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revision 1.3, Thu Nov 30 23:02:10 2006 UTC revision 1.4, Wed Dec 6 23:50:46 2006 UTC
# Line 72  Line 72 
72  # This Sub funtions to open up the table and keep track of the index of what row we are on  # This Sub funtions to open up the table and keep track of the index of what row we are on
73  sub get_table{  sub get_table{
74      my($cgi, $varHash, $file)= @_;      my($cgi, $varHash, $file)= @_;
75      Open(\*TABLE, "$FIG_Config::drug_directory/$file");      Open(\*TABLE, "<$FIG_Config::drug_directory/$file");
76      while (<TABLE>){      while (! eof TABLE){
77          my @lines = split (/\r/,$_);          my @entry = Tracer::GetLine(\*TABLE);
78          for my $i (0..scalar@lines-1) {          &get_best_pdb($cgi, $varHash, @entry);
             my @entry = split (/\t/,$lines[$i]);  
 #           &print_row($entry[5], $entry[9], $entry[3], $entry[1], $i);  
             &get_best_pdb($cgi, $varHash, $i,$file);  
         }  
79      }      }
80  }  }
81    
82    
83  # This Sub funtions to print the Table Row in the correct format.  # This Sub funtions to print the Table Row in the correct format.
84  sub print_column{  sub print_column{
85      my($cgi, $varHash, $pdb, $color, $score,$peg, $func, $lit, $cat, $i) = @_ ;      my($cgi, $varHash, $pdb, $color, $score,$peg, $func, $lit, $cat) = @_ ;
86      my $genome = $peg;      my $genome = $peg;
87      $genome =~ s/fig\|//;      $genome =~ s/fig\|//;
88      $genome =~ s/\.peg\.\d+//;      $genome =~ s/\.peg\.\d+//;
# Line 155  Line 151 
151    
152  #-- we wish to desplay only the best pdbs and those that are relavent  #-- we wish to desplay only the best pdbs and those that are relavent
153  sub get_best_pdb{  sub get_best_pdb{
154      my ($cgi, $varHash, $i, $file)= @_;      my ($cgi, $varHash, @entry)= @_;
155      my @pdbresults =("1ah7","1dhn","1tfu"); # we define what pdb actually have been docked well.      my @pdbresults =("1ah7","1dhn","1tfu"); # we define what pdb actually have been docked well.
     Open(\*TABLE, "$FIG_Config::drug_directory/$file");  
     while (<TABLE>){  
         my @lines = split (/\r/,$_);  
         my @entry = split(/\t/,$lines[$i]);  
156          if (T(4)) {          if (T(4)) {
157              my $line = "Processing line\n";              my $line = "Processing line\n";
158              for (my $i = 0; $i <= $#entry; $i++) {              for (my $i = 0; $i <= $#entry; $i++) {
# Line 171  Line 163 
163          Trace("Analyzing PDB $entry[11].") if T(4);          Trace("Analyzing PDB $entry[11].") if T(4);
164          foreach (@pdbresults){ #look through the results we have          foreach (@pdbresults){ #look through the results we have
165              if ($entry[11] =~ m/$_/gi){ #ifwe have results for the free              if ($entry[11] =~ m/$_/gi){ #ifwe have results for the free
166                  &print_column($cgi, $varHash, $entry[11],'red', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this              &print_column($cgi, $varHash, $entry[11],'red', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
167                  return;                  return;
168              }elsif($entry[14] =~ m/$_/gi){ #if we have resutls for the bound              }elsif($entry[14] =~ m/$_/gi){ #if we have resutls for the bound
169                  &print_column($cgi, $varHash,$entry[14], 'red', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we wnat to display this              &print_column($cgi, $varHash,$entry[14], 'red', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1]); #we wnat to display this
170                  return;                  return;
171              }              }
172          }          }
173          if ($entry[13] eq "0"){ #if the free pdb is perfect          if ($entry[13] eq "0"){ #if the free pdb is perfect
174              &print_column($cgi, $varHash, $entry[11], '', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this          &print_column($cgi, $varHash, $entry[11], '', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
175              return;              return;
176          }elsif($entry[16] eq '0'){ #if the bound  pdb is perfect          }elsif($entry[16] eq '0'){ #if the bound  pdb is perfect
177              &print_column($cgi, $varHash, $entry[14], '', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this          &print_column($cgi, $varHash, $entry[14], '', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
178              return;              return;
179          }elsif($entry[13] =~ /\d\.\d*E\-(\d+)/ ){ #if the eval is like 1.4E-45          }elsif($entry[13] =~ /\d\.\d*E\-(\d+)/ ){ #if the eval is like 1.4E-45
180              if (15 < $1) { #and the exponant is less than 1.0E-15              if (15 < $1) { #and the exponant is less than 1.0E-15
# Line 193  Line 185 
185                          my $efree = $free[0] * 13 ** -$free[1];                          my $efree = $free[0] * 13 ** -$free[1];
186                          my $ebound = $bound[0] * 13 ** -$bound[1];                          my $ebound = $bound[0] * 13 ** -$bound[1];
187                          if ($efree <= $ebound){ #if the free is less than the boutd                          if ($efree <= $ebound){ #if the free is less than the boutd
188                              &print_column($cgi, $varHash, $entry[11], 'black', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this                          &print_column($cgi, $varHash, $entry[11], 'black', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
189                              return;                              return;
190                          }else{                          }else{
191                              &print_column($cgi, $varHash, $entry[14], 'green', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this                          &print_column($cgi, $varHash, $entry[14], 'green', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
192                              return;                              return;
193                          }                          }
194                      }else{ #the bound exponent wasn't less than 15                      }else{ #the bound exponent wasn't less than 15
195                          &print_column($cgi, $varHash, $entry[11], 'blue', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this                      &print_column($cgi, $varHash, $entry[11], 'blue', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
196                          return;                          return;
197                      }                      }
198                  }else{ #the bound pdb didn't even have an exponant                  }else{ #the bound pdb didn't even have an exponant
199                      &print_column($cgi, $varHash, $entry[11], 'yello', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1], $i); #we want to display this                  &print_column($cgi, $varHash, $entry[11], 'yello', $entry[13],$entry[5], $entry[9], $entry[3], $entry[1]); #we want to display this
200                      return; #this takes care the if free is good and bound is bad                      return; #this takes care the if free is good and bound is bad
201                  }#a free pdb is no good becaus eval > 1e-15                  }#a free pdb is no good becaus eval > 1e-15
202              }#free pdb was no good because eval > 1e-15              }#free pdb was no good because eval > 1e-15
203          }elsif($entry[16] =~ /\d\.\d*E\-(\d+)/ ){ #we are now checking if the bound pdb is good          }elsif($entry[16] =~ /\d\.\d*E\-(\d+)/ ){ #we are now checking if the bound pdb is good
204              if (15 < $1) {              if (15 < $1) {
205                  &print_column($cgi, $varHash, $entry[14], 'black', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1], $i);              &print_column($cgi, $varHash, $entry[14], 'black', $entry[16],$entry[5], $entry[9], $entry[3], $entry[1]);
206                  return;                  return;
207              }              }
208        } else {
209            Trace("Peg $entry[5] not printed.") if T(4);
210          }          }
211      }      }
     Trace("No result printed for line $i in file $file.") if T(4);  
 }  
212    
213    
214  # -error interupt--these subs will probably go when bruce sees them  # -error interupt--these subs will probably go when bruce sees them

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