Issue with tutorial.py and tutorial_asym.py

[gustavor101]

Trying to run the tutorial examples both fail with error: File "tutorial_asym.py", line 43, in c.create_receptor_motif_complex(n_motif=2, dock_pose_id=0) File "/storage3/silc-env/lib/python3.8/site-packages/silc/build_molecule.py", line 413, in create_receptor_motif_complex self.dock.receptor, motifs = util.optimize_complex(self.dock.receptor, motifs, expanded_cores) File "/storage3/silc-env/lib/python3.8/site-packages/silc/util.py", line 192, in optimize_complex complex = AllChem.CombineMols(mols[0], mols[1]) Boost.Python.ArgumentError: Python argument types in rdkit.Chem.rdmolops.CombineMols(NoneType, Mol) did not match C++ signature: CombineMols(RDKit::ROMol mol1, RDKit::ROMol mol2, RDGeom::Point3D offset=<rdkit.Geometry.rdGeometry.Point3D object at 0x7f75ebc696c0>) File "tutorial.py", line 43, in c.create_receptor_motif_complex(n_motif=2, dock_pose_id=19, solvate=True) # X-shape, "trans" File "/storage3/silc-env/lib/python3.8/site-packages/silc/build_molecule.py", line 413, in create_receptor_motif_complex self.dock.receptor, motifs = util.optimize_complex(self.dock.receptor, motifs, expanded_cores) File "/storage3/silc-env/lib/python3.8/site-packages/silc/util.py", line 192, in optimize_complex complex = AllChem.CombineMols(mols[0], mols[1]) Boost.Python.ArgumentError: Python argument types in rdkit.Chem.rdmolops.CombineMols(NoneType, Mol) did not match C++ signature: CombineMols(RDKit::ROMol mol1, RDKit::ROMol mol2, RDGeom::Point3D offset=<rdkit.Geometry.rdGeometry.Point3D object at 0x7f15fe62d640>)

[franklhy]

I cannot reproduce this error. It seems that it fails to load the docking configuration from silc/data/tutorial/docking/symmetric_core and silc/data/tutorial/docking/asymmetric_core. Did you modify the tutorial.py and tutorial_asym.py code?

[gustavor101]

No, they are the same files than in the biased_md branch. Here is my conda list:

packages in environment at /storage3/silc-env:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ambertools 23.3 py38hce2aceb_6 conda-forge amberutils 21.0 pypi_0 pypi anyio 4.2.0 pypi_0 pypi argon2-cffi 23.1.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arpack 3.8.0 nompi_h0baa96a_101 conda-forge arrow 1.3.0 pypi_0 pypi asttokens 2.4.1 pypi_0 pypi async-lru 2.0.4 pypi_0 pypi attrs 23.2.0 pypi_0 pypi babel 2.14.0 pypi_0 pypi backcall 0.2.0 pypi_0 pypi beautifulsoup4 4.12.3 pypi_0 pypi bleach 6.1.0 pypi_0 pypi blosc 1.21.5 h0f2a231_0 conda-forge boost 1.82.0 hb563948_6 conda-forge boost-cpp 1.82.0 h44aadfe_6 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py38h17151c0_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.25.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge cffi 1.16.0 pypi_0 pypi charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge comm 0.2.1 pypi_0 pypi contourpy 1.1.1 py38h7f3f72f_1 conda-forge cudatoolkit 11.5.2 hbdc67f6_12 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge debugpy 1.8.0 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi dill 0.3.7 pypi_0 pypi edgembar 0.2 pypi_0 pypi exceptiongroup 1.2.0 pypi_0 pypi executing 2.0.1 pypi_0 pypi fastjsonschema 2.19.1 pypi_0 pypi fftw 3.3.10 nompi_hc118613_108 conda-forge fonttools 4.47.2 py38h01eb140_0 conda-forge fqdn 1.5.1 pypi_0 pypi freetype 2.12.1 h267a509_2 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_h4f84152_100 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.6 pyhd8ed1ab_0 conda-forge importlib-metadata 7.0.1 pypi_0 pypi importlib-resources 6.1.1 pyhd8ed1ab_0 conda-forge importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge ipykernel 6.29.0 pypi_0 pypi ipython 8.12.3 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi jedi 0.19.1 pypi_0 pypi jinja2 3.1.3 pypi_0 pypi joblib 1.3.2 pyhd8ed1ab_0 conda-forge json5 0.9.14 pypi_0 pypi jsonpointer 2.4 pypi_0 pypi jsonschema 4.21.0 pypi_0 pypi jsonschema-specifications 2023.12.1 pypi_0 pypi jupyter-client 8.6.0 pypi_0 pypi jupyter-core 5.7.1 pypi_0 pypi jupyter-events 0.9.0 pypi_0 pypi jupyter-lsp 2.2.2 pypi_0 pypi jupyter-server 2.12.5 pypi_0 pypi jupyter-server-terminals 0.5.1 pypi_0 pypi jupyterlab 4.0.10 pypi_0 pypi jupyterlab-pygments 0.3.0 pypi_0 pypi jupyterlab-server 2.25.2 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py38h7f3f72f_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libboost 1.82.0 h6fcfa73_6 conda-forge libboost-devel 1.82.0 h00ab1b0_6 conda-forge libboost-headers 1.82.0 ha770c72_6 conda-forge libboost-python 1.82.0 py38hae673b5_6 conda-forge libboost-python-devel 1.82.0 py38hb563948_6 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcurl 8.5.0 hca28451_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge libnetcdf 4.9.2 nompi_h9612171_113 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libtiff 4.6.0 ha9c0a0a_2 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.12.4 h232c23b_1 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge markupsafe 2.1.3 pypi_0 pypi matplotlib-base 3.7.3 py38h58ed7fa_0 conda-forge matplotlib-inline 0.1.6 pypi_0 pypi meeko 0.5.0 pypi_0 pypi mistune 3.0.2 pypi_0 pypi mmpbsa-py 16.0 pypi_0 pypi munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbclient 0.9.0 pypi_0 pypi nbconvert 7.14.2 pypi_0 pypi nbformat 5.9.2 pypi_0 pypi ncurses 6.4 h59595ed_2 conda-forge nest-asyncio 1.5.9 pypi_0 pypi netcdf-fortran 4.6.1 nompi_hacb5139_103 conda-forge notebook-shim 0.2.3 pypi_0 pypi numpy 1.24.4 py38h59b608b_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge ocl-icd-system 1.0.0 1 conda-forge openjpeg 2.5.0 h488ebb8_3 conda-forge openmm 8.1.1 py38h172b3f9_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge overrides 7.4.0 pypi_0 pypi packaging 23.2 pyhd8ed1ab_0 conda-forge packmol 20.010 h86c2bf4_0 conda-forge packmol-memgen 2023.2.24 pypi_0 pypi pandas 2.0.3 py38h01efb38_1 conda-forge pandocfilters 1.5.0 pypi_0 pypi parmed 4.2.2 py38h17151c0_1 conda-forge parso 0.8.3 pypi_0 pypi pdb4amber 22.0 pypi_0 pypi perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 10.2.0 py38ha43c96d_0 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pypi_0 pypi platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge pooch 1.8.0 pyhd8ed1ab_0 conda-forge prometheus-client 0.19.0 pypi_0 pypi prompt-toolkit 3.0.43 pypi_0 pypi psutil 5.9.7 pypi_0 pypi pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi py3dmol 2.0.4 pypi_0 pypi pycparser 2.21 pypi_0 pypi pygments 2.17.2 pypi_0 pypi pymsmt 22.0 pypi_0 pypi pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.8.18 hd12c33a_1_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pypi_0 pypi python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge python_abi 3.8 4_cp38 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 pypi_0 pypi pyzmq 25.1.2 pypi_0 pypi rdkit 2023.9.4 pypi_0 pypi readline 8.2 h8228510_1 conda-forge referencing 0.32.1 pypi_0 pypi requests 2.31.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi rpds-py 0.17.1 pypi_0 pypi sander 22.0 pypi_0 pypi scipy 1.10.1 py38h59b608b_3 conda-forge send2trash 1.8.2 pypi_0 pypi setuptools 69.0.3 pyhd8ed1ab_0 conda-forge silc 0.1.0 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.0 pypi_0 pypi soupsieve 2.5 pypi_0 pypi stack-data 0.6.3 pypi_0 pypi terminado 0.18.0 pypi_0 pypi tinycss2 1.2.1 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pypi_0 pypi tornado 6.4 pypi_0 pypi traitlets 5.14.1 pypi_0 pypi types-python-dateutil 2.8.19.20240106 pypi_0 pypi typing-extensions 4.9.0 pypi_0 pypi unicodedata2 15.1.0 py38h01eb140_0 conda-forge uri-template 1.3.0 pypi_0 pypi urllib3 2.1.0 pyhd8ed1ab_0 conda-forge vina 1.2.5 pypi_0 pypi wcwidth 0.2.13 pypi_0 pypi webcolors 1.13 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.7.0 pypi_0 pypi wheel 0.42.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

[gustavor101]

Using rdkit 2023.9.1 instead of rdkit 2023.9.4 solves the issue.

[franklhy]

@gustavor101 I created a new branch named read_receptor which uses MDAnalysis to read the topology and pdb of receptors. Could you please try it with both rdkit 2023.9.1 and rdkit 2023.9.4?

[gustavor101]

Both examples work with either rdkit 2023.9.1 or 2023.9.4 in combination with mdanalysis 2.4.3.