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

#ifndef INCLUDED_protocols_frag_picker_VallResidue_hh
#define INCLUDED_protocols_frag_picker_VallResidue_hh

// unit headers
#include <protocols/frag_picker/VallResidue.fwd.hh>

// project headers
#include <protocols/frag_picker/ContactTypes.hh>

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

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

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

// C++ headers
#include <iostream>
#include <map>

//Auto Headers
#include <core/fragment/BBTorsionSRFD.fwd.hh>
#include <utility/vector1_bool.hh>


namespace protocols {
namespace frag_picker {

/// @brief class for managing a line of the Vall fragment library
class VallResidue: public utility::pointer::ReferenceCount {

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
  virtual ~VallResidue();

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

public:
  /// @brief build a BBTorsionSRFD from this page
  BBTorsionSRFDOP bbtorsion_srfd() const;

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

  /// @brief sets the key id
  void key(Size key) { key_ = key; }

  /// @brief sets the key id
  Size key() { return key_; }

  /// @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 one letter secondary structure STR code
  inline
  char ss_str() const {
    return ss_str_;
  }

  /// @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 x-coordinate of C-beta
  inline Real cbx() const {
    return cbx_;
  }

  /// @brief y-coordinate of C-beta
  inline Real cby() const {
    return cby_;
  }

  /// @brief z-coordinate of C-beta
  inline Real cbz() const {
    return cbz_;
  }

  /// @brief x-coordinate of centroid
  inline Real cenx() const {
    return cenx_;
  }

  /// @brief y-coordinate of centroid
  inline Real ceny() const {
    return ceny_;
  }

  /// @brief z-coordinate of centroid
  inline Real cenz() const {
    return cenz_;
  }

  /// @brief solvent accessible area
  inline Real sa() const {
    return sa_;
  }

  /// @brief solvent accessible area normalized
  inline Real sa_norm() const {
    return sa_norm_;
  }

  /// @brief phi backbone torsion in degrees from DSSP
  inline Real dssp_phi() const {
    return dssp_phi_;
  }

  /// @brief psi backbone torsion in degrees from DSSP
  inline Real dssp_psi() const {
    return dssp_psi_;
  }

  /// @brief all-atom residue depth
  inline Real depth() const {
    return all_atom_residue_depth_;
  }

  /// @brief number of alignments
  inline Size nali() const {
    return nali_;
  }

  /// @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 b factor average for backbone
  inline Real bF() const {
    return bF_;
  }

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

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

  /// @brief secondary chemical shifts
  inline utility::vector1<Real> const & secondary_shifts() {
    return sec_shift_data_;
  }

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

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

  /// @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 one letter secondary structure STR code
  inline
  void ss_str(char const c) {
    ss_str_ = c;
  }

  inline
  void set_ss_from_str() {
    switch(ss_str_) {
      case 'H':
        ss_ = 'H';
        break;
      case 'G':
        ss_ = 'H';
        break;
      case 'I':
        ss_ = 'H';
        break;
      case 'A':
        ss_ = 'E';
        break;
      case 'E':
        ss_ = 'E';
        break;
      case 'M':
        ss_ = 'E';
        break;
      case 'P':
        ss_ = 'E';
        break;
      case 'Q':
        ss_ = 'E';
        break;
      case 'Z':
        ss_ = 'E';
        break;
      case 'B':
        ss_ = 'E';
        break;
      default:
        ss_ = 'L';
    }
  }

  /// @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 x-coordinate of C-beta
  inline
  void cbx(Real const val) {
    cbx_ = val;
  }

  /// @brief y-coordinate of C-beta
  inline
  void cby(Real const val) {
    cby_ = val;
  }

  /// @brief z-coordinate of C-beta
  inline
  void cbz(Real const val) {
    cbz_ = val;
  }

  /// @brief x-coordinate of centroid
  inline
  void cenx(Real const val) {
    cenx_ = val;
  }

  /// @brief y-coordinate of centroid
  inline
  void ceny(Real const val) {
    ceny_ = val;
  }

  /// @brief z-coordinate of centroid
  inline
  void cenz(Real const val) {
    cenz_ = val;
  }


  /// @brief solvent accessible area
  inline
  void sa(Real const val) {
    sa_ = val;
  }

  /// @brief number of alignments
  inline
  void nali(Size const val) {
    nali_ = val;
  }

  /// @brief all-atom residue depth
  inline
  void depth(Real const depth) {
    all_atom_residue_depth_ = depth;
  }

  /// @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 b factor average for backbone
  inline
  void bF(Real const val) {
    bF_ = val;
  }

  /// @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;
  }

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

  inline
  bool has_chemical_shifts() const {
    return sec_shift_data_.size() > 0;
  }

public:
  // methods

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

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

  /// @brief fill internal data from string
  void fill_from_string_version1(String const & line);

  void fill_from_string_residue_depth_version1(String const & line);

  Real distance_squared( VallResidueCOP r );

  Real distance_squared_cb( VallResidueCOP r );

  Real distance_squared_cen( VallResidueCOP r );

  Real distance_squared( VallResidueCOP r, ContactType const & type );

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();
  /// @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_cs();

  /// @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_version1();

  static String format_string_residue_depth_version1();

private:
  // data

  /// @brief integer key for a residue is simply the line number in a vall file
  Size key_;

  /// @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 (3 letter alphabet)
  char ss_;

  /// @brief one letter secondary structure code (STR alphabet - Karplus et. al.)
  char ss_str_;

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

  /// @brief b factor average for backbone
  Real bF_;

  /// @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 x-coordinate of C-beta
  Real cbx_;

  /// @brief y-coordinate of C-beta
  Real cby_;

  /// @brief z-coordinate of C-beta
  Real cbz_;

  /// @brief x-coordinate of centroid
  Real cenx_;

  /// @brief y-coordinate of centroid
  Real ceny_;

  /// @brief z-coordinate of centroid
  Real cenz_;

  /// @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 solvent accessible area
  Real sa_;

  /// @brief normalized solvent accessible area
  Real sa_norm_;

  /// @brief phi backbone torsion in degrees from DSSP program
  Real dssp_phi_;

  /// @brief psi backbone torsion in degrees from DSSP program
  Real dssp_psi_;

  /// @brief number of alignments used for profile
  Size nali_;

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

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

  utility::vector1<Real> sec_shift_data_;

  /// @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_;

  Real all_atom_residue_depth_;

private:
  // static data

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

};

} // frag_picker
} // protocols


#endif /* INCLUDED_protocols_frag_picker_VallResidue_HH */