AntibodyClass.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
/// @brief
/// @author Aroop Sircar

#ifndef INCLUDED_protocols_antibody_AntibodyClass_hh
#define INCLUDED_protocols_antibody_AntibodyClass_hh

// Rosetta Headers
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <protocols/loops/Loops.hh>
#include <utility/vector1.hh>

// C++ Headers

// Utility Headers

///////////////////////////////////////////////////////////////////////////////
namespace protocols {
  namespace antibody {

    /// antibody definition
    class Antibody {

    public:
      /// default constructor
      Antibody();

      /// constructor with arguments
      Antibody( core::pose::Pose& pose_in );
      Antibody( core::pose::Pose& pose_in, bool camelid );
      Antibody( core::pose::Pose& pose_in, std::string cdr_name );

      void set_defaults();

      void set_Fv( core::pose::Pose& pose_in );

      void set_Fv( core::pose::Pose& pose_in, bool camelid );

      void populate_all_cdrs();

      void all_cdr_fold_tree();

      /// align current Fv to native.Fv
      void align_to_native( antibody::Antibody & native );

      core::Size cdrl_[4][3];
      core::Size cdrh_[4][3];
      core::Size lfr_[8][3];
      core::Size hfr_[7][3];

      // Start coordinates of active loop
      core::Size current_start;
      // End coordinates of active loop
      core::Size current_end;

      // Pose containing antibody variable region, Fv
      core::pose::Pose Fv;

      bool kinked_;
      bool extended_;
      utility::vector1< char > Fv_sequence_;

      loops::Loops all_cdr_loops;

      core::kinematics::MoveMap ab_movemap;

    private:

      core::Size cdr_h3_cut_;
      bool camelid_;

      void detect_CDR_H3_stem_type();
      void detect_camelid_CDR_H3_stem_type();
      void detect_regular_CDR_H3_stem_type();
      void update_sequence();
    };


  } //namespace antibody
} //namespace protocols


#endif //INCLUDED_protocols_loops_AntibodyClass_HH