def idx_align()

in data/contact_map_utils.py [0:0]

• 22 lines of code
• 6 McCabe index (conditional complexity)

def idx_align(pdb_seq: str, og_seq: str):
    """Maps indices of original and PDB sequences to mutual alignment
    Args:
        pdb_seq: Sequence of amino acids as extracted from PDB file
        og_seq: Original sequence of amino acids
    Returns:
        Tuple where the first element is a list of integers containing the indices in
        the PDB sequence for which aligned information is available and the second element
        is a list of integers containing the indices in the original sequence
        for which aligned information is available
    """
    alignment = pairwise2.align.globalxx(Seq(og_seq), Seq(pdb_seq))[0]
    og_seq_align = alignment.seqA
    og_idxs = []
    og_offset = 0

    pdb_seq_align = alignment.seqB
    pdb_idxs = []
    pdb_offset = 0
    for i in range(len(pdb_seq_align)):
        valid = True
        pdb_res = pdb_seq_align[i]
        og_res = og_seq_align[i]
        if pdb_res == "-":
            pdb_offset += 1
            valid = False
        if og_res == "-":
            og_offset += 1
            valid = False
        if valid and (pdb_res == og_res):
            pdb_idxs.append(i - pdb_offset)
            og_idxs.append(i - og_offset)

    return pdb_idxs, og_idxs