qp.structure.missing.fix_numbering

qp.structure.missing.fix_numbering(pdb_content)

Handles insertion codes from Modeller.

Modeller resets the residue indices, which we fix with transfer_numbering(). However, transfer_numbering() names residues with insertion codes. For example, 5,5A,5B,5C instead of 5,6,7,8. This function fixes is residue numbering behavior. Takes the generated PDB, fixes the residue numbers and overwrites the PDB.

Parameters:

pdb_content (str) – Contents of a PDB as a str with line breaks.

Returns:

pdb_content – Contents of a PDB as a str with line breaks.

Return type:

str