Split Database Of Mol2 Files Into Chunks Of N Files

Question

[Flow]

I downloaded portions of ZINC database in mol2 format. Each part contains 20000 ligands. I would like to split each one into 100 ligands chunks. I know that with openbabel one can do

babel -i zinc_part.mol2 a.mol2 -m

but the chunks are always individual files. Later one could of course concatenate them, but this can be a mess. I wonder if there are other babel options or another approaches to divided a large mol2 files into chunks of N ligands each.

Answer 1

[Michael Kuhn]

One way could be to take this Perl script to split a file, and add this to the top:

$/ = "@<TRIPOS>MOLECULE";

This would instruct Perl to treat each record as one "line". But you may have to fiddle around with this to make sure your output is valid.

Answer 2

[Egon Willighagen]

Tobias Kind gave 20 solutions on the Blue Obelisk eXchange website.

Answer 3

[morency.lp]

I just fell on the thread and wanted to share my PERL script splitting multi-molecular ZINC mol2 files into single files named ZINCxxxxxxxx.mol2. Command line : perl separe_ligands.pl -f <filename>

#!/usr/bin/perl
use strict;
use warnings;
use Cwd;

my $file="";
my @ligands=();
my $mol2="";
my $workdir=getcwd;

for my $i (0..@ARGV-1)
{
    if ($ARGV[$i] eq "-f") {++$i;$file = $ARGV[$i];}
    if ($ARGV[$i] eq "-w") {++$i;$workdir .= $ARGV[$i];}
}

open IN, "$file";
while (<IN>)
{
    my $line = $_;
    chomp($line);
    if ($line =~ m/@<TRIPOS>MOLECULE/ && $mol2 eq "")
    {
        $mol2.=$line."\n";
    }
    elsif ($line =~ m/@<TRIPOS>MOLECULE/ && $mol2 ne "" )
    {
        my $outfile.=pop(@ligands).".mol2";
        open OUT, ">$outfile";
        print OUT "$mol2";
        close OUT;
        $mol2=$line."\n";
    }
    else
    {
        if($line =~ m/ZINC/) {push(@ligands,$line);}
        $mol2.=$line."\n";
        chomp($line);
    }
}
close IN;
exit;

[morency.lp]

For Unix based OS (no guarantee under Windows).