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14 Commits

Author SHA1 Message Date
Greg Landrum
f23bde46d3 fixes an r-group symmetrization problem (#2324) 
* fixes a r-group symmetrization problem

* clang-tidy

* changes in response to review

* typo
 2019-03-08 09:11:15 -05:00
Ric
a6b26253ff Fix (most of) mem problems (#2123) 
* do not use new on loggers

* del pointers in testDistGeom

* Update Dict hasNonPOD status on bulk update

* delete new Dicts in memtest1.cpp

* fixes in MolSuppliers and testFMCS

* PeriodicTable singleton as unique_ptr

* fix EEM_arrays leak

* fix leaks in testPBF

* fix ParamCollection leak in test UFF

* fix leaks in MMFF

* clear prop dict before read in in pickler

* fix leaks in testFreeSASA

* fix leaks in test3D

* modernize Dict.h & SmilesParse.cpp

* fix leaks in testQuery

* fix leaks in testCrystalFF

* fix leaks in cxsmilesTest

* fix leaks in Catalog & mol cat test

* fix leaks in ShapeUtils & tests

* fix leaks in testSubgraphs1

* fix leaks testFingerprintGenerators

* fix leaks in Catalog/FilterCatalog

* fix leaks in graphmolqueryTest

* these changes reduce bison parse leaks

* fixed leaks in testChirality.cpp

* fix leaks + 2 tests in testMolWriter

* fix 4m leaks in substructLibraryTest

* small improvements to molTautomerTest; still leaks

* fix leaks in testRGroupDecomp

* fix leaks in test; parser still leaks

* fix leaks in itertest

* fix 4m leaks in testDepictor

* fixes in smatest; still leaking due to parser

* fixes in testSLNParse; still leaking due to parser

* flex/bison: always add atoms with ownership; smarts error cleanup

* fix leaks in testReaction

* fix leaks in testSubstructMatch

* fix leaks in resMolSupplierTest

* fix leaks in testChemTransforms + bug in ChemTransforms

* fix leaks in testPickler

* fix leaks in testMolTransform

* fix leaks in testFragCatalog

* fix leak in testSLNParse. Still leaks due to Smiles

* fixed most leaks in testMolSupplier

* pre bison fix

* fix some atom & bond parse problems; others still fail

* bison smiles & smarts, atoms & bonds more or less fixed

* fix leaks in molopstest.cpp

* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp

* fix leaks in moldraw2Dtest1

* fix leaks in testDescriptors

* fix leaks in testInchi

* fix leaks in testUFFForceFieldHelpers

* fix leaks in hanoiTest & new_canon.h

* fix leaks in testMMFFForceField

* fix leaks in graphmolTest1

* fix leaks in testMMFFForceFieldHelpers

* fix leaks in testDistGeomHelpers

* fix leaks in testMolAlign

* initialize occupancy & temp facto with default values

* fix leak in TautomerTransform

* updated suppressions

* fix testStructChecker

* fix logging & py tests

* fix TautomerTransform class/struct issue

* remove misplaced delete in testSLNParse

* deinit in testAvalonLib1

* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp

* fix random testMolWriter/Supplier fails

- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.

* use reset in FFs Params.cpp

* comments on testMMFFForceField

* unrequired 'if's added to mol suppliers

* correct cast in FilterCatalog.h

* use unique_ptr in MACCS Patterns

* remove unrequred if in new_canon

* update & move suppressions
 2018-10-29 14:33:26 +00:00
Paolo Tosco
f7c888844d moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074) 2018-10-11 17:35:23 -04:00
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
Brian Kelley
c5deeb4839 Fix for matchOnlyAtRgroups to allow H replacements as well (#1871) 
R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
 2018-05-21 05:37:15 +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
Brian Kelley
a661489226 Fix/rgroup prefer matching nonhs over hs (#1707) 
* Tweak the scoring function to penalize non h matches considerably.  Only full H rgroups get a one.  Might need to tweak int the future

* Scale the hydrogens as 1/# mols unless they are a full group
 2018-01-09 05:56:37 +01:00
Greg Landrum
1efa8e696e another clang-format run 2017-10-12 06:42:15 +02:00
Greg Landrum
f94e277856 another pass of clang modernize 2017-10-12 06:35:51 +02:00
Greg Landrum
db89172bf8 handle the heavy-atom degree queries differently (#1560) 
* handle the heavy-atom degree queries differently

* Fixes #1563

* add a test for the heavy atom degree option

* Support (and test) adjustHeavyDegree in the cartridge too.

* test results
 2017-09-12 16:10:15 -04:00
Brian Kelley
58ede0f81b Dev/rgroup decomp freefunction (#1557) 
* Adds RGroupDecomp free function and python wrapper

* Fixes subtle bug, adds new RGroupDecomp API

* Updates results for the subtle bug fix.  Verified results were correct.

* Removes smilesCaching.

* Changes RGroupDecompose ordering, adds docstrings and more tests
 2017-09-12 17:41:21 +02:00
Greg Landrum
5a06022704 R group improvements (#1552) 
* Fixes #1550

* might as well update properties on the r groups too

* add option to remove Hs from sidechains;
expose a few more parameters to python;
expose ctor with parameter object to python
 2017-09-08 07:49:05 -04:00
Greg Landrum
62150f7d80 Squashed commit of the following: 
commit 7f7b5268a62eecd260027e0918abbdf62b100034
Merge: 90e9fd3 6dd173d
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Tue Aug 8 01:19:15 2017 +0200

    merge back to master

commit 6dd173dec6
Merge: 45a94bd e11ad49
Author: Brian Kelley <fustigator@gmail.com>
Date:   Thu Aug 3 07:54:26 2017 -0400

    Merge pull request #8 from greglandrum/dev/rgroup-decomposition

    support using generic iterators in ctor;

commit e11ad49068
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Tue Aug 1 06:29:52 2017 +0200

    move notebooks to docs

commit 606c03c28f
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Thu Jul 27 05:13:13 2017 +0200

    support using generic iterators in ctor;
    general comment: this is a useful pattern that we could use elsewhere

commit 45a94bd663
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Wed Jul 26 13:30:23 2017 -0400

    Updates notebooks

commit 8f78ba97d3
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Wed Jul 26 09:00:42 2017 -0400

    Updates notebooks

commit 44728803ae
Merge: d67409d 4d0b00d
Author: Brian Kelley <fustigator@gmail.com>
Date:   Wed Jul 26 08:53:11 2017 -0400

    Merge pull request #7 from greglandrum/dev/rgroup-decomposition

    clean up a couple leaks and some compiler warnings

commit 4d0b00dd2e
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Wed Jul 26 07:47:56 2017 +0200

    clean up a couple leaks and some compiler warnings

commit d67409da0c
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 11:43:14 2017 -0400

    Makes the scoring system more sane

commit 1b5181dc2f
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 10:55:33 2017 -0400

    Finalizes enums

commit 7e9ee61556
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 10:55:18 2017 -0400

    Fixes constructor botched in the last commit

commit aed2a201bf
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:22:42 2017 -0400

    Cleans up some code

commit 95e82a1398
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:14:31 2017 -0400

    Removes unused variable

commit 0b1ed09316
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:14:23 2017 -0400

    Slight optimization by combining two loops

commit ed3340a516
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:53:06 2017 -0400

    Fixes post increments in for loops

commit 25b1678a58
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:53 2017 -0400

    Fixes memory leak and doesn’t call SmartsToMol twice

commit 86c8c42688
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:32 2017 -0400

    Adds header guards

commit b043e38d3a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:25 2017 -0400

    Removes unused variable

commit 631aa77153
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 11 08:10:39 2017 -0400

    Fixes typo in filename

commit d6e0dc753a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 10 14:48:04 2017 -0400

    Fixes c++11 style enums

commit b9a31eae9a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 10 14:00:04 2017 -0400

    Adds RGroupDecomposition attempt
 2017-08-08 01:23:49 +02:00