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awfderry / COLLAPSE

Representation learning for protein functional site analysis
MIT License
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local variable 'af_flag' referenced before assignment #6

Closed BinhongLiu closed 1 year ago

BinhongLiu commented 1 year ago

Hi, it's really a nice tool! Some errors appeared when I test the tool using the demo data.

UnboundLocalError: local variable 'af_flag' referenced before assignment

the log file is attached here: log.txt

I've tried to uninstall and reinstall the torch-geometric and torch-scatter packages, but the error was still there.

Could you help me fix this error? Thanks!

BinhongLiu commented 1 year ago

here are the packages I've installed in the environment.

(collapse) liuhongbin@node7:~/soft/Pockets/COLLAPSE-main$ conda list

packages in environment at /home/liuhongbin/anaconda3/envs/collapse:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge aiofiles 22.1.0 pypi_0 pypi aiosqlite 0.18.0 pypi_0 pypi anyio 3.6.2 pypi_0 pypi aom 3.3.0 h27087fc_1 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 21.3.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi argparse 1.4.0 pypi_0 pypi arrow 1.2.3 pypi_0 pypi asttokens 2.2.1 pypi_0 pypi atom3d 0.2.6 pypi_0 pypi attrs 22.2.0 pypi_0 pypi babel 2.11.0 pypi_0 pypi backcall 0.2.0 pypi_0 pypi beautifulsoup4 4.11.2 pypi_0 pypi biopython 1.81 pypi_0 pypi blas 2.116 mkl conda-forge blas-devel 3.9.0 16_linux64_mkl conda-forge bleach 6.0.0 pypi_0 pypi blosc2 2.0.0 pypi_0 pypi brotlipy 0.7.0 py38h0a891b7_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py38h4a40e3a_3 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 pypi_0 pypi collapse 0.1.0 pypi_0 pypi comm 0.1.2 pypi_0 pypi contourpy 1.0.7 pypi_0 pypi cpuonly 2.0 0 pytorch cryptography 39.0.1 py38h3d167d9_0 conda-forge cycler 0.11.0 pypi_0 pypi cython 0.29.33 pypi_0 pypi debugpy 1.6.6 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi dill 0.3.6 pypi_0 pypi docker-pycreds 0.4.0 pypi_0 pypi easy-parallel 0.1.6 pypi_0 pypi executing 1.2.0 pypi_0 pypi faiss-cpu 1.7.3 py3.8_h2a577fa_0_cpu pytorch fastjsonschema 2.16.2 pypi_0 pypi ffmpeg 4.3 hf484d3e_0 pytorch fonttools 4.38.0 pypi_0 pypi fqdn 1.5.1 pypi_0 pypi freesasa 2.2.0.post3 pypi_0 pypi freetype 2.12.1 hca18f0e_1 conda-forge gitdb 4.0.10 pypi_0 pypi gitpython 3.1.31 pypi_0 pypi gmp 6.2.1 h58526e2_0 conda-forge gnutls 3.6.13 h85f3911_1 conda-forge gvp 0.1.1 pypi_0 pypi h5py 3.8.0 pypi_0 pypi icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.0.0 pypi_0 pypi importlib-resources 5.12.0 pypi_0 pypi ipykernel 6.21.2 pypi_0 pypi ipython 8.10.0 pypi_0 pypi ipython-genutils 0.2.0 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi jedi 0.18.2 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi joblib 1.2.0 pypi_0 pypi jpeg 9e h0b41bf4_3 conda-forge json5 0.9.11 pypi_0 pypi jsonpointer 2.3 pypi_0 pypi jsonschema 4.17.3 pypi_0 pypi jupyter-client 8.0.3 pypi_0 pypi jupyter-core 5.2.0 pypi_0 pypi jupyter-events 0.6.3 pypi_0 pypi jupyter-server 2.3.0 pypi_0 pypi jupyter-server-fileid 0.8.0 pypi_0 pypi jupyter-server-terminals 0.4.4 pypi_0 pypi jupyter-server-ydoc 0.6.1 pypi_0 pypi jupyter-ydoc 0.2.2 pypi_0 pypi jupyterlab 3.6.1 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-server 2.19.0 pypi_0 pypi kiwisolver 1.4.4 pypi_0 pypi lame 3.100 h166bdaf_1003 conda-forge lcms2 2.14 hfd0df8a_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 16_linux64_mkl conda-forge libcblas 3.9.0 16_linux64_mkl conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libdrm 2.4.114 h166bdaf_0 conda-forge libfaiss 1.7.3 h2bc3f7f_0_cpu pytorch libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libhwloc 2.9.0 hd6dc26d_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_mkl conda-forge liblapacke 3.9.0 16_linux64_mkl conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libpciaccess 0.17 h166bdaf_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.20.2 h6239696_0 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.44.2 h166bdaf_0 conda-forge libva 2.17.0 h0b41bf4_0 conda-forge libvpx 1.11.0 h9c3ff4c_3 conda-forge libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.10.3 h7463322_0 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge llvm-openmp 15.0.7 h0cdce71_0 conda-forge lmdb 1.4.0 pypi_0 pypi markupsafe 2.1.2 pypi_0 pypi matplotlib 3.7.0 pypi_0 pypi matplotlib-inline 0.1.6 pypi_0 pypi mistune 2.0.5 pypi_0 pypi mkl 2022.1.0 h84fe81f_915 conda-forge mkl-devel 2022.1.0 ha770c72_916 conda-forge mkl-include 2022.1.0 h84fe81f_915 conda-forge msgpack 1.0.4 pypi_0 pypi multipledispatch 0.6.0 pypi_0 pypi multiprocess 0.70.14 pypi_0 pypi nbclassic 0.5.2 pypi_0 pypi nbclient 0.7.2 pypi_0 pypi nbconvert 7.2.9 pypi_0 pypi nbformat 5.7.3 pypi_0 pypi ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.6 pypi_0 pypi nettle 3.6 he412f7d_0 conda-forge ninja 1.11.1 h924138e_0 conda-forge notebook 6.5.2 pypi_0 pypi notebook-shim 0.2.2 pypi_0 pypi numexpr 2.8.4 pypi_0 pypi numpy 1.24.2 py38h10c12cc_0 conda-forge openh264 2.1.1 h780b84a_0 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.0.8 h0b41bf4_0 conda-forge packaging 23.0 pyhd8ed1ab_0 conda-forge pandas 1.5.3 pypi_0 pypi pandocfilters 1.5.0 pypi_0 pypi parso 0.8.3 pypi_0 pypi pathos 0.3.0 pypi_0 pypi pathtools 0.1.2 pypi_0 pypi pexpect 4.8.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 9.4.0 py38hde6dc18_1 conda-forge pip 23.0.1 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pypi_0 pypi platformdirs 3.0.0 pypi_0 pypi pooch 1.6.0 pyhd8ed1ab_0 conda-forge pox 0.3.2 pypi_0 pypi ppft 1.7.6.6 pypi_0 pypi prometheus-client 0.16.0 pypi_0 pypi prompt-toolkit 3.0.37 pypi_0 pypi protobuf 4.22.0 pypi_0 pypi psutil 5.9.4 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 py-cpuinfo 9.0.0 pypi_0 pypi pycparser 2.21 pyhd8ed1ab_0 conda-forge pyg-lib 0.1.0+pt111cpu pypi_0 pypi pygments 2.14.0 pypi_0 pypi pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pypi_0 pypi pyrr 0.10.3 pypi_0 pypi pyrsistent 0.19.3 pypi_0 pypi pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.8.16 he550d4f_1_cpython conda-forge python-dateutil 2.8.2 pypi_0 pypi python-dotenv 1.0.0 pypi_0 pypi python-json-logger 2.0.7 pypi_0 pypi python_abi 3.8 3_cp38 conda-forge pytorch 1.11.0 py3.8_cpu_0 pytorch pytorch-mutex 1.0 cpu pytorch pytz 2022.7.1 pypi_0 pypi pyyaml 6.0 pypi_0 pypi pyzmq 25.0.0 pypi_0 pypi readline 8.1.2 h0f457ee_0 conda-forge requests 2.28.2 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi scikit-learn 1.2.1 pypi_0 pypi scipy 1.10.1 py38h10c12cc_0 conda-forge seaborn 0.12.2 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi sentry-sdk 1.15.0 pypi_0 pypi setproctitle 1.3.2 pypi_0 pypi setuptools 67.4.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pypi_0 pypi sklearn 0.0.post1 pypi_0 pypi sleef 3.5.1 h9b69904_2 conda-forge smmap 5.0.0 pypi_0 pypi sniffio 1.3.0 pypi_0 pypi soupsieve 2.4 pypi_0 pypi stack-data 0.6.2 pypi_0 pypi svt-av1 1.1.0 h27087fc_1 conda-forge tables 3.8.0 pypi_0 pypi tbb 2021.8.0 hf52228f_0 conda-forge terminado 0.17.1 pypi_0 pypi threadpoolctl 3.1.0 pypi_0 pypi tinycss2 1.2.1 pypi_0 pypi tk 8.6.12 h27826a3_0 conda-forge tomli 2.0.1 pypi_0 pypi torch-cluster 1.6.0 pypi_0 pypi torch-geometric 2.2.0 pypi_0 pypi torch-scatter 2.1.0 pypi_0 pypi torch-sparse 0.6.16 pypi_0 pypi torchaudio 0.11.0 py38_cpu pytorch torchvision 0.12.0 py38_cpu pytorch tornado 6.2 pypi_0 pypi tqdm 4.64.1 pypi_0 pypi traitlets 5.9.0 pypi_0 pypi typing_extensions 4.4.0 pyha770c72_0 conda-forge uri-template 1.2.0 pypi_0 pypi urllib3 1.26.14 pyhd8ed1ab_0 conda-forge wandb 0.13.10 pypi_0 pypi wcwidth 0.2.6 pypi_0 pypi webcolors 1.12 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.5.1 pypi_0 pypi wheel 0.38.4 pyhd8ed1ab_0 conda-forge x264 1!161.3030 h7f98852_1 conda-forge x265 3.5 h924138e_3 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 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 y-py 0.5.9 pypi_0 pypi ypy-websocket 0.8.2 pypi_0 pypi zipp 3.14.0 pypi_0 pypi zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge

awfderry commented 1 year ago

Thanks for your interest in our tool! This issue has been fixed now, see commit [7340a9b].