File Coverage

blib/lib/HackaMol/X/Calculator.pm

Criterion	Covered	Total	%
statement	18	40	45.0
branch	0	16	0.0
condition			n/a
subroutine	6	12	50.0
pod			n/a
total	24	68	35.2

package HackaMol::X::Calculator;
$HackaMol::X::Calculator::VERSION = '0.011';
# ABSTRACT: Abstract calculator class for HackaMol
use 5.008;
use Moose;
use MooseX::StrictConstructor;
use Moose::Util::TypeConstraints;
use namespace::autoclean;
use Carp;

with qw(HackaMol::X::Roles::ExtensionRole);

sub _build_map_in{
  my $sub_cr = sub { return (@_) };
  return $sub_cr;
}

sub _build_map_out{
  my $sub_cr = sub { return (@_) };
  return $sub_cr;
}

sub build_command {
    # exe -options file.inp -moreoptions > file.out
    my $self = shift;
    return 0 unless $self->exe;
    my $cmd;
    $cmd = $self->exe;
    $cmd .= " " . $self->in_fn->stringify    if $self->has_in_fn;
    $cmd .= " " . $self->exe_endops          if $self->has_exe_endops;
    $cmd .= " > " . $self->out_fn->stringify if $self->has_out_fn;

    # no cat of out_fn because of options to run without writing, etc
    return $cmd;
}

sub BUILD {
    my $self = shift;

    if ( $self->has_scratch ) {
        $self->scratch->mkpath unless ( $self->scratch->exists );
    }

    unless ( $self->has_command ) {
        return unless ( $self->has_exe );
        my $cmd = $self->build_command;
        $self->command($cmd);
    }
    return;
}

__PACKAGE__->meta->make_immutable;

1;

__END__

=pod

=head1 NAME

HackaMol::X::Calculator - Abstract calculator class for HackaMol

=head1 VERSION

version 0.011

=head1 SYNOPSIS

   use Modern::Perl;
   use HackaMol;
   use HackaMol::X::Calculator;
   use Path::Tiny;

   my $path = shift || die "pass path to gaussian outputs";

   my $hack = HackaMol->new( data => $path, );

   foreach my $out ( $hack->data->children(qr/\.out$/) ) {

       my $Calc = HackaMol::X::Calculator->new(
           out_fn  => $out,
           map_out => \&output_map,
       );

       my $energy = $Calc->map_output(627.51);

       printf( "%-40s: %10.6f\n", $Calc->out_fn->basename, $energy );

   }

   #  our function to map molec info from output

   sub output_map {
       my $calc = shift;
       my $conv = shift;
       my $re   = qr/-\d+.\d+/;
       my @energys = $calc->out_fn->slurp =~ m/SCF Done:.*(${re})/g;
       return ( $energys[-1] * $conv );
   }

=head1 DESCRIPTION

The HackaMol::X::Calculator extension generalizes molecular calculations using external programs.
The Calculator class consumes the HackaMol::X::Roles::ExtensionRole role, which manage the running of executables...
perhaps on files; perhaps in directories.  This extension is intended to provide a
simple example of interfaces with external programs. This is a barebones use of the ExtensionRole that is
intended to be flexible. See the examples and testing directory for use of the map_in and map_out functions
inside and outside of the map_input and map_output functions.  Extensions with more rigid and encapsulated
APIs can evolve from this starting point. In the synopsis, a Gaussian output is processed for the SCF Done
value (a classic scripting of problem computational chemists).  See the examples and tests to learn how the
calculator can be used to:

  1. generate inputs
  2. run programs
  3. process outputs

via interactions with HackaMol objects.

=head1 ATTRIBUTES

=head2 scratch

If scratch is set, the object will build that directory if needed.  See HackaMol::PathRole for more information about
the scratch attribute.

=head1 SEE ALSO

=over 4

=item *

L<HackaMol>

=item *

L<HackaMol::X::Roles::Extension>

=item *

L<HackaMol::PathRole>

=item *

L<Path::Tiny>

=back

=head1 EXTENDS

=over 4

=item * L<Moose::Object>

=back

=head1 CONSUMES

=over 4

=item * L<HackaMol::Roles::ExeRole>

=item * L<HackaMol::Roles::ExeRole|HackaMol::Roles::PathRole>

=item * L<HackaMol::Roles::PathRole>

=item * L<HackaMol::X::Roles::ExtensionRole>

=back

=head1 AUTHOR

Demian Riccardi <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2015 by Demian Riccardi.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut