[Biopython] Bio.PDB.PDBIO.save renumbers Atom Serial Number

[Hongbo Zhu]

Hi,

The >>Atom Serial Number<< in the .pdb files from the Protein Data Bank
(PDB) are assigned consecutively from 1 to ATOM/HETATM records. This helps
to identify atoms, though it may be risky to rely on that number completely.

Apparently, function Bio.PDB.PDBIO.save() renumbers the  >>Atom Serial
Number<< in newly generated PDB file. This is on one hand consistent with
.pdb file style, on the other hand very confusing, as the same atom gets
different serial numbers. I suggest at least give the users the choice to
keep the original >>Atom Serial Number<< by adding a new parameter to the
save() function of class Bio.PDB.PDBIO.

cheers,
hongbo