I ended up hacking this together when I got into the lab this afternoon. It's ugly, and probably inefficient, but it is entirely within my skillset and it works beautifully for what I need it to do (save for one file, which for some reason gets printed in triplicate, but that is just one case).
#!/usr/bin/perl
use strict;
use warnings;

        # Parse Gaussian '03 output files
        # for the lengths of the bonds
        # in Diaminopolymethine Dyes
        # strictly between Carbon and Nitrogen
        # or Carbon and Carbon
my $infile, my $outfile;
my @inlog, my @inlog_n, my @logged;

chomp($infile = <>);
chomp($outfile = <>);

open FILE, "<$infile";
while(<FILE>)
{
        push @inlog, $_;
}
close FILE;

for(@inlog)
{
        push @inlog_n, grep( /^\s?!{1}?\s*(c|n)/, $_);
}

@inlog = grep( !/h|c{3}?|nc{2}?|(estimate)|c{2}?n{1}?/, @inlog_n );
pop @inlog_n for @inlog_n;

@inlog_n = map{ split( /\s/, $_) } @inlog;
pop @inlog for @inlog;

for(@inlog_n)
{
        push @logged, $_ if $_=~/\d/ && $_!~/[a-zA-Z]/;
}

open LOG, ">$outfile";
for(@logged)
{
        print LOG "$_\n" if $_>=1;
}
close LOG;

[download]

Thanks again for the help! 



C(qw/74 97 104 112/);sub C{while(@_){$c**=$C;print
(map{chr($C!=$c?shift:pop)}$_),$C+=@_%2!=1?1:0}}

[download]

In reply to Re^4: Parsing Guassian '03 Log Files by Andrew_Levenson
in thread Parsing Guassian '03 Log Files by Andrew_Levenson

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