in reply to Parsing Guassian '03 Log Files

Something like:

use strict;
use warnings;

my $file = <<FILE;
  ----------------------------
                       !   Optimized Parameters   !
                       ! (Angstroms and Degrees)  !
 ----------------------                            -------------------
+-----------------------------------------------------
 !      Name          Value   Derivative information (Atomic Units)   
+  !
 ---------------------------------------------------------------------
+---
 !       hc2         1.1136   -DE/DX =    0.0                         
+  !
 !       nc3         1.3392   -DE/DX =    0.0                         
+  !
 !      nch3       117.4979   -DE/DX =    0.0                         
+  !
 !       hn4         0.9929   -DE/DX =    0.0                         
+  !
----------------------------------------------------------------------
+--
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGr
+adGrad
FILE

open my $inFile, '<', \$file;

my $valueStart;
my $valueLength;
my $min = 1.0;
my $max = 2.0;

while (<$inFile>) {
    next unless m/Optimized Parameters/ .. m/GradGradGrad/;
    next unless $valueLength or /^(.*?Name)(\s*Value)/;

    if (! $valueLength) {
        $valueStart = length $1;
        $valueLength = length $2;
        next;
    }

    my $value = substr $_, $valueStart, $valueLength;

    next unless $value =~ /^\s*[+-]?\d+(\.\d*)?\s*$/;
    next if $value < $min or $value > $max;
    print $_;
}

close $inFile;

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Prints:

 !       hc2         1.1136   -DE/DX =    0.0                         
+  !
 !       nc3         1.3392   -DE/DX =    0.0                         
+  !

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Perl is environmentally friendly - it saves trees

Replies are listed 'Best First'.
Re^2: Parsing Guassian '03 Log Files
by Andrew_Levenson (Hermit) on Jan 31, 2008 at 02:15 UTC
    Thank you very much, but unfortunately, I need it to work in such a way that I call the script/program, feed it an input filename and an output filename, and have it work its magic. Each file is of an undetermined length, with sections that need to be parsed f undetermined length, as each file represents a different chain-length of the molecule.

    Sorry that I didn't specify that earlier. 
    


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

    [download]
[reply]
[d/l]

      Well, I couldn't do it all for you - what would you do with all the time you saved?

      You may find help in dealing with the file issues in replies to the thread File read and strip ;).

      Perl is environmentally friendly - it saves trees
[reply]
        Thanks, GF.
        You've been a great help time and again. :) 
        


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

        [download]
[reply]
[d/l]
        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}}

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[reply]
[d/l]
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