File Coverage

blib/lib/HackaMol/Roles/AtomGroupRole.pm

Criterion	Covered	Total	%
statement	262	283	92.5
branch	67	76	88.1
condition	1	2	50.0
subroutine	38	39	97.4
pod	22	28	78.5
total	390	428	91.1

$HackaMol::Roles::AtomGroupRole::VERSION = '0.052';
#ABSTRACT: Role for a group of atoms
use Moose::Role;
use Carp;
use Math::Trig;
use Math::Vector::Real;
use FileHandle;
use Scalar::Util 'reftype';
use List::Util qw(sum);

#use MooseX::Storage;
#with Storage( 'format' => 'JSON', 'io' => 'File', traits => ['OnlyWhenBuilt'] );

my $angste_debye = 4.80320;

has 'atoms' => (
    traits  => ['Array'],
    is      => 'ro',
    isa     => 'ArrayRef[HackaMol::Atom]',
    default => sub { [] },
    handles => {
        unshift_atoms => 'unshift',
        push_atoms    => 'push',
        select_atoms  => 'grep',
        map_atoms     => 'map',
        sort_atoms    => 'sort',
        get_atoms     => 'get',
        set_atoms     => 'set',
        insert_atoms  => 'insert',
        delete_atoms  => 'delete',
        all_atoms     => 'elements',
        count_atoms   => 'count',
        natoms        => 'count',
        clear_atoms   => 'clear',
        has_atoms     => 'count',
    },
    lazy => 1,
);

has 'is_constrained' => (
    is      => 'rw',
    isa     => 'Bool',
    lazy    => 1,
    default => 0,
);

has 'qcat_print' => (
    is      => 'rw',
    isa     => 'Bool',
    lazy    => 1,
    default => 0,
);

has 'info' => (
    is      => 'rw',
    isa     => 'Str',
    lazy    => 1,
    default => "",
);

    # private function used for each coordinate
    # translation of tcl function written by Justin Gullingsrud @ uiuc.edu
    # algorithm reference: Bevington
    # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tcl
    # Fit the points x to x = ai + b, i=0...N-1, and return the value of a
    # a = 12/( (N(N^2 - 1)) ) sum[ (i-(N-1)/2) * xi]
    my $xis = shift || die "expecting array_ref of cartesian coordinate [x y or z]";
    my $n = @$xis;
    my $sum = 0;
    my $d = ($n-1)/2;
    my $i = 0;
    $sum += ($i++ - $d)*$_ foreach @$xis;
    return $sum * 12 / ($n * ( $n * $n - 1)) ;
}

    my $self = shift;
    my $centered_flag = shift;
    my @mvrs = map {$_->xyz} $self->all_atoms;
    die "2 atoms needed for a centered_vector" unless @mvrs > 1;
    my @x = map { $_->[0] } @mvrs;
    my @y = map { $_->[1] } @mvrs;
    my @z = map { $_->[2] } @mvrs;
    my $mvr = V( map { _lsq_slope($_) } \@x,\@y,\@z);
    return $mvr->versor;
}


    # this should be rerun for each selection
    #10.1016/j.jmb.2015.09.024
    my $self = shift;
    unless ( $self->count_atoms > 1 ) {
        warn "calc_bfps> group not large enough\n";
        return;
    }
    my @atoms      = $self->all_atoms;
    my @bfacts     = map { $_->bfact } @atoms;
    my $bfact_mean = sum(@bfacts) / @bfacts;
    my $sd         = 0;
    $sd += ( $_ - $bfact_mean )**2 foreach @bfacts;
    unless ( $sd > 0 ) {
        warn "calc_bfps> no variance in the group bfactors\n";
        return;
    }
    my $bfact_std = sqrt( $sd / ( @bfacts - 1 ) );
    foreach my $atom (@atoms) {
        my $bfp = ( $atom->bfact - $bfact_mean ) / $bfact_std;
        $atom->bfp($bfp);
    }
    return map { $_->bfp } @atoms;
}

    my $self = shift;
    return ( V(0) ) unless ( $self->count_atoms );
    my @atoms   = $self->all_atoms;
    my @vectors = grep { defined } map { $_->get_coords( $_->t ) } @atoms;
    my @charges = grep { defined } map { $_->get_charges( $_->t ) } @atoms;
    my $dipole  = V( 0, 0, 0 );
    if ( $#vectors != $#charges ) {
        carp
          "build_dipole> mismatch number of coords and charges. all defined?";
        return $dipole;
    }
    $dipole += $vectors[$_] * $charges[$_] foreach 0 .. $#charges;
    return ($dipole);
}

    my $self = shift;
    return ( V(0) ) unless ( $self->count_atoms );
    my @atoms     = $self->all_atoms;
    my @m_vectors = map { $_->mass * $_->get_coords( $_->t ) } @atoms;
    my $com       = V( 0, 0, 0 );
    $com += $_ foreach @m_vectors;
    return ( $com / $self->total_mass );
}

    my $self = shift;
    return ( V(0) ) unless ( $self->count_atoms );
    my @atoms   = $self->all_atoms;
    my @vectors = map { $_->get_coords( $_->t ) } @atoms;
    my $center  = V( 0, 0, 0 );
    $center += $_ foreach @vectors;
    return ( $center / $self->count_atoms );
}

    my $self = shift;
    return ( V(0) ) unless ( $self->count_atoms );
    my @atoms     = $self->all_atoms;
    my @z_vectors = map { $_->Z * $_->get_coords( $_->t ) } @atoms;
    my $coz       = V( 0, 0, 0 );
    $coz += $_ foreach @z_vectors;
    return ( $coz / $self->total_Z );
}


    #set group time
    my $self = shift;
    my $t    = shift;
    $self->do_forall( 't', $t );
}

    my $self   = shift;
    my $method = shift;
    do { carp "doing nothing for all"; return } unless (@_);
    my @atoms = $self->all_atoms;
    $_->$method(@_) foreach @atoms;
}

    my $self = shift;
    return (0) unless ( $self->count_atoms );
    my @atoms   = $self->all_atoms;
    my @charges = map { $_->get_charges( $_->t ) } @atoms;
    my $sum     = 0;
    $sum += $_ foreach @charges;
    return ($sum);
}

    my $self = shift;
    return (0) unless ( $self->count_atoms );
    my @masses = map { $_->mass } $self->all_atoms;
    my $sum = 0;
    $sum += $_ foreach @masses;
    return ($sum);
}

    my $self = shift;
    return (0) unless ( $self->count_atoms );
    my @Zs = map { $_->Z } $self->all_atoms;
    my $sum = 0;
    $sum += $_ foreach @Zs;
    return ($sum);
}

    my $self = shift;
    return ( abs( $self->dipole ) * $angste_debye );
}


    # Called with no arguments.
    # Returns a hash with a count of unique atom symbols
    my $self   = shift;
    my $bin_hr = $self->bin_this('symbol');
    return ($bin_hr);
}

    my $self   = shift;
    my $bin_hr = $self->bin_atoms;
    return ( scalar( keys %{$bin_hr} ) );
}


    # return something like C4H10 sort in order of descending Z
    my $self   = shift;
    my $bin_hr = $self->bin_atoms;
    my $z_hr;
    $z_hr->{ $_->symbol } = $_->Z foreach $self->all_atoms;

    my @names = map {
        my $name = $_ . $bin_hr->{$_};
        $name =~ s/(\w+)1$/$1/;
        $name;    # substitue 1 away?
      }
      sort {
        $z_hr->{$b} <=> $z_hr->{$a}    # sort by Z!  see above...
      } keys %{$bin_hr};
    return join( '', @names );
}

    my $self = shift;
    my $tvec = shift or croak "pass MVR translation vector";
    my $tf   = shift;

    my @atoms = $self->all_atoms;
    do { carp "no atoms to translate"; return } unless (@atoms);
    $tf = $atoms[0]->t unless ( defined($tf) );

    foreach my $at (@atoms) {
        my $v = $at->xyz + $tvec;
        $at->set_coords( $tf, $v );
    }
}


    #rotate about origin. having origin allows rotation of subgroup
    #without having to translate everything.
    my $self = shift;
    my $rvec = shift or croak "pass MVR rotation vector";
    my $ang  = shift or croak "pass rotation angle";
    my $orig = shift or croak "pass MVR origin";
    my $tf   = shift;

    my @atoms = $self->all_atoms;
    my $t     = $atoms[0]->t;
    $tf = $t unless ( defined($tf) );
    $rvec = $rvec->versor;    #unit vector

    my @cor = map { $_->get_coords($t) - $orig } @atoms;
    my @rcor = $rvec->rotate_3d( deg2rad($ang), @cor );

    $atoms[$_]->set_coords( $tf, $rcor[$_] + $orig ) foreach 0 .. $#rcor;
}


# args:
#      1. rotation matrix (3x3): ar, each column (cx,cy,cz, below) is a Math::Vector::Real
#      2. translate vector, MVR
#               r' = x*cx + y*cy + z*cz + v_trans
#      3. t final, the final t location for transformed coordinates [defaults to current t]
    my $self  = shift;
    my $rmat  = shift;
    my $trns  = shift;
    my $tf    = shift;
    my @atoms = $self->all_atoms;
    my ( $cx, $cy, $cz ) = @{$rmat};

    my $t = $atoms[0]->t;
    $tf = $t unless ( defined($tf) );

    foreach my $atom (@atoms) {
        my $xyz = $atom->xyz;

        #my ($x,$y,$z) = @{$xyz};
        my $xr = $cx * $xyz;
        my $yr = $cy * $xyz;
        my $zr = $cz * $xyz;

        #my $xyz_new = $x*$cx + $y*$cy + $z*$cz + $trns;
        my $xyz_new = V( $xr, $yr, $zr ) + $trns;
        $atom->set_coords( $tf, $xyz_new );
    }

}

    my @atoms  = shift->all_atoms;
    my $offset = shift;
    $offset = 1 unless defined($offset);
    $atoms[$_]->{serial} = $_ + $offset foreach ( 0 .. $#atoms );
    return $offset;
}

    _print_ts( 'print_xyz', @_ );
}

    _print_ts( 'print_pdb', @_ );
}


    #use one sub for xyz_ts and pdb_ts writing
    my $print_method = shift;

    # two args: \@ts, optional filename
    my $self = shift;
    my $ts   = shift;
    unless ( defined($ts) ) {
        croak "must pass arrayref containing ts";
    }
    my @ts = @$ts;
    unless ( scalar(@ts) ) {
        croak "must pass array with atleast one t";
    }
    my $tmax = $self->tmax;
    my $nt = grep { $_ > $tmax } @ts;
    croak "$nt ts out of bounds" if $nt;

    my $tnow = $self->what_time;

    # take the first out of the loop to setup fh
    $self->gt( shift @ts );
    my $fh = $self->$print_method(@_);

    foreach my $t (@ts) {
        $self->gt($t);
        $fh = $self->$print_method($fh);
    }

    # return to original t
    $self->gt($tnow);
}


    #return hash{$_->method}++
    my $self   = shift;
    my $method = shift;

    return ( {} ) unless $self->count_atoms;

    my @atoms = $self->all_atoms;

    # just test the first one...
    croak "Atom does not do $method" unless $atoms[0]->can($method);

    my $bin;
    $bin->{$_}++ foreach ( map { $_->$method } @atoms );
    return ($bin);

}


    # still not the best implementation! what about atoms without coords?
    my $self = shift;
    my $tbin = $self->bin_this('count_coords');
    my @ts   = keys(%$tbin);
    croak "tmax differences within group" if ( scalar(@ts) > 1 );
    $ts[0] ? return $ts[0] - 1 : return 0;
}

    my $self = shift;
    my $tbin = $self->bin_this('t');
    my @ts   = keys(%$tbin);
    carp "what_time> t differences within group!!" if ( scalar(@ts) > 1 );
    return $ts[0];
}

    my $self              = shift;
    my $add_info_to_blank = shift;

    my $string;
    $string .= $self->count_atoms . "\n" unless $self->qcat_print;
    $string .= $add_info_to_blank if ( defined($add_info_to_blank) );
    $string .= "\n";

    foreach my $at ( $self->all_atoms ) {
        $string .= sprintf( "%3s %10.6f %10.6f %10.6f\n",
            $at->symbol, @{ $at->get_coords( $at->t ) } );
    }
    return $string;
}

    my $self = shift;
    my $fh   = _open_file_unless_fh(shift);

    print $fh $self->string_xyz;

    # my @atoms = $self->all_atoms;
    #print $fh $self->count_atoms . "\n\n" unless $self->qcat_print;
    #foreach my $at (@atoms) {
    #    printf $fh (
    #        "%3s %10.6f %10.6f %10.6f\n",
    #        $at->symbol, @{ $at->get_coords( $at->t ) }
    #    );
    #}

    return ($fh);    # returns filehandle for future writing

}

    my $self = shift;

    my $t     = $self->what_time;
    my @atoms = $self->all_atoms;

    my $string;
    $string .= sprintf( "MODEL       %2i\n", $t + 1 ) unless $self->qcat_print;

    my $atform =
      "%-6s%5i  %-3s%1s%3s%2s%4s%1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n";

    foreach my $at (@atoms) {

        # front pad one space if name length is < 4
        my $form = $atform;
        if ( length $at->name > 3 ) {
            $form =
      "%-6s%5i %4s%1s%3s%2s%4s%1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n";
        }
        $string .= sprintf(
            $form,
            (
                map { $at->$_ }
                  qw (
                  record_name
                  serial
                  name
                  altloc
                  resname
                  chain
                  resid
                  icode
                  )
            ),
            @{ $at->get_coords( $at->t ) },
            $at->occ,
            $at->bfact,
            $at->segid,
            $at->symbol,    # $at->charge
        );
    }
    $string .= "ENDMDL\n" unless $self->qcat_print;
    return $string;
}

    my $self = shift;
    my $fh   = _open_file_unless_fh(shift);

    print $fh $self->string_pdb;

#   my @atoms = $self->all_atoms;
#   printf $fh ( "MODEL       %2i\n", $atoms[0]->t + 1 ) unless $self->qcat_print;
#   my $atform = "%-6s%5i  %-3s%1s%3s %1s%4i%1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n";

#   foreach my $at (@atoms) {
#       # front pad one space if name length is < 4
#       my $form = $atform;
#       if (length $at->name > 3){
#         $form = "%-6s%5i %4s%1s%3s %1s%4i%1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s\n"
#       }
#       printf $fh (
#           $form,
#           (
#               map { $at->$_ }
#                 qw (
#                 record_name
#                 serial
#                 name
#                 altloc
#                 resname
#                 chain
#                 resid
#                 icode
#                 )
#           ),
#           @{ $at->get_coords( $at->t ) },
#           $at->occ,
#           $at->bfact,
#           $at->segid,
#           $at->symbol,    # $at->charge
#       );

    #   }
    #   print $fh "ENDMDL\n" unless $self->qcat_print;

    return ($fh);    # returns filehandle for future writing
}


    my $file = shift;    # could be file or filehandle

    my $fh = \*STDOUT;   # default to standard out
                         # if argument is passed, check if filehandle
    if ( defined($file) ) {
        if ( ref($file) ) {
            if ( reftype($file) eq "GLOB" ) {
                $fh = $file;
            }
            else {
                croak "trying write to reference that is not a GLOB";
            }
        }
        else {
            carp "overwrite $file" if ( -e $file );
            $fh = FileHandle->new(">$file");
        }
    }

    return ($fh);
}

no Moose::Role;

1;


=pod

=head1 NAME

HackaMol::Roles::AtomGroupRole - Role for a group of atoms

=head1 VERSION

version 0.052

=head1 SYNOPSIS

    use HackaMol::AtomGroup;
    use HackaMol::Atom;

    my $atom1 = HackaMol::Atom->new(
        name    => 'O1',
        coords  => [ V( 2.05274, 0.01959, -0.07701 ) ],
        Z       => 8,
    );

    my $atom2 = HackaMol::Atom->new(
        name    => 'H1',
        coords  => [ V( 1.08388, 0.02164, -0.12303 ) ],
        Z       => 1,
    );

    my $atom3 = HackaMol::Atom->new(
        name    => 'H2',
        coords  => [ V( 2.33092, 0.06098, -1.00332 ) ],
        Z       => 1,
    );

    $atom1->push_charges(-0.834);
    $_->push_charges(0.417) foreach ($atom1, $atom2);

    # instance of class that consumes the AtomGroupRole

    my $group = HackaMol::AtomGroup->new(atoms=> [$atom1,$atom2,$atom3]);

    print $group->count_atoms . "\n"; #3
    print $group->total_charge . "\n"; # 0
    print $group->total_mass . "\n";

    my @atoms = $group->all_atoms;

    print $group->dipole_moment . "\n";

    $group->do_forall('push_charges',0);
    $group->do_forall('push_coords',$group->COM);

    $group->gt(1); # same as $group->do_forall('t',1);

    print $group->dipole_moment . "\n";
    print $group->bin_atoms_name . "\n";
    print $group->unique_atoms . "\n";

    $group->translate(V(10,0,0));

    $group->rotate( V(1,0,0),
                         180,
                    V(0,0,0));

    $group->print_xyz ; #STDOUT

    my $fh = $group->print_xyz("hackagroup.xyz"); #returns filehandle
    $group->print_xyz($fh) foreach (1 .. 9);     # boring VMD movie with 10 frames

=head1 DESCRIPTION

The HackaMol AtomGroupRole class provides core methods and attributes for
consuming classes that use groups of atoms. The original implementation of
this role relied heavily on attributes, builders, and clearers.  Such an approach
naturally gives fast lookup tables, but the ability to change atoms and coordinates
made the role to difficult.  Such an approach may be pursued again (without changing
the API) in the future after the API has matured.  The AtomGroupRole calculates all
values for atoms using their own t attributes.

=head1 METHODS

=head2 do_for_all

pass method and arguments down to atoms in group

  $group->do_for_all('t',1); #sets t to 1 for all atoms

=head2 gt

integer argument. wraps do_for_all for setting time within group

  $group->gt(1);

=head2 dipole

no arguments. return dipole calculated from charges and coordinates as Math::Vector::Real object

=head2 COM

no arguments. return center of mass calculated from masses and coordinates as Math::Vector::Real object

=head2 COZ

no arguments. return center of nuclear charge calculated from Zs and coordinates as Math::Vector::Real object

=head2 total_charge

no arguments. return sum of atom charges.

=head2 total_mass

no arguments. return sum of atom masses.

=head2 total_Z

no arguments. return sum of Zs.

=head2 dipole_moment

no arguments. returns the norm of the dipole in debye (assuming charges in electrons, AKMA)

=head2 bin_atoms

Called with no arguments. Returns a hash with a count for each unique atom symbol.

=head2 count_unique_atoms

no arguments. returns the number of unique atoms

=head2 bin_atoms_name

no arguments. returns a string summary of the atoms in the group sorted by decreasing atomic number. For example; OH2 for water or O2H2 for peroxide.

=head2 tmax

return (count_coords-1) if > 0; return 0 otherwise; croaks if not all atoms share the same tmax.

=head2 translate

requires L<Math::Vector::Real> vector argument. Optional argument: integer tf.

Translates all atoms in group by the MVR vector.  Pass tf to the translate
method to store new coordinates in tf rather than atom->t.

=head2 rotate

requires Math::Vector::Real vector, an angle (in degrees), and a MVR vector
origin as arguments. Optional argument: integer tf.

Rotates all atoms in the group around the MVR vector. Pass tf to the translate
method to store new coordinates in tf rather than atom->t.

=head2 print_xyz

optional argument: filename or filehandle.  with no argument, prints xyz formatted output to STDOUT. pass
a filename and an xyz file with that name will be written or overwritten (with warning). pass filehandle
for continuous writing to an open filehandle.

=head2 print_xyz_ts

argument: array_ref containing the values of t to be used for printing.
optional argument: filename or filehandle for writing out to file. For example,

  $mol->print_xyz_ts([0 .. 3, 8, 4], 'fun.xyz');

will write the coordinates for all group atoms at t=0,1,2,3,8,4 to a file, in
that order.

=head2 print_pdb

same as print_xyz, but for pdb formatted output

=head2 print_pdb_ts

same as print_xyz_ts, but for pdb formatted output

=head2 bin_this

argument: Str , return hash_ref of binned $self->Str.

  $hash_ref{$_}++ foreach ( map {$_->$Str} $self->all_atoms );

=head2 what_time

returns the current setting of t by checking against all members of group.

=head2 fix_serial

argument, optional: Int, offset for resetting the serial number of atoms.
Returns the offset.

  $group->fix_serial(0); # serial starts from zero

=head2 centered_vector

calculates least squares fitted vector for the AtomGroup. Returns normalized Math::Vector::Real
object with origin V(0,0,0).

  $mvr = $group->centered_vector; # unit vector origin 0,0,0
  # place two mercury atoms along the vector to visualize the fit
  my $hg_1 = HackaMol::Atom->new(Z => 80, coords => [$group->center]);
  my $hg_2 = HackaMol::Atom->new(Z => 80, coords => [$group->center + $mvr]);

=head1 ARRAY METHODS

=head2 push_atoms, get_atoms, set_atoms, all_atoms, count_atoms, clear_atoms

ARRAY traits for the atoms attribute, respectively: push, get, set, elements, count, clear

=head2 push_atoms, unshift_atoms

push atom on to the end of the atoms array
  or
unshift_atoms on to the front of the array

  $group->push_atoms($atom1, $atom2, @otheratoms);
  $group->unshift_atoms($atom1, $atom2, @otheratoms); # maybe in reverse

=head2 all_atoms

returns array of all elements in atoms array

  print $_->symbol, "\n" foreach $group->all_atoms;

=head2 get_atoms

return element by index from atoms array

  print $group->get_atoms(1); # returns $atom2 from above

=head2 set_atoms

set atoms array by index

  $group->set_atoms(1, $atom1);

=head2 count_atoms

return number of atoms in group

  print $group->count_atoms;

=head2 clear_atoms

clears atoms array

=head1 ATTRIBUTES

=head2 atoms

isa ArrayRef[Atom] that is lazy with public ARRAY traits described in ARRAY_METHODS

=head2 qcat_print

isa Bool that has a lazy default value of 0.  if qcat_print, print all atoms coordinates in one go (no model breaks)

=head1 SEE ALSO

=over 4

=item *

L<HackaMol::AtomGroup>

=item *

L<HackaMol::Bond>

=item *

L<HackaMol::Angle>

=item *

L<HackaMol::Dihedral>

=back

=head1 AUTHOR

Demian Riccardi <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2017 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