ProtSSN

ProtSSN copied to clipboard

Problem when using run_pt.py

3

I met a problem when i testing the pre-train part of your code. I use: bash script/run_pt.sh. to follow your Start Training part in README, and find that the process...

Melonoyk

torch_geometric version

1

Hi, Thanks for your code, and model. Just a freindly notice, it seems that torch_geometric update some functions. The function "propagate" in the egnn_pytorch_geometric.py file doesn't work properly, and have...

yxliu-TAMU

get_node_features函数中二面角phi计算好像不对

1

你好呀，看起来src.dataset.mutant_dataset.py 中第318行`angles[i, 0] = dihedral(c_coords[i], n_coords[i], c_alpha_coords[i], n_coords[i+1])`不对。  感觉正确的计算方式应该是 C(i-1)-N(i)-Cα(i)-C(i)，可以参考西湖大学反转结构算法PIFold的结构特征编码方式（应该更高效）。不过既然这两都是角度特征且不涉及精确的原子坐标计算，对最终结果的影响应该不大。

imSeaton

AssertionError

2

python zeroshot_predict.py --gnn_model_name k20_h512 --mutant_dataset_dir data/mutant_example/no_exp --result_dir result/no_exp --------------- ProtSSN k20_h512 --------------- Processing... Processing A0A5J4FAY1_MICAE: 100%|████████████████████████████████████████████████████████| 1/1 [00:02> Protein names: ['A0A5J4FAY1_MICAE'] >>> Number of proteins: 1 >>> k20_h512 Number of...

QUEST2179

Inputs during training and inference

1

Hi, Excellent work! I am reading ProtSSN and trying to use it, but I have a few questions: 1) The input in downstream tasks is the entire protein, while the...

zchwang

multiple mutation

2

1) Just try the compute_fitness.py and find the output in .../result/ is the score of single mutations like the attached one. But now, we hope to see the score of...

polytide1988