Indexing with Missing Residues about proteinmpnn

[brucejwittmann]

Thanks everyone. @jadolfbr, based on the code you referenced, it looks like the logic is as follows for indexing:

1. Find the smallest and largest residue indices in the PDB file, extracting from the coordinates section.
2. Scan over the range of integers between the smallest and largest integers, recording masks/pads for missing residues.

Based on that logic, in my example with "NXXXXXN", the first "N" would be index "1" and the second index "7" assuming that there were 5 indices between them. If I were to add missing residues at the beginning or end, I would get the same indexing scheme as the first case as those residues will not show up in the coordinates section of the PDB file.

@tony-res, I believe indexing should start at 1 for ProteinMPNN. If you look at example 4 you can see that noted in a comment. Also you can see when masking fixed positions that "1" is subtracted from the input array.

I think it's important to note that the index in the code @jadolfbr copied is not the same as the index for freezing positions. The index in the copied code is direct from the PDB file, while the indices in the example I linked are 1-indexed to the relative position of a residue in the file.

[jadolfbr]

Yes, nice. Also, it’s 1-indexed for each chain - not necessarily for the whole PDB.

…

On Mon, Dec 4, 2023 at 8:47 PM Bruce Wittmann ***@***.***> wrote: Thanks everyone. @jadolfbr <https://github.com/jadolfbr>, based on the code you referenced, it looks like the logic is as follows for indexing: 1. Find the smallest and largest residue indices in the PDB file, extracting from the coordinates section. 2. Scan over the range of integers between the smallest and largest integers, recording masks/pads for missing residues. Based on that logic, in my example with "NXXXXXN", the first "N" would be index "1" and the second index "7" assuming that there were 5 indices between them. If I were to add missing residues at the beginning or end, I would get the same indexing scheme as the first case as those residues will not show up in the coordinates section of the PDB file. @tony-res <https://github.com/tony-res>, I believe indexing should start at 1 for ProteinMPNN. If you look at example 4 <https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_4.sh#L23C1-L23C88> you can see that noted in a comment. Also you can see when masking fixed positions <https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/protein_mpnn_utils.py#L310> that "1" is subtracted from the input array. I think it's important to note that the index in the code @jadolfbr <https://github.com/jadolfbr> copied is not the same as the index for freezing positions. The index in the copied code is direct from the PDB file, while the indices in the example I linked are 1-indexed to the relative position of a residue in the file. — Reply to this email directly, view it on GitHub <#77 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZDHREF2YATJSRL43GQZK3YHZ4JLAVCNFSM6AAAAAA7QLOLHSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZZHA3DAMJVHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[tony-res]

From what I've seen the second "N" would be at position 2. What I do is I just replace the "X" with "" and then count.

sequence_no_gaps = sequence_with_gaps.replace("X","")

That said, I forget if the index starts at 0 or at 1. I think it starts at 0. So

--position_list "0 1"

rather than

--position_list "1 2"

As a sanity check I always use a python script to go through the output .fa file and calculate the changes. A good Python library for that is from collections import Counter.

For example,

>>> from collections import Counter
>>> word = "mississippi"
>>> counter = {}

>>> for letter in word:
            counter[letter] = counter.get(letter, 0) + 1

>>> counter
{'m': 1, 'i': 4, 's': 4, 'p': 2}

Some cool code to handle everything: https://huggingface.co/spaces/simonduerr/ProteinMPNN/blob/main/app.py#L382

[jadolfbr]

protein_mpnn_utils.py, line 125; I commented out a few of the places where 'gaps' are being added for sequence numbering.
Becomes this:

try:
    for resn in range(min_resn,max_resn+1):
      if resn in seq:
        for k in sorted(seq[resn]): seq_.append(aa_3_N.get(seq[resn][k],20))
      #else: seq_.append(20)
      if resn in xyz:
        for k in sorted(xyz[resn]):
          for atom in atoms:
            if atom in xyz[resn][k]: xyz_.append(xyz[resn][k][atom])
            else: xyz_.append(np.full(3,np.nan))
      #else:
      #  for atom in atoms: xyz_.append(np.full(3,np.nan))
    print("Seq_", seq_)