Hello Rasmus, I too had this problem a while ago while trying to build the RDKit on Windows, but since I was only interested in the C++ API I gave up on the Python wrappers altogether.
Since this is somewhat related, I’m seizing the opportunity for a suggestion: given how convenient it is to install Boost (and everything else) with vcpkg, would it be possible to contribute the RDKit to vcpkg as well? For Windows users wanting to use the C++ API currently the only option is to build the RDKit from source. On Linux it’s possible to use the RDKit libraries of the Anaconda distribution, but on Windows it doesn’t ship with actual .lib or .dlls but .pyd files instead. I would give this a shot myself but I’m probably not knowledgeable enough to get it working. Best regards, Alan From: Rasmus "Termo" Lundsgaard<mailto:termope...@gmail.com> Sent: 14 April 2020 10:25 To: RDKit Discuss<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] compile py wrappers with vcpkg boost 1.72 I now figured out that the problem is with static build boost libraries. It works fine with dynamic build boost libraries. Why does the python wrapping not work with static build boost libraries, and is it possible for it to work with static libraries? Regards Rasmus On Wed, Apr 8, 2020 at 7:58 PM Rasmus "Termo" Lundsgaard <termope...@gmail.com<mailto:termope...@gmail.com>> wrote: Dear all. I am trying to compile RDKit with boost from vcpkg which by standard use latest which is boost 1.72, and link against python37. All none python crests pass fine, but most python tests keeps failing for me with something the "did not match C++ signature" error. Here is a minimal example that fails: In [7]: mol = Chem.MolFromSmiles('CCCC') In [8]: mol.GetNumAtoms() Out[8]: 4 In [9]: mol.Debug() Atoms: 0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 Bonds: 0 0->1 order: 1 conj?: 0 aromatic?: 0 1 1->2 order: 1 conj?: 0 aromatic?: 0 2 2->3 order: 1 conj?: 0 aromatic?: 0 In [10]: molh = Chem.AddHs(mol) --------------------------------------------------------------------------- ArgumentError Traceback (most recent call last) <ipython-input-10-9a58211410d1> in <module> ----> 1 molh = Chem.AddHs(mol) ArgumentError: Python argument types in rdkit.Chem.rdmolops.AddHs(Mol) did not match C++ signature: AddHs(RDKit::ROMol mol, bool explicitOnly=False, bool addCoords=False, boost::python::api::object onlyOnAtoms=None, bool addResidueInfo=False) Do you have any idea of why that is? My only suspiscion right now is if it can because it is linking to the found numpy (which is in and conda environment I am using for testing), if this is using another boost version, can that be it? my cmake call: cmake -DPy_ENABLE_SHARED=1 \ -DPYTHON_EXECUTABLE=/home/hafnium/miniconda3/envs/py37/bin/python3 \ -DRDK_BUILD_COORDGEN_SUPPORT=OFF \ -DRDK_INSTALL_INTREE=OFF \ -DRDK_INSTALL_STATIC_LIBS=OFF \ -DRDK_BUILD_CPP_TESTS=ON \ -DRDK_USE_BOOST_IOSTREAMS=OFF \ -DBoost_NO_SYSTEM_PATHS=ON \ -DCMAKE_INSTALL_PREFIX=/home/hafnium/Hflabs-sync/HFgit/External/rdkit/rdkit-install \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_TOOLCHAIN_FILE=/home/hafnium/Hflabs-sync/vcpkg/scripts/buildsystems/vcpkg.cmake \ .. The following tests FAILED: 17 - pyAlignment (Failed) 21 - pyForceFieldConstraints (Failed) 41 - pyDepictor (Failed) 62 - pyChemReactions (Failed) 63 - pyChemReactionEnumerations (Failed) 64 - pyChemReactionSanitize (Failed) 70 - pyFilterCatalog (Failed) 72 - pyFragCatalog (Failed) 87 - pyMolDescriptors (Child aborted) 88 - pyMolDescriptors3D (Failed) 93 - pyTestGenerator (Failed) 94 - pyTestMHFP (Failed) 96 - pyPartialCharges (Failed) 98 - pyMolTransforms (Failed) 103 - pyForceFieldHelpers (Failed) 105 - pyDistGeomHelpers (Failed) 107 - pyMolAlign (Failed) 109 - pyChemicalFeatures (Failed) 111 - pyShapeHelpers (Failed) 113 - pyMolCatalog (Failed) 117 - pyMolDraw2D (Failed) 119 - pyFMCS (Failed) 123 - pyMolHash (Failed) 125 - pyMMPA (Failed) 127 - pyReducedGraphs (Failed) 130 - pySubstructLibrary (Failed) 132 - pyRGroupDecomposition (Failed) 134 - pyMolInterchange (Failed) 137 - pyGraphMolWrap (Failed) 138 - pyTestConformerWrap (Failed) 139 - pyTestTrajectory (Failed) 140 - pyTestSGroups (Failed) 142 - pyTestPropertyLists (Failed) 151 - pyMolStandardize (Failed) 153 - pyScaffoldNetwork (Failed) 157 - pyMatCalc (Failed) 160 - pySimDivPickers (Failed) 161 - pyRanker (Failed) 163 - pyFeatures (Failed) 164 - pythonTestDbCLI (Failed) 165 - pythonTestDirML (Failed) 166 - pythonTestDirDataStructs (Failed) 168 - pythonTestDirSimDivFilters (Failed) 169 - pythonTestDirVLib (Failed) 170 - pythonTestDirChem (Failed)
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