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Re^4: Parsing Guassian '03 Log Files

by Andrew_Levenson (Hermit)
on Jan 31, 2008 at 20:01 UTC ( #665428=note: print w/ replies, xml ) Need Help??


in reply to Re^3: Parsing Guassian '03 Log Files
in thread Parsing Guassian '03 Log Files

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;

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}}


Comment on Re^4: Parsing Guassian '03 Log Files
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Re^5: Parsing Guassian '03 Log Files
by GrandFather (Cardinal) on Jan 31, 2008 at 20:25 UTC

    You can clean that up a little:

    #!/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 Carb +on and # Carbon chomp (my $infile = <>); chomp (my $outfile = <>); open FILE, '<', $infile or die "Unable to open $infile: $!"; my @inlog = grep {/\d/ && ! /[a-zA-Z]/ && $_ >= 1} map {split (/\s/, $_)} grep {!/h|c{3}?|nc{2}?|(estimate)|c{2}?n{1}?/} grep {/^\s?!{1}?\s*(c|n)/} <FILE>; close FILE; open LOG, '>', $outfile or die "Unable to create $outfile: $!"; print LOG join "\n", @inlog; close LOG;

    Your version had some rather odd constructs. The pop loops to clear out arrays were perhaps the strangest. Much better to:

    @array = ();

    The while loop to slurp the file is better as:

    @array = <FILE>;

    The construct my $infile, my $outfile; is odd. Either my ($var1, $var1); or use two separate statements:

    my $var1; my $var2;

    However you should declare your variables as close to their first use as possible so it is not often that you need to declare a bunch of variables in one place like that anyway. See too the file name variable declarations in my version of your code above.

    You should always use the three parameter version of open and you should always check the result.


    Perl is environmentally friendly - it saves trees
      Ooh, @array = ();? Nice. Yeah, I completely forgot how to empty an array, so I... made my own way. I guess we know now why I'm a chemistry major now instead of Computer Science, haha.

      If its okay, i'm going to test your script and replace mine in the bin? Or not, I'll figure it out when I get back to the lab.
      Again, thanks.
      C(qw/74 97 104 112/);sub C{while(@_){$c**=$C;print (map{chr($C!=$c?shift:pop)}$_),$C+=@_%2!=1?1:0}}

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