shiwentao00 / graphsite-classifier Goto Github PK

I am trying to use the procedures and scripts to create the .mol2, .pops, and .profile files, but it appears the separate_pdb_chains.py does not seem to actually separate the chains as it should. It is potential I am just using it wrong, but I can not get it to seperate the pdb files into chains as it appears this script should do.

In step 2 of the inference section, it says that I am supposed to create a file that looks something like "unseen-pocket-lists.yaml". I have looked for this example file and I can't seem to find it anywhere. Could this please be added so I can make the yml file correctly? Thanks

Sorry, in the process of reproducing your work, I found that the data set pointed to by the URL was deleted. Could you provide your data set again, thank you very much.

I am having issues generating input files for the binding pockets (Step-7 and Step-8) as outlined in the instructions at https://github.com/shiwentao00/Graphsite-classifier/blob/master/docs/data_curation/readme.md.

I am getting an error message while attempting to screen small molecules for unknown binding pockets, and my troubleshooting has led me to believe the issue may be with generating mol files using step 7 and step 8 in above link. I have not been able to replicate the exact input mol2 files, for example using the pdb code 1a0f with a trained data set.

Looks like obabel is not writing all the information of the bond connectivity at the end of the file @< "TRIPOS>" BOND while converting the pdb into mol file. (i can be wrong on it).

I would greatly appreciate it if you could offer any advice on this matter.

After installation of dependencies ... I am training the model Graphsite-classifier. getting the following error.
Please advise on this matter ..
Thank you

Traceback (most recent call last):
File "/home/nmrbox/spenumutchu/workflow2023/56Graphsite_classifer/Graphsite-classifier-master/gnn/train_classifier.py", line 8, in
from dataloader import read_cluster_file_from_yaml
File "/home/nmrbox/spenumutchu/workflow2023/56Graphsite_classifer/Graphsite-classifier-master/gnn/dataloader.py", line 6, in
from torch_geometric.data import Data, Dataset
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch_geometric/init.py", line 4, in
import torch_geometric.data
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch_geometric/data/init.py", line 1, in
from .data import Data
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch_geometric/data/data.py", line 20, in
from torch_sparse import SparseTensor
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch_sparse/init.py", line 18, in
torch.ops.load_library(spec.origin)
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch/_ops.py", line 255, in load_library
ctypes.CDLL(path)
File "/home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/ctypes/init.py", line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: /home/nmrbox/spenumutchu/anaconda3/envs/56Graphsite-classifier_py37/lib/python3.9/site-packages/torch_sparse/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

Hi,

I am attempting to replicate the binding pockets that you generated using the default fpocket parameters, but I have noticed significant differences in the results. I am not sure what the optimal parameters to use are. Could you provide some guidance on this matter?

Thank you.