3D-Generative-SBDD

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Clarification on Pocket2Mol model training with CrossDocked2020 dataset

1

Hello, I appreciate your excellent work. I am also attempting to train this model on a larger dataset and have started with the CrossDocked2020-v1.3 dataset, which has an RMSD <...

mahmoud-ekhani

Cannot get valid molecule from running sample.py for a long time

14

I read your paper which looks great. I tried to run according to the instruction, sample.py, using the sample.yml and the two model ckpts downloaded from google drive. I waited...

simmed00

Run sample.py failed: OSError: libc10_cuda.so: cannot open shared object file: No such file or directory

1

--------------------------------------------- Error Information -------------------------------------- (SBDD-3D) root@10-90-43-152:/home/jenkins/zhuyuxiao/SBDD_Project/3D-Generative-SBDD# python sample.py ./configs/sample.yml --data_id {i} Traceback (most recent call last): File "sample.py", line 7, in from torch_geometric.data import Batch File "/home/miniconda3/envs/SBDD-3D/lib/python3.8/site-packages/torch_geometric/__init__.py", line 4, in...

zyx5256

error in sample.py

1

thanks for your great work! i got the error when running sample.py: ValueError: zero-size array to reduction operation maximum which has no identity the reason is query_tmp = [], after...

futianfan

Hi, your work is very fantastic! May I ask two questions? What is the meaning of the numbers (for example 0.367042 as below) in the data/crossdocked_pocket10/index.pkl? The index is like...

ChengchengGutenTag

Hi, Can you please explain the data structure of crossdocked_pocket10? For example: `1eqc_A_rec_1eqc_cts_lig_tt_docked_0_pocket10.pdb` So here if we split using `_` what are the terms like `1eqc`, `cts` etc. Same for...

ss62171