examples/contributed/nmrpdb_parse.pl

   1 #!/usr/bin/perl
   2 use strict;
   3
   4 # This program will read in an NMR derived PDB file containing
   5 # multiple conformers, and will allow the user to extract either
   6 # one or all of the models to separate files.
   7 #
   8 # Although the program will run interactively, the command line
   9 # usage is "nmrsplit [input.file] [number of model to extract]"
  10 #
  11 #
  12 #
  13 # Written 13/12/00 by Simon Andrews (simon.andrews@bbsrc.ac.uk)
  14
  15 # Submitted to bioperl script project 2001/08/06
  16
  17 # Description:  Script which reads  an NMR-derived  multiple structure
  18 # PDB file, and will either extract a single structure from it, or
  19 # will  extract all of the structures into single  files.  This  is
  20 # useful when you want to  work with a single representative structure
  21 # from an NMR  ensemble - especially in conjunction  with the OLDERADO
  22 # database (http://neon.chem.le.ac.uk/olderado/) which  finds  the
  23 # most representative structure from an ensemble.
  24
  25
  26 my $Input = $ARGV[0];   # File to be read
  27 my $Pullout = $ARGV[1]; # Specific model to extract
  28 my @Pdbfile;            # Array for whole PDB file
  29 my $Header = "";        # String to hold the PDB header
  30 my $Model = "";         # String to hold individual models
  31 my $Output;             # Prefix for output files
  32 my $Modno = 1;          # Number of the model being processed
  33
  34 while () {
  35     if ($Input) {
  36
  37         if (-r $Input) {
  38             last;
  39         }else{
  40             print "\"$Input\" does not exist, or could not be read\n";
  41         }
  42     }
  43
  44     print "\nEnter name of multiple PDB file: ";
  45     $Input = <STDIN>;
  46     chomp $Input;
  47     $Input =~ s/^\s*//;
  48     $Input =~ s/\s*$//;
  49
  50     next;
  51 }
  52
  53 while () {
  54     if ($Pullout) {
  55
  56         if ($Pullout =~ /^\d+$/){
  57             if ($Pullout == int $Pullout) {
  58                 last;
  59             }else {
  60                 print "\"$Pullout\" should be an integer\n";
  61             }
  62         }else  {
  63             print "\"$Pullout\" should be a number\n";
  64         }
  65     }
  66
  67     print "\nEnter number of specific model to extract (Return for none): ";
  68     $Pullout = <STDIN>;
  69     chomp $Pullout;
  70     $Pullout =~ s/^\s*//;
  71     $Pullout =~ s/\s*$//;
  72
  73     last unless ($Pullout);
  74     next;
  75 }
  76
  77
  78 ($Output = $Input) =~ s/\.\w*$//; # Take off everything after the last . to use as prefix
  79
  80
  81 open (PDB,$Input) || die "Can't open $Input because $!";
  82
  83
  84
  85 ########## Read the header information ####################
  86
  87
  88 while (<PDB>) {
  89     if (/^MODEL\b/){last;}
  90     $Header = $Header . $_;
  91 }
  92
  93
  94 ######### Read the separate models #######################
  95
  96
  97 while () {
  98
  99     model();
 100     if ($Model) {      # Check if we're past the last model
 101         if ($Pullout) {          # Check if we're writing one or all
 102             last if ($Modno > $Pullout);# No point continuing if we've got the one we want
 103             readout();
 104         }else   {
 105             writeout();
 106         }
 107         $Model = "";
 108         ++$Modno;
 109     }else  {
 110         last;
 111     }
 112 }
 113 --$Modno;     # Correct last increment which didn't find a model
 114
 115 if (($Pullout) & ($Modno < $Pullout)) {
 116     print "\nCannot find model $Pullout : Only $Modno models in this file\n";
 117 }
 118
 119 #################### subroutines start here ##########################
 120
 121
 122 sub model {
 123
 124     while (<PDB>) {
 125         if (/^(MODEL\b|END\b|MASTER\b)/){next;}
 126         # Stops you getting MODEL... at the top of the output
 127         # and makes sure there isn't a file containing just END or MASTER
 128
 129         if (/^ENDMDL\b/){last;}    # Check for the end of the model
 130         $Model = $Model . $_;      # Append the line to $Model
 131     }
 132 }
 133
 134 sub writeout  {  # Used when all files are being written out
 135
 136     if (-e "$Output\_$Modno.pdb"){  # Check whether we're overwriting anything
 137
 138         print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? ";
 139         my $Question = <STDIN>;
 140         unless ($Question =~ /^y/i) {
 141             print "\nSkipping $Output\_$Modno.pdb";
 142             return;
 143         }
 144     }
 145
 146     open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!";
 147     print "\nWriting $Output\_$Modno.pdb ...";
 148     print OUT $Header;
 149     print OUT $Model;
 150     print OUT "END\n";  # Adds and END statement to the PDB file
 151
 152     close OUT || die "Couldn't close $Output\_$Modno.pdb because $!";
 153 }
 154
 155
 156 sub readout {
 157
 158     if ($Modno == $Pullout) {
 159
 160         if (-e "$Output\_$Modno.pdb") { # Check whether we're overwriting anything
 161
 162             print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? ";
 163             my $Question = <STDIN>;
 164             unless ($Question =~ /^y/i) {
 165                 print "\nModel not extracted\n";
 166                 $Model = "";
 167                 return;
 168             }
 169         }
 170
 171         open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!";
 172         print "\nWriting $Output\_$Modno.pdb ...\n";
 173         print OUT $Header;
 174         print OUT $Model;
 175         print OUT "END\n"; # Adds and END statement to the PDB file
 176
 177         close OUT || die "Couldn't close $Output\_$Modno.pdb because $!";
 178
 179         $Model = "";  # Stops the reading after this model
 180     }else  {
 181         print "\nReading Model $Modno ...";
 182     }
 183 }