DecoyStruct.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:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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/io/raw_data/DecoyStruct.hh
///
/// @brief silent input file reader for mini

#ifndef INCLUDED_core_io_raw_data_DecoyStruct_hh
#define INCLUDED_core_io_raw_data_DecoyStruct_hh

// mini headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

// AUTO-REMOVED #include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/chemical/VariantType.hh>
// AUTO-REMOVED #include <core/chemical/ChemicalManager.hh>

// AUTO-REMOVED #include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/conformation/ResidueFactory.hh>

#include <core/io/raw_data/RawStruct.hh>

#include <core/chemical/ResidueTypeSet.fwd.hh>

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

// Numeric headers
#include <numeric/xyzVector.hh>

// C++ Headers
// AUTO-REMOVED #include <vector>
#include <string>
#include <map>

#include <utility/vector1.hh>


namespace core {
namespace io {
namespace raw_data {

  class DecoyStruct : public RawStruct {
  public:

    // the constructor:
    DecoyStruct( Size const nres_in )
    {
      nres_        = nres_in;
      fullatom_    = false;
      resize( nres_in );
    }

    DecoyStruct()
    {
      nres_        = 0;
      fullatom_    = false;
      decoy_tag_   = "empty";
    }

    DecoyStruct(
      core::pose::Pose const& pose,
      std::string tag = "empty_tag",
      bool fa = false
    );

    // resize everything appropriately
    void resize(
      Size const nres_in
    );

    // destructor
    ~DecoyStruct() {}

    //DecoyStruct & operator= (DecoyStruct const & src);

    void fill_pose(
      core::pose::Pose & pose
    );

    void fill_pose(
      core::pose::Pose & pose,
      core::chemical::ResidueTypeSet const& residue_set
    );

    // fills the res array
    //void set_sequence(std::string const & sequence);

    virtual void print_conformation( std::ostream& output ) const;

    /// @brief calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this
    /// DecoyStruct and the C-alpha atoms from this DecoyStruct.
    virtual Real get_debug_rmsd();

    /// @brief data getters/setters
    bool fullatom() const {
      return fullatom_;
    }

    Real phi( unsigned int seqpos ) const {
      return phi_[seqpos];
    }

    Real psi( unsigned int seqpos ) const {
      return psi_[seqpos];
    }

    Real omega( unsigned int seqpos ) const {
      return omega_[seqpos];
    }

    char secstruct( unsigned int seqpos ) const {
      return secstruct_[seqpos];
    }

    utility::vector1< Real > chi( unsigned int seqpos ) const {
      return chi_[ seqpos ];
    }

    Vector coords( unsigned int seqpos ) const {
      return coords_[seqpos];
    }


    void fullatom( bool fullatom ) {
      fullatom_ = fullatom;
    }

    void phi( unsigned int seqpos, Real phi ) {
      phi_[seqpos] = phi;
    }

    void psi( unsigned int seqpos, Real psi ) {
      psi_[seqpos] = psi;
    }

    void omega( unsigned int seqpos, Real omega ) {
      omega_[seqpos] = omega;
    }

    void secstruct( unsigned int seqpos, char ss ) {
      secstruct_[seqpos] = ss;
    }

    void chi( unsigned int seqpos, utility::vector1< Real > chis ) {
      chi_[seqpos] = chis;
    }

    void coords( unsigned int seqpos, Vector coords ) {
      coords_[seqpos] = coords;
    }


  protected:
    bool fullatom_;

    utility::vector1< char > secstruct_;
    utility::vector1< Real > phi_;
    utility::vector1< Real > psi_;
    utility::vector1< Real > omega_;
    utility::vector1< utility::vector1< Real > > chi_;
    utility::vector1< Vector > coords_;

  }; // class DecoyStruct
} // namespace silent
} // namespace io
} // namespace core

#endif