Revised codes for no toxin chains, Manual epitope design

[Hyeongsun]

Excellent work, I tried to generate antibody for COVID NP protein.

So, I revised the code as below;

if name == 'main': ckpt = './checkpoints/cdrh3_design.ckpt' root_dir = './demos/data' pdbs = [os.path.join(rootdir, '6wzo.pdb') for in range(4)] toxin_chains = [] remove_chains = None receptor_chains = ["A", "B", "C", "D"] epitope_defs = [os.path.join(root_dir, c + '_epitope.json') for c in receptor_chains] identifiers = [f'{c}_antibody' for c in receptor_chains]

I manually design epitope.json file as;

A_epitope.json [ ["A", [299, ""]], ["A", [300, ""]], ["A", [302, ""]], ["A", [303, ""]], ["A", [305, ""]], ["A", [306, ""]], ["A", [345, ""]], ["A", [347, ""]], ["A", [348, ""]], ["A", [349, ""]] ] However, I encounter the messeges as;

/home/jhs9301/anaconda3/envs/dyMEAN/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /home/jhs9301/anaconda3/envs/dyMEAN/lib/python3.8/site-packages/numpy/core/_methods.py:184: RuntimeWarning: invalid value encountered in divide ret = um.true_divide( /mnt/c/Users/jhs93/Downloads/dyMEAN-main/dyMEAN-main/data/dataset.py:63: RuntimeWarning: invalid value encountered in cast X[0] = center # set center

I guess the invalid values were obtained in Epitope data.

Epitope data: {'X': array([[[-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808], [-9223372036854775808, -9223372036854775808, -9223372036854775808]]]), 'S': [22], 'residue_pos': [0], 'xloss_mask': [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]}

Then, How can i fix the problem? please let me know.

[kxz18]

Hi, thanks for your interest in our work. Could you try replacing the insert code with a space instead of an empty string? The code base is using biopython to parse the PDB file, and the biopython package uses a space to denote an empty insert code. This mismatch might be the cause of the problem.

[Hyeongsun]

Thanks! It was fixed. there is one more question. Is there any way to obtain the complex structure of an antibody sequence that I already know and an antigen? I wanna optimize the already developed antibody but there is no complex structure.

[kxz18]

Hi, I've updated the API for structure prediction here. Corresponding explanations are also updated in README. You can have a try!