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Layne-Huang / PMDM

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Missing geometry.py in the models folder when sample molecules for given customized pockets #3

Closed FeilongWuHaa closed 5 months ago

FeilongWuHaa commented 6 months ago

Hi，

when I try to sample molecules for our customized pockets with command: "python -u sample_for_pdb.py --ckpt ./500.pt --pdb_path 3WZE/pocket.pdb --num_atom 32 --num_samples 100 --sampling_type generalized"

But, I got an error: "File "/home/PMDM/sample_for_pdb.py", line 13, in from models.epsnet import get_model File "/home/PMDM/models/epsnet/init.py", line 1, in from .MDM_pocket_coor_shared import MDM_full_pocket_coor_shared File "/home/PMDM/models/epsnet/MDM_pocket_coor_shared.py", line 15, in from ..encoders.schnet_geo import SchNetEncoder # wufeil File "/home/PMDM/models/encoders/schnet_geo.py", line 8, in from ..geometry import get_distance ModuleNotFoundError: No module named 'models.geometry' "

It looks like the geometry.py file is missing in the models folder

FeilongWuHaa commented 6 months ago

Similarly, I did not find the SchNetEncoder_protein function in the project, which is required by MDM_pocket_coor_shared.py in ./models/epsnet:

" from ..encoders import (EGNN_Sparse_Network, SchNetEncoder, SchNetEncoder_protein, get_edge_encoder) "

Layne-Huang commented 6 months ago

Hi,

Thanks for pointing it out. We have uploaded the corresponding files. Please check them.