Chemistry::ESPT::Aprmcrd - AMBER prmcrd file object.

Chemistry-ESPT documentation Contained in the Chemistry-ESPT distribution.

Index

Code Index:

NAME

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Chemistry::ESPT::Aprmcrd - AMBER prmcrd file object.

SYNOPSIS

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    use Chemistry::ESPT::Aprmcrd;

    my $prmcrd = Chemistry::ESPT::Aprmcrd->new();

DESCRIPTION

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This module provides methods to quickly access data contained in an AMBER prmcrd file. AMBER prmcrd files can only be read currently.

ATTRIBUTES

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All attributes are currently read-only and get populated by reading the assigned ESS file. Attribute values are accessible through the $Aprmcrd->get() method.

CARTCOORD

NATOMS x 3 matrix containing Cartesian coordinates

METHODS

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Method parameters denoted in [] are optional.

$prmcrd->new()

Creates a new Aprmcrd object

$prmcrd->analyze(filename [spin])

Analyze the spin results in file called filename. Spin defaults to Alpha.

VERSION

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0.02

SEE ALSO

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Chemistry::ESPT::ESSfile, http://amber.scripps.edu

AUTHOR

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Dr. Jason L. Sonnenberg, <sonnenberg.11@osu.edu>

COPYRIGHT AND LICENSE

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Copyright 2008 by Dr. Jason L. Sonnenberg

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. I would like to hear of any suggestions for improvement.

Chemistry-ESPT documentation Contained in the Chemistry-ESPT distribution. 
package Chemistry::ESPT::Aprmcrd;

use base qw(Chemistry::ESPT::ESSfile);
use strict;
use warnings;


our $VERSION = '0.02';


## the object constructor **

sub new {
	my $invocant = shift;
	my $class = ref($invocant) || $invocant;
	my $prmcrd = Chemistry::ESPT::ESSfile->new();

	$prmcrd->{PROGRAM} = "AMBER";
	$prmcrd->{TYPE} = "prmcrd";

	# molecular info
	$prmcrd->{CARTCOORD} = [];		# Current cartesian coordinates

	bless($prmcrd, $class);
	return $prmcrd;
}


## methods ##


# set filename & spin then digest the file
sub analyze : method {
	my $prmcrd = shift;
	$prmcrd->prepare(@_);
	$prmcrd->_digest();
	return;
}


## subroutines ##

sub _digest {

my $prmcrd = shift;

# flags & counters
my $counter = 0;
my $Titleflag = 1;

# open filename for reading or display error
open(PRMCRDFILE,$prmcrd->{FILENAME}) || die "Could not read $prmcrd->{FILENAME}\n$!\n";

# grab everything which may be useful
while (<PRMCRDFILE>){
	# skip blank lines
	next if /^$/;

	# title; first line of text
	if ( $Titleflag == 1 && /^[\w\d\-\(\)]+/ ) {
		chomp($_);
		s/\s+$//;
		$prmcrd->{TITLE} = $_;
		$Titleflag = 0;
		next;
	}
	# number of atoms
	if ( $Titleflag == 0 && /^\s+(\d+)$/ ) {
		$prmcrd->{NATOMS} = $1;
		next;
	}
        # current cartesian coordinates
        # store in an N x 3 array for the time being
        # switch to PerlMol objects in the future
        if ( /^\s+((?:-*\d+\.\d+\s+){1,6})/ ) {
		my @carts = split /\s+/, $1;
                for (my $i=0; $i<scalar(@carts); $i++) {
                        push @{ $prmcrd->{CARTCOORD} [$counter] }, $carts[$i];
                        $counter++ if $#{$prmcrd->{CARTCOORD} [$counter]}  == 2;
                }
                next;
        }

}
}


1;
__END__