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a75018fe385b0a36901bcb074ebbca0c4e84a9d5
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77 Commits

Author SHA1 Message Date
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
5cd27a242f Fix typo (#2862) 
* Fix typo

* Reflect the comments

* Fix more typos
 2019-12-31 06:43:27 +01:00
Eisuke Kawashima
7c6d9cf4e9 Unset executable flag (#2833) 2019-12-19 08:29:32 +01:00
Paolo Tosco
d714f5128f Fixes #2839 (#2840) 
* - fixes #2839

* clang format
 2019-12-11 16:22:53 +01:00
Paolo Tosco
fea3f00c3f - removed RDKIT_SIMDIVPICKERS_EXPORT which should not be there (#2740) 
and prevents DLLs from building on Windows
 2019-10-28 17:18:32 -04:00
Greg Landrum
5de8007b43 Merge branch 'e-kwsm-misc' 2019-10-25 04:49:23 +02:00
Greg Landrum
6cfc8f36a7 [WIP] Add Leader picker implementation (#2724) 
* initial commit of Roger's contrib

* add the new file to the headers list

* clang-format

* stub of the python wrapper

* code added for testing

* code added for testing

* add LeaderPicker.seq.h

* default pickSize value

* first crude python wrapper

* Add C++ tests for the LeaderPicker
combine the thread and non-thread versions

* that was not really a test

* support providing a functor from Python

* no longer need the .seq header

* temporarily disable the threaded version to allow CI runs to pass

* some refactoring and cleanup
 2019-10-24 13:14:15 +02:00
Eisuke Kawashima
185ec927ab Unset executable flag 2019-10-10 20:18:43 +09:00
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
Greg Landrum
24f1737839 Remove a bunch of Python2-related warts (#2315) 
* remove all of the "from __future__" imports

* remove the first batch of rdkit.six imports/uses

* next step of rdkit.six removal

* removing xrange, range, and some maps

* next round of removals

* next round of cleanups

* fix inchi test

* last bits of "from rdkit.six" are gone

* and the last of the six stuff is gone

* strange importlib problem
 2019-03-06 20:43:49 -05:00
Greg Landrum
699f0b8c5b fix a problem with the random pickers test (#2310) 2019-03-04 22:34:25 -05:00
Greg Landrum
4d14a819e6 Fixes #2245 (#2250) 
* not yet done

* update docs, python tests, and the release notes

* updates in response to review
 2019-01-31 00:03:39 -05:00
Ric
91008ff11d Address compile warnings & trivial improvements (#2097) 
* Address compile warnings & trivial improvements

* revert unwanted initializers; use RDUNUSED_PARAM for unused params

* revert fix in testRDFcustom; marked with 'TO DO' comment
 2018-10-12 06:39:32 -04:00
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
Dan N
8bed437c5f Addresses several minor warning messages during the build (#1935) 
* Address minor compilation warning messages

Addresses trivial compilation warning messages:

    [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o
    rdkit/Code/GraphMol/AddHs.cpp:497:9: warning: unused variable 'dblBond' [-Wunused-variable]
      Bond *dblBond = nullptr;
            ^
    1 warning generated.

    [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o
    rdkit/Code/GraphMol/Chirality.cpp:1738:62: warning: unused parameter 'mol' [-Wunused-parameter]
    bool isBondCandidateForStereo(const Bond *bond, const ROMol &mol) {
                                                                 ^
    1 warning generated.

    [ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o
    rdkit/Code/GraphMol/molopstest.cpp:4694:12: warning: unused variable 'nm' [-Wunused-variable]
        ROMol *nm = MolOps::renumberAtoms(*m, nVect);
               ^
    rdkit/Code/GraphMol/molopstest.cpp:6941:16: warning: unused variable 'm' [-Wunused-variable]
            RWMol *m = SmilesToMol(smiles);
                   ^
    2 warnings generated.

    [ 42%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o
    rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:14: warning: unused parameter 'argc' [-Wunused-parameter]
    int main(int argc, char *argv[]) {
                 ^
    rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:26: warning: unused parameter 'argv' [-Wunused-parameter]
    int main(int argc, char *argv[]) {
                             ^
    2 warnings generated.

    [ 55%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o
    rdkit/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:176:20: warning: unused variable 'NUM_FUNCS' [-Wunused-const-variable]
    const unsigned int NUM_FUNCS =
                       ^
    1 warning generated.

    [ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o
    rdkit/Code/GraphMol/StructChecker/ReCharge.cpp:405:17: warning: unused variable 'atom' [-Wunused-variable]
        const Atom &atom = *Mol.getAtomWithIdx(i);
                    ^
    1 warning generated.

    [ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o
    rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:12: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        if (-1 == ti || -1 == tj) continue;
            ~~ ^  ~~
    rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:24: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        if (-1 == ti || -1 == tj) continue;
                        ~~ ^  ~~
    2 warnings generated.

    [ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o
    rdkit/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:428:9: warning: unused variable 'res' [-Wunused-variable]
        int res = decomp.add(*mol);
            ^
    1 warning generated.

    [ 96%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o
    rdkit/Code/SimDivPickers/testPickers.cpp:19:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      return abs((double)i - (double)j);
             ^
    rdkit/Code/SimDivPickers/testPickers.cpp:19:10: note: use function 'std::abs' instead
      return abs((double)i - (double)j);
             ^~~
             std::abs
    1 warning generated.

* Close open file handles during build set-up

Under Python3, the update_pains.py file generated warning
messages like:

    == Done updating pains files
    /Code/GraphMol/FilterCatalog/update_pains.py:140: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/../../../Data/Pains/wehi_pains.csv'
mode='r' encoding='UTF-8'>
      for smiles, name in csv.reader(open(PAINS_CSV)):
    /Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_a.in' mode='r'
encoding='UTF-8'>
      t = open(filename).read()
    /Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_b.in' mode='r'
encoding='UTF-8'>
      t = open(filename).read()
    /Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_c.in' mode='r'
encoding='UTF-8'>
      t = open(filename).read()
 2018-06-26 13:57:22 -07:00
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
890886d770 speedup the NumBitsInCommon operation (#1785) 
* patch to speedup tanimoto calculation

* make it build on windows

* cleanup a bit

* followup from review
 2018-04-02 05:01:07 +02:00
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
f94e277856 another pass of clang modernize 2017-10-12 06:35:51 +02:00
Greg Landrum
87786c08b5 Merge branch 'master' into modern_cxx 
# Conflicts:
#	.travis.yml
#	Code/GraphMol/FileParsers/MolFileParser.cpp
#	Code/GraphMol/FileParsers/MolFileStereochem.cpp
#	Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
#	Code/GraphMol/MolAlign/testMolAlign.cpp
#	Code/GraphMol/MolDraw2D/MolDraw2D.cpp
#	Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
#	Code/GraphMol/QueryOps.cpp
#	Code/GraphMol/ROMol.cpp
#	Code/GraphMol/SmilesParse/test.cpp
#	Code/GraphMol/Trajectory/Trajectory.cpp
#	Code/GraphMol/Wrap/Atom.cpp
#	Code/GraphMol/Wrap/Bond.cpp
#	Code/GraphMol/new_canon.cpp
#	Code/RDGeneral/testDict.cpp
#	Code/SimDivPickers/Wrap/MaxMinPicker.cpp
 2017-10-05 05:58:38 +02:00
Greg Landrum
96b092177e [WIP] add threshold argument to maxmin picker (#1587) 
* add threshold argument

* expose the new options to python
not yet tested, but it at least compiles

* support threshold on the python side;
fix a bug with the way the threshold is returned
 2017-09-26 12:49:33 -04:00
Greg Landrum
fd3524f77c Optimization of the MaxMin diversity picker (#1574) 
* initial submission; needs review

* minor

* line endings

* remove cache functionality since it's now redundant

* add test data

* add a test

* changes from review
 2017-09-17 09:13:14 -04:00
Greg Landrum
85488fb3ae fixes #1421 (#1422) 
* fixes #1421

* change suggested in review
 2017-07-02 10:24:26 +02:00
Greg Landrum
a19d6fec0b fixes #1421 (#1422) 
* fixes #1421

* change suggested in review
 2017-05-22 17:29:00 -04:00
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
Brian Kelley
5d3a2a7262 Merge pull request #797 from greglandrum/fix/cleanup_register_execption 
Remove extra calls to python::register_exception_translator
 2016-03-12 08:03:45 -05:00
Greg Landrum
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +01:00
Greg Landrum
a2f2c9805f add a basic test of specific results for the lazy picker 2016-02-25 16:25:10 +01:00
Greg Landrum
ed62f46a4d require numpy 1.7, not 1.8 2015-12-01 04:39:28 +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
d07f2ccd05 replace oldnumeric imports 2015-11-28 02:38:58 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Greg Landrum
1cde397acb merge commit 2015-10-30 02:58:46 +01:00
Brian Kelley
237861136b Fixes more Boost warning suppression 2015-10-18 16:08:11 -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
Greg Landrum
a743cff4d7 Fixes #573 2015-09-20 04:44:39 +02:00
Andrew Dalke
6d66534743 removed bare except statements 2015-09-07 13:27:14 +02:00
Riccardo Vianello
e6a1327822 Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 21:40:40 +01:00
Riccardo Vianello
95f60d21bc python3 portability fixes for pandas and the ipython notebook 2014-09-11 23:49:45 +02:00
Greg Landrum
7946261aae Fixes #294 
also adds direct diversity picking using fingerprints from python (efficiency win)
 2014-08-07 09:22:11 +02:00
Greg Landrum
fac600885b fix the simdivfilters problem with python3. This has now been tested on py3 and should, hopefully, not cause the travis build to fail 2014-08-05 05:26:25 +02:00
Greg Landrum
d2fdb3d075 Fixes #294 2014-08-03 12:03:35 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
bf2416032e docstring cleanup 2012-01-07 15:10:42 +00:00
Greg Landrum
b993f89afe remove the bjam-based build system 2010-09-27 03:54:07 +00:00