I feel there is a code problem here。

[0dpwpb0]

SurfDock/datasets/process_mols.py

Line 504 in 6420335

dis_matx_ca = distance_matrix(ca_pos, center_pos)

dis_matx_ca = distance_matrix(ca_pos, center_pos) feels a bit strange, I think it should be dis_matx_ca = distance_matrix(ca_pos, ca_pos)?If my understanding is incorrect, please feel free to correct me.

[liyifei1717-del]

Have you encountered this issue before when running eval_samples.sh? How did you resolve it?

-------------------------------- Step3 : Get Pocket ESM Embedding ----------------------------
Traceback (most recent call last):
File "/sharedata/home/lyf/SurfDock/datasets/esm_embedding_preparation.py", line 51, in
df = pd.read_csv(args.protein_ligand_csv)
File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file

[0dpwpb0]

Have you encountered this issue before when running eval_samples.sh? How did you resolve it?

-------------------------------- Step3 : Get Pocket ESM Embedding ---------------------------- Traceback (most recent call last): File "/sharedata/home/lyf/SurfDock/datasets/esm_embedding_preparation.py", line 51, in df = pd.read_csv(args.protein_ligand_csv) File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv return _read(filepath_or_buffer, kwds) File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init self._engine = self._make_engine(f, self.engine) File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine return mapping[engine](f, **self.options) File "/sharedata/home/lyf/miniconda3/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

You might not have installed pymesh properly, and pymesh2 did not generate the surface mesh PLY file: '1a0q_protein_processed_8A.ply', so reading test_samples.csv results in empty data.