NAME

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

VERSION

version 0.039

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; # 

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.

METHODS

read_file_atoms

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

returns a list of HackaMol::Atom objects

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

ATTRIBUTES

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.

SEE ALSO

• HackaMol

• HackaMol::Roles::ReadXyzRole

• HackaMol::Roles::ReadPdbRole

• HackaMol::Roles::ReadPdbqtRole

• HackaMol::Roles::ReadZmatRole

• HackaMol::Atom

• HackaMol::Molecule

CONSUMES

• HackaMol::Roles::NERFRole

• HackaMol::Roles::ReadPdbRole

• HackaMol::Roles::ReadPdbqtRole

• HackaMol::Roles::ReadXyzRole

• HackaMol::Roles::ReadYAMLRole

• HackaMol::Roles::ReadYAMLRole

• HackaMol::Roles::ReadZmatRole

AUTHOR

Demian Riccardi <demianriccardi@gmail.com>

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.