VallResidue.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   core/fragment/picking_old/vall/VallResidue.hh
/// @brief  class for managing a line of the Vall fragment library
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_VallResidue_hh
#define INCLUDED_core_fragment_picking_old_vall_VallResidue_hh


// unit headers
#include <core/fragment/picking_old/vall/VallResidue.fwd.hh>

// type headers
#include <core/types.hh>

// project headers
#include <core/chemical/AA.hh>
#include <core/fragment/BBTorsionSRFD.hh>

// utility headers
#include <utility/pointer/owning_ptr.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

// C++ headers
#include <iostream>

#include <utility/vector1.hh>




namespace core {
namespace fragment {
namespace picking_old {
namespace vall {


/// @brief class for managing a line of the Vall fragment library
class VallResidue {


public: // typedefs


  typedef core::Size Size;
  typedef core::Real Real;
  typedef std::string String;

  typedef core::fragment::BBTorsionSRFD BBTorsionSRFD;
  typedef core::fragment::BBTorsionSRFDOP BBTorsionSRFDOP;


public: // construct/destruct


  /// @brief default constructor
  VallResidue();


  /// @brief string constructor
  VallResidue( String const & line );


  /// @brief copy constructor
  VallResidue( VallResidue const & rval );


  /// @brief default destructor
  ~VallResidue();


public: // copy assignment


  /// @brief copy assignment
  VallResidue & operator =( VallResidue const & rval );


public: // conversion


  /// @brief build a BBTorsionSRFD of the given type from this page
  /// @param[in] srfd_type BBTorsionSRFD::create() will be called from this object.
  /// @return A BBTorsionSRFD of the given type initialized with the backbone
  ///  torsion information from this page.
  BBTorsionSRFDOP bbtorsion_srfd( BBTorsionSRFD const & srfd_type = BBTorsionSRFD() ) const;


public: // accessors


  /// @brief id of fragment source (e.g. pdb name)
  inline
  String const & id() const {
    return id_;
  }


  /// @brief one letter amino acid code
  inline
  char aa() const {
    return aa_;
  }


  /// @brief one letter secondary structure code
  inline
  char ss() const {
    return ss_;
  }


  /// @brief residue sequence number in source
  inline
  Size resi() const {
    return resi_;
  }


  /// @brief x-coordinate of C-alpha
  inline
  Real x() const {
    return x_;
  }


  /// @brief y-coordinate of C-alpha
  inline
  Real y() const {
    return y_;
  }


  /// @brief z-coordinate of C-alpha
  inline
  Real z() const {
    return z_;
  }


  /// @brief phi backbone torsion in degrees
  inline
  Real phi() const {
    return phi_;
  }


  /// @brief psi backbone torsion in degrees
  inline
  Real psi() const {
    return psi_;
  }


  /// @brief omega backbone torsion in degrees
  inline
  Real omega() const {
    return omega_;
  }


  /// @brief per amino acid profile data
  inline
  utility::vector1< Real > const & profile() const {
    return profile_;
  }


  /// @brief stores the 1-based indexing for accessing this residue
  ///  via VallSection::operator []
  inline
  Size position_index() const {
    return position_index_;
  }


  /// @brief stores the 1-based indexing for accessing the VallSection
  ///  this residue is located in via VallLibrary::operator []
  inline
  Size section_index() const {
    return section_index_;
  }


public: // mutators


  /// @brief id of fragment source (e.g. pdb name)
  inline
  void id( String const & s ) {
    id_ = s;
  }


  /// @brief one letter amino acid code
  inline
  void aa( char const c ) {
    aa_ = c;
  }


  /// @brief one letter secondary structure code
  inline
  void ss( char const c ) {
    ss_ = c;
  }


  /// @brief residue sequence number in source
  inline
  void resi( Size const i ) {
    resi_ = i;
  }


  /// @brief x-coordinate of C-alpha
  inline
  void x( Real const val ) {
    x_ = val;
  }


  /// @brief y-coordinate of C-alpha
  inline
  void y( Real const val ) {
    y_ = val;
  }


  /// @brief z-coordinate of C-alpha
  inline
  void z( Real const val ) {
    z_ = val;
  }


  /// @brief phi backbone torsion in degrees
  inline
  void phi( Real const val ) {
    phi_ = val;
  }


  /// @brief psi backbone torsion in degrees
  inline
  void psi( Real const val ) {
    psi_ = val;
  }


  /// @brief omega backbone torsion in degrees
  inline
  void omega( Real const val ) {
    omega_ = val;
  }


  /// @brief per amino acid profile data
  inline
  void profile( utility::vector1< Real > const & v ) {
    profile_ = v;
  }


  /// @brief stores the 1-based indexing for accessing this residue
  ///  via VallSection::operator []
  inline
  void position_index( Size const idx ) {
    position_index_ = idx;
  }


  /// @brief stores the 1-based indexing for accessing the VallSection
  ///  this residue is located in via VallLibrary::operator []
  inline
  void section_index( Size const idx ) {
    section_index_ = idx;
  }


public: // query


  /// @brief has profile info?
  inline
  bool has_profile() const {
    return profile_.size() > 0;
  }


public: // methods


  /// @brief fill internal data from string
  void fill_from_string( String const & line );


private: // static methods


  /// @brief return a vector specifying the order of profile data in Vall
  static utility::vector1< core::chemical::AA > order_vector();


  /// @brief return a formatting string for fill_from_string() dependent
  ///  upon actual type of core::Real and core::Size
  /// @remarks This is necessary for sscanf; wrong type can give wrong
  ///  input.
  static String format_string();


private: // data


  /// @brief id of fragment source (e.g. pdb name)
  String id_;


  /// @brief one letter amino acid code
  char aa_;


  /// @brief one letter secondary structure code
  char ss_;


  /// @brief residue sequence number in source
  Size resi_;


  /// @brief x-coordinate of C-alpha
  Real x_;


  /// @brief y-coordinate of C-alpha
  Real y_;


  /// @brief z-coordinate of C-alpha
  Real z_;


  /// @brief phi backbone torsion in degrees
  Real phi_;


  /// @brief psi backbone torsion in degrees
  Real psi_;


  /// @brief omega backbone torsion in degrees
  Real omega_;


  /// @brief per amino acid profile data
  utility::vector1< Real > profile_;


  /// @brief stores the 1-based indexing for accessing this residue
  ///  via VallSection::operator []
  Size position_index_;


  /// @brief stores the 1-based indexing for accessing the VallSection
  ///  this residue is located in via VallLibrary::operator []
  Size section_index_;


private: // static data


  /// @brief order of amino acid profile data in Vall
  static utility::vector1< core::chemical::AA > order_;


  /// @brief formatting string for fill_from_string()
  static String format_;


};


/// @brief wrapper for a collection of VallResidue
class VallResidues : public utility::vector1< VallResidue > {


public: // typedefs


  /// @brief Page typedef required to satisfy concept
  typedef VallResidue Page;


};


} // vall
} // picking_old
} // fragment
} // core


#endif /* INCLUDED_core_fragment_picking_old_vall_VallResidue_HH */