joblib Parallel issue with specific complex '3m1s' in the PDBBind data

It could be a problem with RDKit. My version is “rdkit 2021.09.4”.

import pickle
pdbbind_dir = "PDBBind_processed/"
name = '3m1s'
lig = read_molecule(os.path.join(pdbbind_dir, name, f'{name}_ligand.sdf'), sanitize=True,
                    remove_hs=True)
if lig == None:  # read mol2 file if sdf file cannot be sanitized
    lig = read_molecule(os.path.join(pdbbind_dir, name, f'{name}_ligand.mol2'), sanitize=True,
                        remove_hs=True)
# lig = Chem.MolFromSmiles('O=C[Ru+9]12345(C6=C1C2C3=C64)n1c2ccc(O)cc2c2c3c(c4ccc[n+]5c4c21)C(=O)NC3=O')
pickle.dump(lig, open("test.pkl", "bw"))
pickle.load(open("test.pkl", "rb"))

RuntimeError: invalid value in pickle

[gaozhangyang]

Thanks for the wonderful work!

I solved the problem by replacing following codes in process_mol.py:

coords = lig.GetConformer().GetPositions()==>coords = get_rdkit_coords(lig).numpy()

and removing some training complexes:

3zs1 3p3h 4jfv 4acu 3w8o 4mdn 2jld 3m1s 3p3j 4jfw 5tgy 4dcy 3p44 4i60 4jhq

and validation complexes:

4xkc 3p55 3rj7

[HannesStark]

Sorry for the late reply, I somehow missed your question @lejlot . Here is a list of versions: _libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
absl-py 1.0.0 pypi_0 pypi asttokens 2.0.5 pypi_0 pypi beautifulsoup4 4.10.0 pypi_0 pypi biopandas 0.2.9 pypi_0 pypi blas 1.0 mkl
bottleneck 1.3.2 py37heb32a55_1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2021.10.26 h06a4308_2
cachetools 4.2.4 pypi_0 pypi cairo 1.16.0 hf32fb01_1
certifi 2021.10.8 py37h06a4308_0
charset-normalizer 2.0.7 pypi_0 pypi cloudpickle 2.0.0 pypi_0 pypi colorama 0.4.4 pypi_0 pypi cudatoolkit 10.2.89 hfd86e86_1
cycler 0.11.0 pypi_0 pypi dgl-cuda10.2 0.7.2 py37_0 dglteam dgllife 0.2.8 pypi_0 pypi executing 0.8.2 pypi_0 pypi ffmpeg 4.3 hf484d3e_0 pytorch filelock 3.4.0 pypi_0 pypi fontconfig 2.13.1 h6c09931_0
fonttools 4.28.1 pypi_0 pypi freetype 2.11.0 h70c0345_0
future 0.18.2 pypi_0 pypi gdown 4.2.0 pypi_0 pypi giflib 5.2.1 h7b6447c_0
glib 2.69.1 h5202010_0
gmp 6.2.1 h2531618_2
gnutls 3.6.15 he1e5248_0
google-auth 2.3.3 pypi_0 pypi google-auth-oauthlib 0.4.6 pypi_0 pypi grpcio 1.42.0 pypi_0 pypi hyperopt 0.2.7 pypi_0 pypi icecream 2.1.1 pypi_0 pypi icu 58.2 he6710b0_3
idna 3.3 pypi_0 pypi importlib-metadata 4.8.2 pypi_0 pypi intel-openmp 2021.4.0 h06a4308_3561
joblib 1.1.0 pypi_0 pypi jpeg 9d h7f8727e_0
kiwisolver 1.3.2 pypi_0 pypi lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.35.1 h7274673_9
libboost 1.73.0 h3ff78a5_11
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 9.3.0 h5101ec6_17
libiconv 1.15 h63c8f33_5
libidn2 2.3.2 h7f8727e_0
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.3.0 hd4cf53a_17
libtasn1 4.16.0 h27cfd23_0
libtiff 4.2.0 h85742a9_0
libunistring 0.9.10 h27cfd23_0
libuuid 1.0.3 h7f8727e_2
libuv 1.40.0 h7b6447c_0
libwebp 1.2.0 h89dd481_0
libwebp-base 1.2.0 h27cfd23_0
libxcb 1.14 h7b6447c_0
libxml2 2.9.12 h03d6c58_0
lz4-c 1.9.3 h295c915_1
markdown 3.3.6 pypi_0 pypi matplotlib 3.5.0 pypi_0 pypi mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py37h7f8727e_0
mkl_fft 1.3.1 py37hd3c417c_0
mkl_random 1.2.2 py37h51133e4_0
ncurses 6.3 h7f8727e_2
nettle 3.7.3 hbbd107a_1
networkx 2.6.3 pyhd3eb1b0_0
numexpr 2.7.3 py37h22e1b3c_1
numpy 1.21.2 py37h20f2e39_0
numpy-base 1.21.2 py37h79a1101_0
oauthlib 3.1.1 pypi_0 pypi olefile 0.46 py37_0
openh264 2.1.0 hd408876_0
openssl 1.1.1l h7f8727e_0
packaging 21.3 pypi_0 pypi pandas 1.3.4 py37h8c16a72_0
pcre 8.45 h295c915_0
pillow 8.4.0 py37h5aabda8_0
pip 21.0.1 py37h06a4308_0
pixman 0.40.0 h7f8727e_1
pot 0.8.0 pypi_0 pypi protobuf 3.19.1 pypi_0 pypi py-boost 1.73.0 py37ha9443f7_11
py4j 0.10.9.2 pypi_0 pypi pyaml 21.10.1 pypi_0 pypi pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pygments 2.10.0 pypi_0 pypi pyparsing 3.0.6 pypi_0 pypi pysocks 1.7.1 pypi_0 pypi python 3.7.11 h12debd9_0
python-dateutil 2.8.2 pyhd3eb1b0_0
pytorch 1.10.0 py3.7_cuda10.2_cudnn7.6.5_0 pytorch pytorch-mutex 1.0 cuda pytorch pytz 2021.3 pyhd3eb1b0_0
pyyaml 6.0 pypi_0 pypi rdkit 2020.09.1.0 py37hd50e099_1 rdkit readline 8.1 h27cfd23_0
requests 2.26.0 pypi_0 pypi requests-oauthlib 1.3.0 pypi_0 pypi rsa 4.7.2 pypi_0 pypi scikit-learn 1.0.1 pypi_0 pypi scipy 1.7.1 py37h292c36d_2
setuptools 58.0.4 py37h06a4308_0
setuptools-scm 6.3.2 pypi_0 pypi six 1.16.0 pyhd3eb1b0_0
soupsieve 2.3.1 pypi_0 pypi sqlite 3.36.0 hc218d9a_0
tensorboard 2.7.0 pypi_0 pypi tensorboard-data-server 0.6.1 pypi_0 pypi tensorboard-plugin-wit 1.8.0 pypi_0 pypi threadpoolctl 3.0.0 pypi_0 pypi tk 8.6.11 h1ccaba5_0
tomli 1.2.2 pypi_0 pypi torchaudio 0.10.0 py37_cu102 pytorch torchvision 0.11.1 py37_cu102 pytorch tqdm 4.62.3 pypi_0 pypi typing_extensions 3.10.0.2 pyh06a4308_0
urllib3 1.26.7 pypi_0 pypi werkzeug 2.0.2 pypi_0 pypi wheel 0.37.0 pyhd3eb1b0_1
xz 5.2.5 h7b6447c_0
zipp 3.6.0 pypi_0 pypi zlib 1.2.11 h7b6447c_3
zstd 1.4.9 haebb681_0