Licko0909
commented
2 years ago Hello! I am very interested in your project, and I want to try to predict the antibody structure( PDB:1IGT) by using your model, but THERE are some problems in the process.
I have successfully installed the environment according to your requirement.txt, but I cannot use it. The error message is as follows:
I find there( requirement.txt) are no requirements for CUDA and Python versions.
Here is a list of my environments
# packages in environment at /home/LChuang/anaconda3/envs/igfold2: # # Name Version Build Channel _libgcc_mutex 0.1 main defaults _openmp_mutex 5.1 1_gnu defaults absl-py 1.0.0 pypi_0 pypi aiohttp 3.8.1 pypi_0 pypi aiosignal 1.2.0 pypi_0 pypi antiberty 0.0.5 pypi_0 pypi argon2-cffi 21.3.0 pyhd3eb1b0_0 defaults argon2-cffi-bindings 21.2.0 py38h7f8727e_0 defaults asttokens 2.0.5 pyhd3eb1b0_0 defaults async-timeout 4.0.2 pypi_0 pypi attrs 21.4.0 pyhd3eb1b0_0 defaults backcall 0.2.0 pyhd3eb1b0_0 defaults beautifulsoup4 4.11.1 py38h06a4308_0 defaults biopython 1.79 pypi_0 pypi bleach 4.1.0 pyhd3eb1b0_0 defaults ca-certificates 2022.4.26 h06a4308_0 defaults cachetools 5.1.0 pypi_0 pypi certifi 2022.5.18.1 py38h06a4308_0 defaults cffi 1.15.0 py38hd667e15_1 defaults charset-normalizer 2.0.12 pypi_0 pypi click 8.1.3 pypi_0 pypi cycler 0.11.0 pypi_0 pypi debugpy 1.5.1 py38h295c915_0 defaults decorator 5.1.1 pyhd3eb1b0_0 defaults defusedxml 0.7.1 pyhd3eb1b0_0 defaults einops 0.3.0 pypi_0 pypi entrypoints 0.4 py38h06a4308_0 defaults executing 0.8.3 pyhd3eb1b0_0 defaults filelock 3.7.0 pypi_0 pypi frozenlist 1.3.0 pypi_0 pypi fsspec 2022.3.0 pypi_0 pypi future 0.18.2 pypi_0 pypi fvcore 0.1.5.post20220512 pypi_0 pypi ghost-py 0.2.3 pypi_0 pypi google-auth 2.6.6 pypi_0 pypi google-auth-oauthlib 0.4.6 pypi_0 pypi grpcio 1.46.1 pypi_0 pypi huggingface-hub 0.6.0 pypi_0 pypi idna 3.3 pypi_0 pypi igfold 0.0.8 pypi_0 pypi importlib-metadata 4.11.3 pypi_0 pypi importlib_resources 5.2.0 pyhd3eb1b0_1 defaults invariant-point-attention 0.1.4 pypi_0 pypi iopath 0.1.9 pypi_0 pypi ipykernel 6.9.1 py38h06a4308_0 defaults ipython 8.3.0 py38h06a4308_0 defaults ipython_genutils 0.2.0 pyhd3eb1b0_1 defaults jedi 0.18.1 py38h06a4308_1 defaults jinja2 3.0.3 pyhd3eb1b0_0 defaults joblib 1.1.0 pypi_0 pypi jsonschema 4.4.0 py38h06a4308_0 defaults jupyter_client 7.2.2 py38h06a4308_0 defaults jupyter_core 4.10.0 py38h06a4308_0 defaults jupyterlab_pygments 0.1.2 py_0 defaults kiwisolver 1.4.2 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1 defaults libffi 3.3 he6710b0_2 defaults libgcc-ng 11.2.0 h1234567_0 defaults libgomp 11.2.0 h1234567_0 defaults libsodium 1.0.18 h7b6447c_0 defaults libstdcxx-ng 11.2.0 h1234567_0 defaults markdown 3.3.7 pypi_0 pypi markupsafe 2.0.1 py38h27cfd23_0 defaults matplotlib 3.4.3 pypi_0 pypi matplotlib-inline 0.1.2 pyhd3eb1b0_2 defaults mistune 0.8.4 py38h7b6447c_1000 defaults multidict 6.0.2 pypi_0 pypi nb_conda 2.2.1 py38h06a4308_1 defaults nb_conda_kernels 2.3.1 py38h06a4308_0 defaults nbbrowserpdf 0.2.0 pypi_0 pypi nbclient 0.5.13 py38h06a4308_0 defaults nbconvert 6.4.4 py38h06a4308_0 defaults nbformat 5.3.0 py38h06a4308_0 defaults ncurses 6.3 h7f8727e_2 defaults nest-asyncio 1.5.5 py38h06a4308_0 defaults notebook 6.4.11 py38h06a4308_0 defaults numpy 1.21.2 pypi_0 pypi oauthlib 3.2.0 pypi_0 pypi openssl 1.1.1o h7f8727e_0 defaults packaging 21.3 pyhd3eb1b0_0 defaults pandas 1.4.2 pypi_0 pypi pandocfilters 1.5.0 pyhd3eb1b0_0 defaults parso 0.8.3 pyhd3eb1b0_0 defaults pexpect 4.8.0 pyhd3eb1b0_3 defaults pickleshare 0.7.5 pyhd3eb1b0_1003 defaults pillow 9.1.1 pypi_0 pypi pip 21.2.4 py38h06a4308_0 defaults portalocker 2.4.0 pypi_0 pypi prometheus_client 0.13.1 pyhd3eb1b0_0 defaults prompt-toolkit 3.0.20 pyhd3eb1b0_0 defaults protobuf 3.20.1 pypi_0 pypi ptyprocess 0.7.0 pyhd3eb1b0_2 defaults pure_eval 0.2.2 pyhd3eb1b0_0 defaults py3dmol 1.8.0 pypi_0 pypi pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pycparser 2.21 pyhd3eb1b0_0 defaults pydeprecate 0.3.1 pypi_0 pypi pygments 2.11.2 pyhd3eb1b0_0 defaults pyparsing 3.0.9 pypi_0 pypi pypdf2 1.27.12 pypi_0 pypi pyrosetta 2022.6+release.28566d4 pypi_0 pypi pyrsistent 0.18.0 py38heee7806_0 defaults python 3.8.13 h12debd9_0 defaults python-dateutil 2.8.2 pyhd3eb1b0_0 defaults python-fastjsonschema 2.15.1 pyhd3eb1b0_0 defaults pytorch-lightning 1.5.10 pypi_0 pypi pytorch-ranger 0.1.1 pypi_0 pypi pytorch3d 0.3.0 pypi_0 pypi pytz 2022.1 pypi_0 pypi pyyaml 6.0 pypi_0 pypi pyzmq 22.3.0 py38h295c915_2 defaults readline 8.1.2 h7f8727e_1 defaults regex 2022.4.24 pypi_0 pypi requests 2.26.0 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rsa 4.8 pypi_0 pypi sacremoses 0.0.53 pypi_0 pypi scipy 1.8.1 pypi_0 pypi seaborn 0.11.2 pypi_0 pypi send2trash 1.8.0 pyhd3eb1b0_1 defaults setuptools 59.5.0 pypi_0 pypi six 1.16.0 pyhd3eb1b0_1 defaults soupsieve 2.3.1 pyhd3eb1b0_0 defaults sqlite 3.38.3 hc218d9a_0 defaults stack_data 0.2.0 pyhd3eb1b0_0 defaults tabulate 0.8.9 pypi_0 pypi tensorboard 2.9.0 pypi_0 pypi tensorboard-data-server 0.6.1 pypi_0 pypi tensorboard-plugin-wit 1.8.1 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.13.1 py38h06a4308_0 defaults testpath 0.5.0 pyhd3eb1b0_0 defaults tk 8.6.11 h1ccaba5_1 defaults tokenizers 0.11.6 pypi_0 pypi torch 1.7.1 pypi_0 pypi torch-optimizer 0.3.0 pypi_0 pypi torchmetrics 0.8.2 pypi_0 pypi torchvision 0.8.2 pypi_0 pypi tornado 6.1 py38h27cfd23_0 defaults tqdm 4.62.1 pypi_0 pypi traitlets 5.1.1 pyhd3eb1b0_0 defaults transformers 4.18.0 pypi_0 pypi typing-extensions 4.2.0 pypi_0 pypi typing_extensions 4.1.1 pyh06a4308_0 defaults urllib3 1.26.9 pypi_0 pypi wcwidth 0.2.5 pyhd3eb1b0_0 defaults webencodings 0.5.1 py38_1 defaults werkzeug 2.1.2 pypi_0 pypi wheel 0.37.1 pyhd3eb1b0_0 defaults xz 5.2.5 h7f8727e_1 defaults yacs 0.1.8 pypi_0 pypi yapf 0.31.0 pypi_0 pypi yarl 1.7.2 pypi_0 pypi zeromq 4.3.4 h2531618_0 defaults zipp 3.8.0 py38h06a4308_0 defaults zlib 1.2.12 h7f8727e_2 defaults
Based on the above, I installed the matching module and was able to run IgFold successfully
conda install pytorch==1.7.1 torchvision==0.8.2 torchaudio==0.7.2 cudatoolkit=11.0 -c pytorch
anar-rzayev
Hello! I am very interested in your project, and I want to try to predict the antibody structure( PDB:1IGT) by using your model, but THERE are some problems in the process.
I have successfully installed the environment according to your requirement.txt, but I cannot use it. The error message is as follows:
I find there( requirement.txt) are no requirements for CUDA and Python versions.
Here is a list of my environments