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Saoge123 / PocketFlow

an autoregressive flow model incorporated with chemical acknowledge for generating drug-like molecules inside protein pockets
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question when Spliting Pocket #10

Open DM0815 opened 1 month ago

DM0815 commented 1 month ago

when conducting Spliting Pocket function. I want to use my .pdb and .sdf file. I met a error as foolows： we can not compute the atoms on the surface of protein, because pymol can not be imported Traceback (most recent call last): File "produce1xc6.py", line 6, in pocketblock, = SplitPocket._split_pocket_with_surface_atoms(pro, lig, dist_cutoff) File "/home/dmeng/protein/PocketFlow/pocket_flow/utils/process_raw.py", line 68, in _split_pocket_with_surface_atoms protein.compute_surface_atoms() File "/home/dmeng/protein/PocketFlow/pocket_flow/utils/ParseFile.py", line 465, in compute_surface_atoms pymol.cmd.load(self.pdb_file) NameError: name 'pymol' is not defined BTW, I installed your env file successfully and can run your code of Molecular generation. Can you give some suggestions. Thanks.

DM0815 commented 1 month ago

when I conducted pip3 install pymol. It reminds that Requirement already satisfied: pymol in ****/envs/pocketflow/lib/python3.8/site-packages (2.4.1)

[notice] A new release of pip is available: 23.3.2 -> 24.2 [notice] To update, run: pip install --upgrade pip

Saoge123 commented 3 weeks ago

Hi, sorry for reply late. It seems to be uncorrect installation of pymol. You can try: 'conda install -c schrodinger pymol' or the commands in https://anaconda.org/schrodinger/pymol