<div dir="ltr">Hi Fred,<div><br></div><div>You can pass the QUIET=1 option to the PDBParser(). That should silence warnings.</div><div><br></div><div>Cheers,</div><div><br></div><div>João</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2014-07-22 19:14 GMT+01:00 Frederico Moraes Ferreira <span dir="ltr"><<a href="mailto:ferreirafm@usp.br" target="_blank">ferreirafm@usp.br</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Biopythonees,<br>
Has anybody happen to know how to suppress warnings when reading PDBs with hydrogenated waters?<br>
<br>
from Bio.PDB.PDBParser import PDBParser<br>
struct = PDBParser().get_structure('<u></u>tmp', pdbf)<br>
<br>
My PDBs came from MD so as all water molecules have hydrogens causing thousands of warnings like:<br>
...<br>
/usr/lib64/python2.7/site-<u></u>packages/Bio/PDB/PDBParser.py:<u></u>284: PDBConstructionWarning: PDBConstructionException: Atom 2H defined twice in residue <Residue HOH het=W resseq=2640 icode= > at line 71037.<br>
Exception ignored.<br>
Some atoms or residues may be missing in the data structure.<br>
% message, PDBConstructionWarning)<br>
...<br>
<br>
Thanks in advance.<br>
Fred<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
-- <br>
Dr. Frederico Moraes Ferreira<br>
University of Sao Paulo<br>
Heart Institute, School of Medicine<br>
Laboratoy of Immunology<br>
Av. Dr. Enéas de Carvalho Aguiar, 44<br>
05403-900 Sao Paulo - SP<br>
Brasil<br>
<br>
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</font></span></blockquote></div><br></div>