1. RAM problem.
RAM is 512MB and swap 1GB.
A file typically is 1.2MB
No. of lines (atoms) 20,000.
Note: This is in test phase, but it can increase by about 10-50 fold.

2. Graph Theory problem.
This unfortunately is not a Graph-Theory problem, but more of a gas-phase problem. I need to find out all the 'interacting-pairs' (ie pairs of atoms close enough) to do a more complicated analysis.

3. FORTRAN object file.
Ok, may be I can make this piece into a library file, so that I should be able to use it as a POSIX funtion?

4. Grid-wise calculation.
Promising. :) I thought, but was a bit lazy to try. After brute-force I began to wonder if it would be worth the effort... Thanks. :)

5. Chemistry::Bond::Find
Yes, I must try this. :) Mine's is a protein with hell-lot of water, and I have to find water-protein hydrogen bonds. At least based on distance alone. Will get back to you. itub. :D

6. Using square of distance.
Well, yes, I was already using the square of the distance, and yes, it is on PDB files. :)

7. Using x:y:z boxinfo.
Yes. I thought of it, but was lazy as I thought I need to put in lot of code. But now I am convinced it won't be so much. Thanks a lot BrowserUk. :)

8. The code: 
#     Open each PDB
      foreach my $pdb_file (<$pdb_list>) {
         {  
            chomp($pdb_file);
            my $tmp_file; # We would open the PDB with this handle
            open($tmp_file, "< $pdb_file") or (die "Cannot open PDB: $
+!");

#           Read X,Y,Z coordinates
            my @X; # X-coordinates
            my @Y; # Y-coordinates
            my @Z; # Z-coordinates
            my @pdb_tmp=<$tmp_file>;
            foreach (@pdb_tmp) {
               if (substr($_,0,3) eq "ATO") {
                  push @X, substr($_,30,8);
                  push @Y, substr($_,38,8);
                  push @Z, substr($_,46,8);
               }
            }

#           Find the interaction pairs. Also strore the best angle, sh
+ould it
#           occur again with another proton. Also keep track of the wa
+ters
#           that have made h-bond with the solute atoms.
            my @sel_wat;  # Array of water molecule (numbers) selected
            my %hbond;    # $hbond[$tag1:$tag2][0]=distance
                          # $hbond[$tag1:$tag2][0]=angle

#           Solute as donor and water as acceptor
            {
               my @atom_cov; # Polar solute atom that is already cover
+ed.
               for (my $i=0; $i <= $#pol_h; $i++) {
#                 If this donor is not already covered, then go ahead.
                  if ( ! defined($atom_cov[$pol_h[$i][1]]) ) {
                     for (my $j=0; $j <= $#wat_a; $j++) {
                        my $dx=$X[$pol_h[$i][1]]-$X[$wat_a[$j]];
                        my $dy=$Y[$pol_h[$i][1]]-$Y[$wat_a[$j]];
                        my $dz=$Z[$pol_h[$i][1]]-$Z[$wat_a[$j]];

                        my $distSq=($dx*$dx)+($dy*$dy)+($dz*$dz);
                        if ($distSq <= $hb_dist) {
                           $atom_cov[$pol_h[$i][1]]=1;
                           print $idty[$pol_h[$i][1]], " ", 
                                 $idty[$wat_a[$j]], $distSq,"\n";
                        }
                     }
                  }
               }
            }
         }
      }

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In reply to Re: Re: Processing data with lot of math... by qhayaal
in thread Processing data with lot of math... by qhayaal

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