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Release_2020_09
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31 Commits

Author SHA1 Message Date
Greg Landrum
45b9aef28b clang-tidy modernize-use-default-member-init and modernize-use-emplace (#3190) 
* run clang-tidy with modernize-use-default-member-init

* results from modernize-use-emplace

* one uniform initialization per line
otherwise SWIG is unhappy

Co-authored-by: Brian Kelley <fustigator@gmail.com>
 2020-05-28 09:07:58 +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
ec366c1ab7 Dev/pvs studio cleanups2 (#2877) 
* a round of cleanups courtesy of PVS studio

* add a test to make sure that a warning is a false alarm

* bug fix

* Fix a UFF bug

* more PVS studio cleanups

* next round of PVS studio cleanups

* completely remove the chances for that bug

* changes in response to review

* add an additional test
+ a bit of reformatting that snuck in
 2020-01-22 15:10:58 +01:00
Eisuke Kawashima
5cd27a242f Fix typo (#2862) 
* Fix typo

* Reflect the comments

* Fix more typos
 2019-12-31 06:43:27 +01:00
Greg Landrum
ea0e8f674e Preserve bond direction in fragmentOnBonds (#2484) 
* Sketch of a solution to preserve bond direction in fragmentOnBonds

* A bit of cleanup work based on Andrew's original commit for #1039
Add a couple of tests too

* forgot to save a file before the commit
 2019-06-10 13:08:50 -04:00
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
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
Greg Landrum
f6bbba411d Fix github1734 (#1741) 
* Fixes #1734
still want some additional testing though

* formatting

* typo

* add python tests

* response to review
re-enable some forgotten tests
 2018-02-15 20:24:40 -05:00
Greg Landrum
ba12d98ad0 Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers (#1713) 
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers

* Actually delete atoms and bonds...

* RWMol::clear now calls destroy to handle atom/bond deletion

* Changes broken Atom lookup for windows/gcc

* Adds tests for running with valgrind

* Adds test designed for valgrind and molecule deletions

* Removes RNG, actually tests bond deletions

* update swig wrappers

* deal with most recent changes on the main branch
 2018-01-07 14:19:47 -05:00
Greg Landrum
636a0f6e69 Cleanup a bunch of compiler warnings (#1697) 
* remove a bunch of compiler warnings

* remove some more warnings on windows (there are still plenty to go...)
 2017-12-22 12:59:52 +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
Greg Landrum
b0f140a55c Fixes #511 2016-03-29 16:56:15 +02:00
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
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Greg Landrum
7fa02f748b Fixes #430 2015-02-04 13:45:47 +01:00
Greg Landrum
2fbea33612 Fixes #429 2015-02-04 10:20:13 +01:00
Greg Landrum
3f23c91eba did not have the version for breakSomeBonds() quite right 2014-11-22 10:42:17 +01:00
Greg Landrum
1725e22cca allow tracking the number of cuts made by the fragmentation code on a per-atom basis 2014-11-22 07:57:39 +01:00
Greg Landrum
2187437649 fix a couple typos 2014-07-07 15:57:27 +02:00
Greg Landrum
288feb7a8a support partial fragmentation on bonds; 
Fixes #288
 2014-07-02 05:47:02 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
6c354852d1 small cleanups 2013-11-07 10:57:18 +01:00
Greg Landrum
95c6c7f261 fragmentOnBonds() fix 2013-11-02 07:17:42 +01:00
Greg Landrum
ea42bf5465 BRICS-related bug fixes 2013-02-05 04:56:10 +00:00
Greg Landrum
89398a10c2 make sure computed props get cleared 2013-01-31 04:54:28 +00:00
Greg Landrum
84d6ddb3f3 add fragmentOnBRICSBonds() 2013-01-30 06:31:06 +00:00
Greg Landrum
fa2b82b606 breaking all BRICS bonds now works 2013-01-29 16:22:27 +00:00
Greg Landrum
00655e7bd6 backup commit; may not build 2013-01-29 06:28:31 +00:00