File Coverage

blib/lib/HackaMol/Roles/MolReadRole.pm

Criterion	Covered	Total	%
statement	52	72	72.2
branch	18	34	52.9
condition			n/a
subroutine	12	13	92.3
pod	2	4	50.0
total	84	123	68.2

package HackaMol::Roles::MolReadRole;
$HackaMol::Roles::MolReadRole::VERSION = '0.051';
# ABSTRACT: Read files with molecular information
use Moose::Role;
use Carp;
use Math::Vector::Real;
use HackaMol::PeriodicTable qw(%KNOWN_NAMES);
use FileHandle;
use YAML::XS qw(LoadFile);
use HackaMol::Atom;    #add the code,the Role may better to understand

with qw(
        HackaMol::Roles::ReadYAMLRole
        HackaMol::Roles::ReadZmatRole
        HackaMol::Roles::ReadPdbRole
        HackaMol::Roles::ReadPdbxRole
        HackaMol::Roles::ReadPdbqtRole
        HackaMol::Roles::ReadXyzRole
);

has 'hush_read' => (
    is      => 'rw',
    isa     => 'Int',
    lazy    => 1,
    default => 0,
);


sub read_string_atoms {
    my $self   = shift;
    my $string = shift;
    my $type   = shift or croak "must pass format: xyz, pdb, cif, pdbqt, zmat, yaml";

    open (my $fh, '<', \$string) or croak "unable to open string";

    my $atoms;

    if ( $type eq 'pdb' ) {
        ($atoms) = $self->read_pdb_atoms($fh);
    }
    elsif ( $type eq 'pdbqt') {
        $atoms = $self->read_pdbqt_atoms($fh);
    }
    elsif ( $type eq 'xyz') {
        $atoms = $self->read_xyz_atoms($fh);
    }
    elsif ( $type eq 'zmat') {
        $atoms = $self->read_zmat_atoms($fh);
    }
    elsif ( $type eq 'cif') {
        $atoms = $self->read_cif_atoms($fh);
    }
    elsif ( $type eq 'yaml') {
        $fh->close;
        $fh = Loadtype($type);
        $atoms = $self->read_yaml_atoms($fh);
    }
    else {
        croak "$type format not supported";
    }
    return (@{$atoms});
}

sub read_file_pdb_parts{
    my $self = shift;
    my $file = shift;

    my $fh   = FileHandle->new("<$file") or croak "unable to open $file";
    return $self->read_pdb_parts($fh);
}

sub read_file_cif_parts {
    # temporary, this is getting out of hand!
    my $self = shift;
    my $file = shift;

    my $fh   = FileHandle->new("<$file") or croak "unable to open $file";
    my $info = $self->read_cif_info($fh);
    my @models = $self->read_cif_atoms($fh);
    #$info = $self->read_cif_info($fh,$info);
    my @mols = map {
        HackaMol::Molecule->new(
          name => "model." . $_->[0]->model_num,
          atoms => $_
        ) } @models;
    return ($info, \@mols);
}

sub read_file_atoms {
    my $self = shift;
    my $file = shift;

    my $fh   = FileHandle->new("<$file") or croak "unable to open $file";

    my $atoms;

    if ( $file =~ m/\.pdb$/ ) {
        ($atoms) = $self->read_pdb_atoms($fh);
    }
    elsif ( $file =~ m/\.pdbqt$/ ) {
        $atoms = $self->read_pdbqt_atoms($fh);
    }
    elsif ( $file =~ m/\.cif$/ ) {
        $atoms = $self->read_cif_atoms($fh);
    }
    elsif ( $file =~ m/\.xyz$/ ) {
        $atoms = $self->read_xyz_atoms($fh);
    }
    elsif ( $file =~ m/\.zmat$/ ) {
        $atoms = $self->read_zmat_atoms($fh);
    }
    elsif ( $file =~ m/\.yaml$/) {
        $fh->close;
        $fh = LoadFile($file);
        $atoms = $self->read_yaml_atoms($fh);
    }
    else {
        croak "$file format not supported";
    }
    return (@{$atoms});
}

no Moose::Role;

1;

__END__

=pod

=head1 NAME

HackaMol::Roles::MolReadRole - Read files with molecular information

=head1 VERSION

version 0.051

=head1 SYNOPSIS

   use HackaMol;

   my $hack   = HackaMol->new( name => "hackitup" );

   # build array of carbon atoms from pdb [xyz,pdbqt] file
   my @carbons  = grep {
                        $_->symbol eq "C"
                       } $hack->read_file_atoms("t/lib/1L2Y.pdb");

   my $Cmol     = HackaMol::Molecule->new(
                        name => "carbonprotein",
                        atoms => [ @carbons ]
                  );

   $Cmol->print_pdb;
   $Cmol->print_xyz;

   # build molecule from xyz [pdb,pdbqt] file
   my $mol    = $hack->read_file_mol("some.xyz");
   $mol->print_pdb; #

=head1 DESCRIPTION

The HackaMol::Role::MolReadRole role provides methods for reading common structural files.  Currently,
pdb, pdbqt, Z-matrix, and xyz are provided.  The methods are all provided in separate roles.  Adding
additional formats is straightforward:

    1. Add a Role that parses the file and returns a list of HackaMol::Atoms.

    2. Add the code here to consume the role and call the method based on the file ending.

=head1 METHODS

=head2 read_file_atoms

one argument: the name of a file (.xyz, .pdb, .pdbqt, .zmat)

returns a list of HackaMol::Atom objects

=head2 read_string_atoms

two arguments: 1. a string with coordinates properly formatted; 2. format (xyz, pdb, pdbqt, zmat, yaml)

returns a list of HackaMol::Atom objects

=head1 ATTRIBUTES

=head2 hush_read

isa Int that is lazy (default 0). $hack->hush_read(1) will quiet some warnings that may be ignored under some instances.
$hack->hush_read(-1) will increase info printed out for some warnings.

=head1 SEE ALSO

=over 4

=item *

L<HackaMol>

=item *

L<HackaMol::Roles::ReadXyzRole>

=item *

L<HackaMol::Roles::ReadPdbRole>

=item *

L<HackaMol::Roles::ReadPdbqtRole>

=item *

L<HackaMol::Roles::ReadZmatRole>

=item *

L<HackaMol::Atom>

=item *

L<HackaMol::Molecule>

=back

=head1 CONSUMES

=over 4

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

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

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

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

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

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

=item * L<HackaMol::Roles::ReadYAMLRole|HackaMol::Roles::ReadZmatRole|HackaMol::Roles::ReadPdbRole|HackaMol::Roles::ReadPdbxRole|HackaMol::Roles::ReadPdbqtRole|HackaMol::Roles::ReadXyzRole>

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

=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