes #1903 (#1971)
* Fixes #1903

* update SWIG bindings too
2018-07-25 09:14:17 +02:00
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
Greg Landrum
3f136946e3 Start using "*" instead of "[*]" in SMILES (#1788) 2018-03-23 15:52:52 -04:00
Matt Swain
e57b7a9bc8 Use numpy not numeric for boost 1.65+ - fixes #1581 (#1664)
boost python numeric no longer exists in boost 1.65, so check boost version and conditionally use boost python numpy.
2017-11-20 05:44:19 +01:00
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
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
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +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
e37296d7c7 post review 2015-11-14 08:08:14 +01:00
Brian Kelley
54311dff9c Suppresses warnings in tests 2015-10-18 16:09:58 -04:00
Brian Kelley
daa7e62258 Fixes signed conversion issues (use rdcast) 2015-10-18 15:16:38 -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
4a9d2cbabd tests don't actually need static libs 2015-09-18 04:52:10 +02:00
Greg Landrum
f072c4c2b3 fix a python3 build problem 2015-09-16 14:44:50 +02:00
Greg Landrum
d854911647 further progress 2015-09-11 11:22:45 +02:00
Greg Landrum
10c57f9177 get python wrapper working and add a few tests 2015-09-11 11:22:45 +02:00
Greg Landrum
de2ae071ee update feature defs to match intent of paper: S only an acceptor in rare cases 2015-09-11 11:22:45 +02:00
Greg Landrum
70f26f21bb builds now 2015-09-11 11:22:45 +02:00
Greg Landrum
59b7f91102 add some testing 2015-09-11 11:22:45 +02:00
Greg Landrum
af92a112ac seems to be working, needs tests 2015-09-11 11:21:43 +02:00
Greg Landrum
51ebc9da1e backup commit 2015-09-11 11:21:43 +02:00