VIP_Mover.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.

#ifndef INCLUDED_protocols_vip_VIP_Mover_HH
#define INCLUDED_protocols_vip_VIP_Mover_HH

#include <protocols/vip/VIP_Report.hh>

namespace protocols {
namespace vip {

class VIP_Mover
{

                core::pose::Pose initial_pose;
    core::pose::Pose cavity_pose;
    core::pose::Pose final_pose;
    utility::vector1<core::conformation::ResidueOP> temp_residues;
    utility::vector1<core::Size> temp_positions;
    utility::vector1<core::Real> temp_energies;
    utility::vector1<core::conformation::ResidueOP> favorable_residues;
    utility::vector1<core::Size> favorable_positions;
    utility::vector1<core::Real> favorable_energies;
    core::Size number_cavities;
    utility::vector1<core::Size> cavity_balls;
    utility::vector1<std::string> favorable_mutations;
    utility::vector1<core::Size> void_neighbors;
    utility::vector1<core::Size> void_mutatables;
    core::Real final_energy;

    utility::vector1<core::Size> excluded_positions;

  public:
    VIP_Mover();
    VIP_Mover(
                        core::pose::Pose,
                        core::pose::Pose,
                        core::pose::Pose,
                        utility::vector1<core::conformation::ResidueOP>,
                        utility::vector1<core::Size>,
                        utility::vector1<core::Real>,
                        utility::vector1<core::conformation::ResidueOP>,
                        utility::vector1<core::Size>,
                        utility::vector1<core::Real>,
                        core::Size,
                        utility::vector1<core::Size>,
                        utility::vector1<std::string>,
                        utility::vector1<core::Size>,
                        utility::vector1<core::Size>,
      core::Real);
    virtual ~VIP_Mover();

    void set_initial_pose( core::pose::Pose );
    void minimize_conformation();
    void compute_number_cavities();
    void get_cavity_positions();
    void apply_holes();
    void dump_pdb_to_file( core::pose::Pose &, std::string );
    void get_neighbors();
    void try_point_mutants();
    void relax_favorable_poses();
    void cull_mutatable_residues();
    void sort_fill_energies();
    core::Real get_cav_approx( core::Size );
    // Undefined, commenting out to fix PyRosetta build  void print_favorable_mutations();
    void skip_relax();
    void sort_relaxed_poses();
    void print_pack_report();
    void print_relax_report();
    void nook_finder();
    void cranny_packer();

    void set_excluded_positions();

    core::Real get_final_energy(){
      return final_energy;}
    core::pose::Pose get_final_pose(){
      return final_pose;}
    void apply();


};

bool are_seqs_different( core::pose::Pose & p1, core::pose::Pose & p2 );

}}
#endif