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(root_dir, '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!