CentroidRelax.hh

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/// @file protocols/relax/CentroidRelax.hh
/// @brief Centroid-based relax, using Frank Dimaio's updated centroid statistics
/// @author Jared Adolf-Bryfogle (jadolfbr@gmail.com)

#ifndef INCLUDED_protocols_relax_CENTROIDRELAX_HH
#define INCLUDED_protocols_relax_CENTROIDRELAX_HH


//Core Headers
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/kinematics/MoveMap.hh>

//Protocol Headers
#include <protocols/relax/RelaxProtocolBase.hh>
#include <protocols/simple_moves/ReturnSidechainMover.hh>
#include <protocols/moves/Mover.hh>

//Utility Headers
#include <utility/vector1.hh>

namespace protocols{
    namespace relax{
        using namespace core::scoring;
        using namespace protocols::simple_moves;
        using namespace core::kinematics;
        using namespace core::pack::task;
        using core::Size;
        using std::string;
        using core::Real;
        using core::pose::Pose;
        using utility::vector1;
           
///@brief Relax a pose using Frank Dimaio's smooth centroid statistics.
///Currently under optimization.
///
///@details Minimize a centroid representation of a pose. Ramp VDW/Rama or both.  
///
///May tweak structure by up to ~2.5 A without constraints.  
///Use custom constraints or coordinate constraints through relax options for best results.
///Using starting coordinate constraints, structure is tweaked by ~.3/.4 A
///Use increased VDW radii option for bb to improve bb-geometry when not using constraints
///
///
class CentroidRelax : public RelaxProtocolBase {
public:
    CentroidRelax();
    CentroidRelax(MoveMapOP mm);
    CentroidRelax(MoveMapOP mm, ScoreFunctionOP cen_scorefxn_in);
        
    //Specific functions for Mover...
    virtual ~CentroidRelax();
    
    virtual string get_name() const;

    virtual protocols::moves::MoverOP clone() const;
    
    void set_defaults();
    
    void set_rounds(Size rounds);
    
    ///@brief use larger VDW radii for atoms - bb for now - default True (Courtesy of Frank Dimaio)
    void set_use_increased_vdw_radii(bool use);
    
    ///@brief Sets to use Rama2b instead of Rama - default True
    void set_use_rama2b(bool use);
    
    ///@brief Ramp Rama according to centroid relax parameters
    void set_ramp_rama(bool use);
    
    ///@brief Ramp VDW according to centroid relax parameters
    void set_ramp_vdw(bool use);
    
    ///@brief Sets main scorefunction used for centroid minimization.
    void set_score_function(ScoreFunctionOP cen_score);
    
    ///@brief Sets fullatom scorefunction - only used for scoring the full atom pose before and after protocol.
    void set_fa_score_function(ScoreFunctionOP fa_score);

    ///@brief Sets the minimizer type.
    void set_min_type(string min);
    
    ///@brief Sets to use the cartesian minimizer.
    void set_cartesian(bool cart);
    
    ///@brief If a fullatom pose is passed, should we repack sidechains according to movemap?
    void do_final_repack(bool repack_sc);
    
    ///@brief Applies the protocol, See notes
    ///
    ///@details Setting ramp_rama and ramp_vdw to false switches to the BASIC protocol 
    /// which is rounds of the centroid minmover
    virtual void apply( Pose & pose );

private:
    
    ///@brief Load the default parameters from the default file.
    void read_default_parameters();
    
    ///@brief used internally to setup extra stuff for movemap.
    void setup_class_movemap_and_constraints(Pose & pose);
    
    ///@brief increase VDW radii for backbone to help geometry and decrease rmsd
    void setup_increased_vdw_radii();
    
    bool use_increased_vdw_radii_;
    bool ramp_rama_;
    bool ramp_vdw_;
    Size rounds_;
    bool cartesian_mode_;
    bool repack_sc_;
    ScoreFunctionOP cen_scorefxn_;
    ScoreFunctionOP fa_scorefxn_;
    MoveMapOP movemap_;
    ScoreType rama_type_;
    
    ///@brief Container for ramp settings
    struct parameters{
        vector1< Real > vdw_params;
        vector1< Real > rama_params;
        vector1< Real > min_params;
        vector1< Real > cst_params;
        };
        
    parameters def_parameters;    
        
};
    }
}

#endif  //#ifndef INCLUDED_protocols/relax_CENTROIDRELAX_HH