File Coverage

blib/lib/HackaMol/Roles/SymopRole.pm

Criterion	Covered	Total	%
statement	12	40	30.0
branch			n/a
condition			n/a
subroutine	4	5	80.0
pod	1	1	100.0
total	17	46	36.9

package HackaMol::Roles::SymopRole;
$HackaMol::Roles::SymopRole::VERSION = '0.000_02'; # TRIAL

$HackaMol::Roles::SymopRole::VERSION = '0.00002';#ABSTRACT: Fill your coordinates using symmetry operations
use Moose::Role;
use Math::Vector::Real;
use Carp;

sub apply_pdbstr_symops {

  my $self   = shift;
  my $symops = shift;
  my $mol    = shift;

  my $t = $mol->tmax+1;

  my %sym_op = (); # a hash to store them!
  #this regex may be general enough to work on entire pdb
  foreach my $line ( grep { m/REMARK 350\s+(BIOMT|SMTRY)\d+\s+\d+/ } split( '\n' , $symops ) ){
    my @entries = split(' ', $line);
    push @{$sym_op{$entries[3]}}, V(@entries[4,5,6,7]);
  }


  foreach my $symop (sort {$a<=>$b} keys %sym_op){
    my @mat_d = @{$sym_op{$symop}};
    my $cx = V(map{$_->[0]} @mat_d);
    my $cy = V(map{$_->[1]} @mat_d);
    my $cz = V(map{$_->[2]} @mat_d);
    my $dxyz = V(map{$_->[3]} @mat_d);

    foreach my $atom ($mol->all_atoms){
        my ($x,$y,$z) = @{$atom->xyz};
        my $xyz_new = $x*$cx + $y*$cy + $z*$cz + $dxyz;
        $atom->set_coords($t,$xyz_new);
    }
    $t++;
  }

}

no Moose::Role;

1;

__END__

=pod

=head1 NAME

HackaMol::Roles::SymopRole - Fill your coordinates using symmetry operations

=head1 VERSION

version 0.000_02

=head1 DESCRIPTION

The goal of HackaMol::Roles::SymopRole is to simplify the application of
symmetry operations.  This role is not loaded with the core; it
must be applied as done in the synopsis.  This role is envisioned for
instances of the HackaMol class, which provides builder.

=head1 METHODS

=head2 apply_pdbstr_symops

takes two arguments:

      1. a string with one or more symmetry operations.  As the name of the method suggests, the method works for strings formatted as in a
         typical protein databank file.  It will filter for lines containing the SMTRY or BIOMT pattern.

      2. the molecule with the initial coordinates

The method applies the symmetry operators and adds the coordinates to each atom of the molecule.

=head1 SYNOPSIS

       ## Symmetry operations using copy and pasted from the PDB

       my $symops = '
         REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
         REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
         REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
         REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
         REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000     -125.59400
         REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000     -125.48300
         REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
       '; # from pdb

       say $mol->tmax ; # says 0

       $bldr->apply_pdbstr_symops($symops,$mol);  # will add coordinates for each, even the identity op (the first three)

       $mol->tmax ;     # says 2


       my $enzyme = $mol->select_group("chain E");
       my $inhib  = $mol->select_group("chain I");

=head1 WARNING

This is still under active development and may change or just not work.  I still need to add warnings to help with bad
selections.  Let me know if you have problems or suggestions!

=head1 AUTHOR

Demian Riccardi <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2016 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