Model is adding an amino acid to the original sequence about proteinmpnn

[tony-res]

I've tracked it down a little more. I think it is coming from the script that creates the parsed_pdbs.jsonl file because that file looks like this:

{"seq_chain_H": "EVQLVESGP-GLVQPGKSLRLSCVASGFTF----SGYGMHWVRQAPGKGLEWIALIIYD--ESNKYYADSVK-GRFTISRDNSKNTLYLQMSSLRAEDTAVFYCAKVKFYDTPAPNDYWGQGTLVTVSS", "coords_chain_H": {"N_chain_H": [[-11.394, -4.934, -17.026], [-9.415, -5.505, -14.037], [-7.515, -2.819, -12.586], [-4.768, -1.263, -10.961], [-2.865, 1.551, -10.077], [-0.044, 2.882, -8.846], [1.493, 5.892, -7.505], [3.436, 8.866, -6.619], [6.281, 8.208, -5.929], [NaN, NaN, NaN], [9.799, 8.533, -4.849], [13.014, 10.127, -3.929], [13.389, 10.802, -0.512], [14.366, 12.408, 2.32], [15.559, 11.094, 5.561], [13.32, 11.104, 8.369], [11.537, 12.932, 7.067], [8.281, 13.081, 5.352], [6.011, 11.214, 3.226], [3.476, 10.527, 0.716], [1.955, 8.134, -0.727], [-0.102, 7.201, -3.541], [-2.64, 5.229, -4.93], [-4.499, 4.565, -7.639], [-7.528, 2.983, -8.404], [-9.327, 0.896, -10.749], [-11.897, -0.72, -12.862], [-13.244, -2.535, -11.189], [-15.546, -2.74, -8.358], [-14.286, -0.709, -6.165], [NaN, NaN, NaN], [NaN, NaN, NaN], [NaN, NaN, NaN], [NaN, NaN, NaN], 

Note that the P is there. So the code seems to be buggy in this script parse_multiple_chains.py

[tony-res]

I printed out an intermediate variable seq in parse_multiple_chains.py. It gives me this:

Note that at position 111, there is a dictionary with two values rather than one. That's where the bug is coming from. I'll see if I can find a patch and submit it.

[tony-res]

It's this. The PDB file is IMGT numbered. The parse code is assuming that it is just an integer. So the 112A and the 112 positions are getting lumped together.

[tony-res]

            if resn[-1].isalpha(): 
                print(resn)
                resa,resn = resn[-1],int(resn[:-1])-1
                print(resn)
            else: 
                resa,resn = "",int(resn)-1

Note that if the position has an alphabetic character (e.g. "112A"), then it removes the character and subtracts 1 from the integer. So "112A" is listed as position 111.

[tony-res]

I created a patch and did a PR.