[Biopython] PDBParser Class --> Output

[João Rodrigues]

Back to this question. Haven't had much time to look at it and it turned out
to be a bit more complicated than what I thought. Permissive is an attribute
of the PDBParser module and since the assignment takes place in the Atom
module I don't see a straightforward way of pulling this off.

However, and although there is the very simple solution of playing with the
warnings module, the solution I offer is to allow a second level of
"permissiveness" (PERMISSIVE=2) where all warnings are supressed.

Cheers,

J