[Bioperl-l] dssp script

Ed Green ed at compbio.berkeley.edu
Fri Jan 21 12:09:04 EST 2005


Dear Peter,

These two are in fact bugs that I will fix. The first results because of 
  the presence of 'termination residues' that don't have residue 
numbers. Their residue numbers, then, can't be compared numerically. 
Fortunately, this bug won't result in wrong results as we want this 
comparison to always be false anyway. The solution to this is to first 
check if either of the termination residue signals are set and if so, 
don't do this numerical comparison.

The second, blank line(s) at end of file will also be fixed.

Beware that there is, I think, a bug in your script. It appears that you 
are attempting to iterate over all residues. However, iterating A:1 .. 
A:max doesn't get it done because of the crazy way residues can be 
numbered in PDB files: you'll miss all the residues with altloc codes 
(A:27A, A:27B, A:27C, e.g.).

To make this easy an iterator is called for. It will just return all 
'real' residues for the pdb file or for a specified chain - I'll try to 
get that done this weekend.

Regards,
Ed Green

Robinson, Peter wrote:
> Dear BioPerlers,
> 
> I am writing a script to use the BioPerl DSSP module to print out a list of phi and psi angles for all applicable residues  of all chains. Although the results are correct, I get the following error message at the end of each chain:
> 
> Argument "" isn't numeric in numeric eq (==) at /usr/local/share/perl/5.8.4/Bio/Structure/SecStr/DSSP/Res.pm line 1168.
> 
> and I am not quite sure where it is coming from. Perhaps I am using the wrong part of the API, but I am trying to get a list of all residues for each chain as follows:
> 
> foreach my $ch (@chains) {
>   my $ss_elements_pts = $dssp->secBounds($ch);
>   print "Chain $ch:\n";
>   my $pos = 0;
>   my $max = 0;
>   foreach my $stretch (@{$ss_elements_pts}) {
>     my $start = $stretch->[0];
>     my $end = $stretch->[1]; 
>     if ($end =~ m/(\d+)/) { $end = $1; }
>    
>     if ($end  > $max) { $max = $end; }
>   }
>   ## END is now the last residue in this chain
>   for my $res (1..$max) {
>     my $residueID = $res . ":" . $ch;
>     my ($phi,$psi,$SS,$SSsum,$AA);
>     eval { $phi = $dssp->resPhi($residueID);};
> 	etc.
> 
> The full script is appended to the bottom of this mail.
> 
> 
> I also noticed what might be a minor bug in the module DSSP/Res.pm; when I use dsspcmbi to analyze a PDB file, it produces a results file with an empty last line. This causes a crash:
> 
> Use of uninitialized value in chomp at /usr/local/share/perl/5.8.4/Bio/Structure/SecStr/DSSP/Res.pm line 1284, <GEN1> line 955.
> 
> 
>  If I manually remove this last empty line, there was no error. By adding the following line at Res.pm l.1284, you can fix the problem:
> 
> 
>  while ( chomp( $cur = <$file> ) ) {
>       next if ($cur =~ m/^\s*$/);  *********************************************
> 	$res_num = substr( $cur, 0, 5 );
> 	$res_num =~ s/\s//g;
> 	$self->{ 'Res' }->[ $res_num ] = &_parseResLine( $cur );
>     }
> }
> 
> 
> 
> 
> Thanks in adavance for any tips! Peter
> Peter N. Robinson, M.D.
> Institute of Medical Genetics
> Charité University Hospital
> Augustenburger Platz 1
> 13353 Berlin
> Germany
> ++49-30-450 569124
> peter.robinson at charite.de
> http://www.charite.de/ch/medgen/robinson
> Beware of bugs in the above code; I have only proved it correct, not tried it. -Donald Knuth, computer scientist (1938- )
> 
> ########################
> 
> #!/usr/bin/perl -w
> use IO::File;
> use Bio::Structure::SecStr::DSSP::Res;
> use Data::Dumper;
> 
> 
> =pod
> parseDSSP.pl
> Script to parse the output of DSSP using the BioPerl module
> Bio::Structure::SecStr::DSSP::Res. To use it, process a PDB
> file with dssp or dsspcmbi, and pass the resulting file to 
> this script. For more information on dssp and BioPerl see the
> module documentation at http://bioperl.org
> 
> @email peter.robinson at charite.de
> 21 January, 2005
> 
> =cut
> 
> 
> 
> my $file = "pdb43ca.dssp";
> my $dssp = new Bio::Structure::SecStr::DSSP::Res('-file'=> "$file");
> 
> my $pdbID = $dssp->pdbID();
> my $auth  = $dssp->pdbAuthor();
> my $cmpd = $dssp->pdbCompound();
> my $pdb_date = $dssp->pdbDate();
> my $header = $dssp->pdbHeader();
> my $pdbSource = $dssp->pdbSource();
> 
> print "PDB entry $pdbID \n\tauthor:\t$auth",
>   "\n\tCompound:\t$cmpd",
>   "\n\tDate:\t$pdb_date",
>   "\n\tHeader:\t$header",
>   "\n\tsource:\t$pdbSource\n\n";
> 
> my $totalRes = $dssp->numResidues();
> print "Total residue count (all chains):$totalRes\n";
> 
> 
> my $surArea= $dssp->totSurfArea();
> print "Total accessible surface area:\t$surArea  (square Ang)\n";
> 
> 
> my $chainRef = $dssp->chains();
> my @chains = sort  @{$chainRef};
> print "Chain[s]:\n";
> foreach my $ch (@chains) {
>   print "\t$ch";
> }
> print "\n";
> 
> my $hb = $dssp->hBonds();
> print "H BONDS.\n";
> print "TYPE O(I)-->H-N(J): $hb->[0]\n",
>    "IN PARALLEL BRIDGES: $hb->[1]\n",
>    "IN ANTIPARALLEL BRIDGES $hb->[2]\n",
>    "TYPE O(I)-->H-N(I-5) $hb->[3]\n",
>    "TYPE O(I)-->H-N(I-4) $hb->[4]\n",
>    "TYPE O(I)-->H-N(I-3) $hb->[5]\n",
>    "TYPE O(I)-->H-N(I-2) $hb->[6]\n",
>    "TYPE O(I)-->H-N(I-1) $hb->[7]\n",
>    "TYPE O(I)-->H-N(I+0) $hb->[8]\n",
>    "TYPE O(I)-->H-N(I+1) $hb->[9]\n",
>    "TYPE O(I)-->H-N(I+2) $hb->[10]\n",
>    "TYPE O(I)-->H-N(I+3) $hb->[11]\n",
>    "TYPE O(I)-->H-N(I+4) $hb->[12]\n",
>    "TYPE O(I)-->H-N(I+5) $hb->[13]\n",
>   "\n";
> 
>    
>  
> foreach my $ch (@chains) {
>   my $ss_elements_pts = $dssp->secBounds($ch);
>   print "Chain $ch:\n";
>   my $pos = 0;
>   my $max = 0;
>   foreach my $stretch (@{$ss_elements_pts}) {
>     my $start = $stretch->[0];
>     my $end = $stretch->[1]; 
>     if ($end =~ m/(\d+)/) { $end = $1; }
>    
>     if ($end  > $max) { $max = $end; }
>   }
>   ## END is now the last residue in this chain
>   for my $res (1..$max) {
>     my $residueID = $res . ":" . $ch;
>     my ($phi,$psi,$SS,$SSsum,$AA);
>     eval { $phi = $dssp->resPhi($residueID);};
>     eval { $psi = $dssp->resPsi($residueID);};
>     eval { $SS = $dssp->resSecStr($residueID);};
>     eval { $SSsum = $dssp->resSecStrSum($residueID);};
>     $AA = $dssp->resAA($residueID);
>     $phi = $phi || "n/a";
>     $psi = $psi || "n/a";
>     $SS = $SS || "-";
>     my $SSclass;
>     if ($SSsum eq "H") { $SSclass = "helix"; }
>     elsif ($SSsum eq "T") { $SSclass = "turn"; }
>     elsif ($SSsum eq "B") { $SSclass = "beta"; }
>     else { $SSclass = $SSsum; }
>     print "$residueID) [$AA] phi:$phi psi:$psi SecStruct: $SS ($SSclass) \n";
>   }
> }
> 
> 
> 
> 
> 
> 
> 
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