chaitjo / geometric-rna-design Goto Github PK

Hi,

Congrats on the great work. As I understand data/seqid_split.pt data/das_split.pt and data/structsim_split.pt contains the train, test, validation idx for different splits. And the corresponding pdbid_<chain> for those can be extracted from processed_df.csv. Can you provide this preprocessed processed_df.csv file or directly the PDB ids for easier access?

Thanks!

Hi @chaitjo,

Thanks for your great work first!
Could you provide a pretrained checkpoint to run inference directly?

Best regards,
Han

Dear authors,

Thank you so much for such great work. I'm really interested in it.
I got an issue here, after getting processed.pt, I tried to run main.py. It uses das_split.pt to split the data into train, val and test, right? But I got an "index out of range" error. I wonder if you have any clues why this happened? By the way, I saw under the data folder, you have three '_split.pt' files, can you please tell me the difference between them?

Error log:
46 Traceback (most recent call last):
47 File "/home/yjwang/geometric-rna-design/main.py", line 246, in
48 main(config, device)
49 File "/home/yjwang/geometric-rna-design/main.py", line 39, in main
50 train_list, val_list, test_list = get_data_splits(config, split_type=config.split)
51 File "/home/yjwang/geometric-rna-design/main.py", line 119, in get_data_splits
52 train_list = index_list_by_indices(data_list, train_idx_list)
53 File "/home/yjwang/geometric-rna-design/main.py", line 113, in index_list_by_indices
54 return [lst[index] for index in indices]
55 File "/home/yjwang/geometric-rna-design/main.py", line 113, in
56 return [lst[index] for index in indices]
57 IndexError: list index out of range

Thanks in advance,
yuehua

作者你好，
请问我在复现实验的时候，出现了eval 和 test的时间很长的现象，这是正常情况吗？

因为数据集和原始数据集有了一些更新，导致出现了很多新的数据（这些数据中有部分的 sec_struc中 左括号数量多于右括号，导致计算对应的adj的时候报错），于是我对原始的代码做了如下修改，将计算过程放到了try里面，如果是错误的就跳出：

def dotbracket_to_adjacency(sec_struct: str) -> np.ndarray: """ Convert secondary structure in dot-bracket notation to adjacency matrix. """ n = len(sec_struct) adj = np.zeros((n, n), dtype=np.int8) stack = [] empty_count = 0 for i, db_char in enumerate(sec_struct): if db_char == '(': stack.append(i) elif db_char == ')': try: j = stack.pop() adj[i, j] = 1 adj[j, i] = 1 except IndexError: break return adj

其他地方都没有改变

大概eval 和 test 每个都要接近8小时，查看占用，发现gpu长时间不用，一直是cpu在跑一个叫做contrafold的进程，希望大佬解惑。

Hello,

Thanks for your paper and open source codes. Currently I am working on the implementation of your codes. I found one problem which is missing from tools.ribonanzanet.network import RibonanzaNet in notebooks/design.ipynb. How can I solve this issue?

Thanks in advance!

Best,