[Bioperl-l] Structure::IO::pdb update needed to comply with PDB file format specification change
Scott.Markel at accelrys.com
Sat Nov 3 00:13:59 UTC 2012
In tracking down a regression test failure we discovered that the Structure::IO::pdb module is out of date relative to the PDB file format specification (http://www.wwpdb.org/docs.html). PDB now writes out to column 79, while pdb.pm is still using the old line length of 71. Our regression failure was caused by a reformatting of 1CRN; journal titles started getting truncated.
Some of the Perl lines are really simple, e.g.,
$keywds = $self->_read_PDB_singlecontline("KEYWDS","11-70",\$buffer);
with others being just a little more detailed, e.g.,
my ($rec, $subr, $cont, $rol) = unpack "A6 x6 A4 A2 x1 A51", $_;
It doesn't look like pdb.pm has changed in about 1.5 years. Is there a current module owner? Or someone else working on this?
If not, we're willing to either compile a list of needed changes (walking through the PDB file format specification and comparing the corresponding column indices in pdb.pm) or provide a new version of the entire file. Please let us know which is preferred.
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: smarkel at accelrys.com
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