AA.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @author Phil Bradley


#ifndef INCLUDED_core_chemical_AA_hh
#define INCLUDED_core_chemical_AA_hh


// Unit headers

// Project headers

// Utility headers

// C++ headers
// Commented by inclean daemon #include <string>

// AUTO-REMOVED #include <basic/Tracer.fwd.hh>

#include <ostream>



namespace core {
namespace chemical {

// temporary -- probably an enum?
///////////////////////////////////////////////////////////////////////////
/// @brief enumeration for amino acids and nucleotides types with the total
/// number as num_aa_types
///////////////////////////////////////////////////////////////////////////
// BUT DONT CODE TO THESE AS INTS!!!!!!
enum AA {
  // protein 1-20
  aa_ala = 1,
  aa_cys,
  aa_asp,
  aa_glu,
  aa_phe,
  aa_gly,
  aa_his,
  aa_ile,
  aa_lys,
  aa_leu,
  aa_met,
  aa_asn,
  aa_pro,
  aa_gln,
  aa_arg,
  aa_ser,
  aa_thr,
  aa_val,
  aa_trp,
  aa_tyr,
  num_canonical_aas = aa_tyr,
  // dna 21-24
  na_ade,
  first_DNA_aa = na_ade,
  na_cyt,
  na_gua,
  na_thy,
  last_DNA_aa = na_thy,
  // rna 25-28
  na_rgu,
  na_rad,
  na_rcy,
  na_ura,
  // virtual
  aa_vrt,

  // unknown
  aa_unk,
  num_aa_types = aa_unk //keep this guy last
};

//////////////////////////////////////////////////////////
/// @brief give a AA string name and return its enum type
//////////////////////////////////////////////////////////
AA
aa_from_name( std::string const & name );

///////////////////////////////////////////////////////
/// @brief give a enum type and return the string name
///////////////////////////////////////////////////////
std::string
name_from_aa( AA  aa );

///////////////////////////////////////////////////////
/// @brief give a enum type and return the string name
///////////////////////////////////////////////////////
char
oneletter_code_from_aa( AA aa );

///////////////////////////////////////////////////////////
/// @brief give a 1 letter code and return the string name
///////////////////////////////////////////////////////////
AA
aa_from_oneletter_code( char onelettercode );

bool
oneletter_code_specifies_aa( char onelettercode );

/// @brief input operator for AA enum type
std::istream & operator >>( std::istream & is, AA & aa );
/// @brief output operator for AA enum type
std::ostream & operator <<( std::ostream & os, AA const & aa );


} // chemical
} // core

#endif