[Bioperl-l] pdb.pm and annotations
Sungsam Gong
sung at bio.cc
Wed Dec 16 12:55:16 EST 2009
Hi,
Wanted to get pubmed identifier from a PDB file using Bio::Structure,
so hacked the code.
Knew that Bio::Structure::IO::pdb.pm get relevant info from either
'JRNL' or 'REMARK 1'.
However could not see any actual code parsing 'PMID'.
>From pdb.pm, what I see:
sub _read_PDB_jrnl {
...
$auth = $self->_concatenate_lines($auth,$rol) if ($subr eq "AUTH");
$titl = $self->_concatenate_lines($titl,$rol) if ($subr eq "TITL");
$edit = $self->_concatenate_lines($edit,$rol) if ($subr eq "EDIT");
$ref = $self->_concatenate_lines($ref ,$rol) if ($subr eq "REF");
$publ = $self->_concatenate_lines($publ,$rol) if ($subr eq "PUBL");
$refn = $self->_concatenate_lines($refn,$rol) if ($subr eq "REFN");
...
}
sub _read_PDB_remark_1 {
...
$auth = $self->_concatenate_lines($auth,$rol) if
($subr eq "AUTH");
$titl = $self->_concatenate_lines($titl,$rol) if
($subr eq "TITL");
$edit = $self->_concatenate_lines($edit,$rol) if
($subr eq "EDIT");
$ref = $self->_concatenate_lines($ref ,$rol) if
($subr eq "REF");
$publ = $self->_concatenate_lines($publ,$rol) if
($subr eq "PUBL");
$refn = $self->_concatenate_lines($refn,$rol) if
($subr eq "REFN");
...
}
>From my script, I did:
($struc->annotation->get_Annotations('reference'))[0]->authors
($struc->annotation->get_Annotations('reference'))[0]->title
or
my $hash_ref=($struc->annotation->get_Annotations('reference'))[0]->hash_tree
for my $key (keys %{$hash_ref}) {
print $key,": ",$hash_ref->{$key},"\n";
}
Any plan to include a code chopping 'PMID' out?
Or did I miss something?
Cheers,
Sung
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