Open sistar2020 opened 3 months ago
Hi there,
We have carefully read your issue. To reproduce your problem, please let me know your OS environment and anaconda version.
Here is the info:
$ lsb_release -a
Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy
$ conda --version
conda 23.11.0
$ conda list
# packages in environment at /opt/anaconda310/envs/DeepBioisostere:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
blas 1.0 mkl
boost 1.78.0 py39hda80f44_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
bottleneck 1.3.7 py39ha9d4c09_0
brotli 1.0.9 h5eee18b_8
brotli-bin 1.0.9 h5eee18b_8
bzip2 1.0.8 h5eee18b_6
ca-certificates 2024.3.11 h06a4308_0
cairo 1.16.0 h19f5f5c_2
certifi 2024.6.2 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
contourpy 1.2.1 pypi_0 pypi
cudatoolkit 11.3.1 h2bc3f7f_2
cycler 0.12.1 pypi_0 pypi
expat 2.6.2 h6a678d5_0
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonttools 4.53.0 pypi_0 pypi
freetype 2.12.1 h4a9f257_0
glib 2.78.4 h6a678d5_0
glib-tools 2.78.4 h6a678d5_0
greenlet 3.0.1 py39h6a678d5_0
icu 73.2 h59595ed_0 conda-forge
idna 3.7 pypi_0 pypi
importlib-resources 6.4.0 pypi_0 pypi
importlib_resources 6.1.1 py39h06a4308_1
intel-openmp 2023.1.0 hdb19cb5_46306
jinja2 3.1.4 pypi_0 pypi
joblib 1.4.2 py39h06a4308_0
jpeg 9e h5eee18b_1
kiwisolver 1.4.5 pypi_0 pypi
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libbrotlicommon 1.0.9 h5eee18b_8
libbrotlidec 1.0.9 h5eee18b_8
libbrotlienc 1.0.9 h5eee18b_8
libdeflate 1.17 h5eee18b_1
libffi 3.4.4 h6a678d5_1
libgcc-ng 13.2.0 h77fa898_9 conda-forge
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libglib 2.78.4 hdc74915_0
libgomp 13.2.0 h77fa898_9 conda-forge
libiconv 1.16 h5eee18b_3
libopenblas 0.3.21 h043d6bf_0
libpng 1.6.39 h5eee18b_0
libstdcxx-ng 13.2.0 hc0a3c3a_9 conda-forge
libtiff 4.5.1 h6a678d5_0
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.44.2 h5eee18b_0
libwebp-base 1.3.2 h5eee18b_0
libxcb 1.15 h7f8727e_0
libzlib 1.2.13 h4ab18f5_6 conda-forge
lz4-c 1.9.4 h6a678d5_1
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.9.0 pypi_0 pypi
matplotlib-base 3.8.4 py39h1128e8f_0
mkl 2023.1.0 h213fc3f_46344
mkl-service 2.4.0 py39h5eee18b_1
mkl_fft 1.3.8 py39h5eee18b_0
mkl_random 1.2.4 py39hdb19cb5_0
ncurses 6.4 h6a678d5_0
numexpr 2.8.7 py39h85018f9_0
numpy 1.26.4 py39h5f9d8c6_0
numpy-base 1.26.4 py39hb5e798b_0
openjpeg 2.4.0 h3ad879b_0
openssl 3.0.14 h5eee18b_0
packaging 24.1 pypi_0 pypi
pandas 2.2.2 py39h6a678d5_0
pcre2 10.42 hebb0a14_1
pillow 10.3.0 py39h5eee18b_0
pip 24.0 py39h06a4308_0
pixman 0.40.0 h7f8727e_1
pybind11-abi 4 hd3eb1b0_1
pycairo 1.23.0 py39hd1222b9_0
pyparsing 3.1.2 pypi_0 pypi
python 3.9.19 h955ad1f_1
python-dateutil 2.9.0post0 py39h06a4308_2
python-tzdata 2023.3 pyhd3eb1b0_0
python_abi 3.9 2_cp39 conda-forge
pytorch 1.11.0 py3.9_cuda11.3_cudnn8.2.0_0 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2024.1 py39h06a4308_0
rdkit 2022.09.4 py39hb00a813_1 conda-forge
readline 8.2 h5eee18b_0
reportlab 3.5.67 py39hfdd840d_1
requests 2.32.3 pypi_0 pypi
scikit-learn 1.4.2 py39h1128e8f_1
scipy 1.13.1 py39h5f9d8c6_0
seaborn 0.13.2 py39h06a4308_0
setuptools 69.5.1 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlalchemy 2.0.30 py39h5eee18b_0
sqlite 3.45.3 h5eee18b_0
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 2.2.0 pyh0d69192_0
tk 8.6.14 h39e8969_0
torch-cluster 1.6.0 pypi_0 pypi
torch-geometric 2.1.0 pypi_0 pypi
torch-scatter 2.0.9 pypi_0 pypi
torch-sparse 0.6.15 pypi_0 pypi
tqdm 4.66.4 pypi_0 pypi
typing-extensions 4.11.0 py39h06a4308_0
typing_extensions 4.11.0 py39h06a4308_0
tzdata 2024a h04d1e81_0
unicodedata2 15.1.0 py39h5eee18b_0
urllib3 2.2.1 pypi_0 pypi
wheel 0.43.0 py39h06a4308_0
xz 5.4.6 h5eee18b_1
zipp 3.19.2 pypi_0 pypi
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.5 hc292b87_2
At line 696 of "scripts/dataset.py", I inserted the code between "#----". Changed version of the file looks as below:
class FragmentLibrary(Dataset):
FRAGMENT_LIBRARY_CSV = "fragment_library.csv"
FRAG_FEATURES = "frag_features.pkl"
FRAG_BRICS_MASKINGS = "frag_brics_maskings.pkl"
def __init__(
self,
frag_lib: pd.DataFrame,
smi_to_frag_features: Dict[SMILES, PairData],
frag_brics_maskings: Dict[Tuple[int], List[torch.BoolTensor]] = None,
num_cores: int = None, # used only when parsing fragment library
):
super().__init__()
#-----------------------------------------------------------------------------------------
frag_lib['MISSING'] = 0
for i,row in frag_lib.iterrows():
smi = row["FRAG-SMI"]
if smi not in smi_to_frag_features:
frag_lib.at[i,'MISSING'] = 1
frag_lib = frag_lib[frag_lib.MISSING == 0]
frag_lib.drop('MISSING', axis=1, inplace=True)
#-----------------------------------------------------------------------------------------
# Save the data in attributes
self.frags_smis = frag_lib["FRAG-SMI"].to_numpy()
self.frags_freq = torch.from_numpy(frag_lib["FRAG-FREQ"].to_numpy()).long()
self.data_type = frag_lib["DATA-TYPE"].to_numpy()
self.brics_type = frag_lib["BRICS-TYPE"].tolist() # for sampling
After doing this, things went OK.
$ python example.py
...
Generator initialization finished.
Option 1. Generate with DeepBioisostere.
Elapsed time: 8.666834831237793
Option 2. Generate with a specific leaving fragment.
Elapsed time: 6.4382524490356445
I tried to install DeepBioisostere as below:
So far, it was successful. But when I tried to run "python example.py", I got the following error:
I thought this may be due to the version problem in rdkit. So I installed the latest rdkit as follow:
conda install rdkit
Then the above error was gone but got the following errors:
Any help?