I want to reproduce the code used to process raw data

[iehaoang]

Hello, we have encountered some issues. Some file paths that appear in file data/data_processing.ipynb do not exist and are not explained, which makes it impossible for us to reproduce the code for processing the original data. We hope to receive your help in updating the files or explaining the specific paths in the crossdock dataset. Thank you

[OdinZhang]

You can try https://github.com/HaotianZhangAI4Science/SurfGen/blob/main/data/surface_maker/generate_surface.ipynb. The file in data/data_processing.ipynb just the decomposition of compute_inp_surface!
By the way, I guess the error you met can be attributed to the environment problem. Please manually assign the utils path, like

import os # in python
os.environ["LD_LIBRARY_PATH"] = '/home/haotian/Molecule_Generation/SurfBP/dataset/install_software/APBS-3.0.0.Linux/lib'
msms_bin="/home/haotian/Molecule_Generation/SurfBP/dataset/install_software/APBS-3.0.0.Linux/bin/msms"
apbs_bin = '/home/haotian/Molecule_Generation/SurfBP/dataset/install_software/APBS-3.0.0.Linux/bin/apbs'
pdb2pqr_bin="/home/haotian/Molecule_Generation/SurfBP/dataset/install_software/pdb2pqr-linux-bin64-2.1.1/pdb2pqr"
multivalue_bin="/home/haotian/Molecule_Generation/SurfBP/dataset/install_software/APBS-3.0.0.Linux/share/apbs/tools/bin/multivalue"