DesignContrast.hh

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// (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
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// (C) 199x-2008 University of Washington
// (C) 199x-2008 University of California Santa Cruz
// (C) 199x-2008 University of California San Francisco
// (C) 199x-2008 Johns Hopkins University
// (C) 199x-2008 University of North Carolina, Chapel Hill
// (C) 199x-2008 Vanderbilt University

/// @file   core/io/sequence_comparation/DesignContrast.hh
///
/// @brief
/// @author Yi Liu

#ifndef INCLUDED_core_io_sequence_comparation_DesignContrast_hh
#define INCLUDED_core_io_sequence_comparation_DesignContrast_hh

// Unit headers
#include <core/io/sequence_comparation/DesignContrast.fwd.hh>

// mini headers
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/pose/util.hh>

// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/file/FileName.hh>
// AUTO-REMOVED #include <utility/io/izstream.hh>

#include <utility/vector1.hh>



namespace core {
namespace io {
namespace sequence_comparation {

using utility::file::FileName;
using utility::vector1;
/// @brief DesignContrast contains information for comparing the native protein sequence to
/// designed protein sequence. And output the compare resultes to a special formated file which
/// can be used for statistics calculations

  class DesignContrast {
  public :
    /// @brief default constructor
    DesignContrast  (){ }

    // @brief copy constructor
    DesignContrast (DesignContrast const & dc);

    /// @brief default de-constructor
    virtual ~DesignContrast(){
    clear();
    }
    /// @brief Set number of neighbors for all residues in pose
    void setNeighbors(pose::Pose & pose);

    /// @brief Get number of neighbors for all residues in pose
    vector1<int> & getNeighbors();
    vector1<int> const & getNeighbors() const;

    /// @brief Set secondary structure for all residues in pose
    void setSecStruct(pose::Pose & pose);

    /// @brief Get secondary structure for all residues in pose
    vector1<std::string> & getSecStruct();
    vector1<std::string> const & getSecStruct() const;

    /// @brief Get pdb file names from the pdb list files.
    void setNames (); // vector1<std::string> & pdb_file_names ); the pdb_file_names is a private member

    ///
    vector1<FileName> & getPdbNames();
    vector1<FileName> const & getPdbNames() const;

    vector1<FileName> & getListNames();
    vector1<FileName> const & getListNames() const;

    void setPdbCodes();

    vector1<std::string> & getPdbCodes();
    vector1<std::string> const & getPdbCodes() const;

    /// @brief this function will output the sequence comparing result between native pose and designed pose
    void output_sqc_file (
                          pose::Pose & native_pose,
                          pose::Pose & decoy_pose,
                          std::string const & single_code,
                          std::ofstream & sqc
                          );

    /// @brief clear function to clear all datas in this class.
    void clear();

  private:
    vector1<FileName> list_file_names_;
    //vector1<std::string> pdb_file_names_;
    vector1<FileName> pdb_file_names_;
    vector1<int> nneighbs_;
    vector1<std::string> secstructs_;
    vector1<std::string> pdb_codes_;
  };
} // namespace sequence_comparation
} // namespace io
} // namespace core

#endif //INCLUDED_core_io_sequence_comparation_DesignContrast_HH