SingleGrid.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   protocols/qsar/scoring_grid/SingleGrid.hh
/// @author Sam DeLuca


#ifndef INCLUDED_protocols_qsar_scoring_grid_SingleGrid_hh
#define INCLUDED_protocols_qsar_scoring_grid_SingleGrid_hh

#include <protocols/qsar/scoring_grid/SingleGrid.fwd.hh>
#include <protocols/qsar/scoring_grid/GridBase.hh>
#include <protocols/qsar/qsarMap.fwd.hh>

#include <core/grid/CartGrid.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>

#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.fwd.hh>

#include <numeric/interpolation/spline/SplineGenerator.hh>
#include <numeric/xyzVector.hh>

#include <list>

#ifdef WIN32
  #include <protocols/qsar/qsarMap.hh>
#endif


namespace protocols {
namespace qsar {
namespace scoring_grid {

class SingleGrid : public GridBase
{
public:

  SingleGrid(std::string type);
  virtual ~SingleGrid();
  /// @brief initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).
  virtual void initialize(core::Vector const & center, core::Real width, core::Real resolution);
  /// @brief set the chain around which to calculate the grid
  virtual void set_chain(char chain);
  /// @brief get the chain around which the grid is calculated
  char get_chain();
  /// @brief populate the grid with values based on a passed pose
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center, core::Size const & ligand_chain_id_to_exclude)=0;
  /// @brief populate the grid with values based on a passed pose
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center,utility::vector1<core::Size> ligand_chain_ids_to_exclude)=0;
  /// @brief populate the grid with values based on a passed pose
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center)=0;
  /// @brief setup a grid based on RosettaScripts input
  virtual void parse_my_tag(utility::tag::TagPtr const tag)=0;
  /// @brief serialize the SingleGrid to a json_spirit object
  virtual utility::json_spirit::Value serialize();
  /// @brief deserialize a json_spirit object to a SingleGrid
  virtual void deserialize(utility::json_spirit::mObject data);
  /// @brief return a constant reference to the grid
  core::grid::CartGrid<core::Real> const &  get_grid();
  ///@brief set the grid type
  void set_type(std::string type);
  /// @brief return the grids type
  virtual std::string get_type();
  /// @brief set the center of the grid
  void set_center(core::Vector center);
  /// @brief get the center of the grid
  core::Vector get_center();
  /// @brief get the max score value in the grid
  core::Real get_min_value() const;
  /// @brief get the minimum score value in the grid
  core::Real get_max_value() const;
  /// @brief get the value of a single point in the grid based on pdb coordinates
  core::Real get_point(core::Real x, core::Real y, core::Real z);
  /// @brief get the value of a single point in the grid based on pdb coordinates
  core::Real get_point(core::Vector coords);
  /// @brief get dimensions of the grid
  numeric::xyzVector<core::Size> get_dimensions();
  /// @brief get the pdb coordinates based on grid point coordinates
  core::Vector get_pdb_coords(int x, int y, int z);
  /// @brief get the pdb coordinates based on grid point coordinates
  core::Vector get_pdb_coords(core::grid::CartGrid<core::Real>::GridPt gridpt);
  /// @brief return the current score of a residue using the current grid
  virtual core::Real score(core::conformation::Residue const & residue, core::Real const max_score, qsarMapOP qsar_map);
  /// @brief return the current score of an atom using the current grid
  virtual core::Real atom_score(core::conformation::Residue const & residue, core::Size atomno, qsarMapOP qsar_map);
  void grid_to_kin(utility::io::ozstream & out, core::Real min_val, core::Real max_val, core::Size stride);
  //void grid_rotamer_trials(core::pose::Pose &  pose, core::Size residue_id, int const min_score);
    /// @brief check to see if residue is in grid
    virtual bool is_in_grid(core::conformation::Residue const & residue);

  std::list<std::pair<core::Vector, core::Real> > get_point_value_list_within_range(core::Real lower_bound, core::Real upper_bound,core::Size stride);

  virtual void dump_BRIX(std::string const & prefix);

  //Various mathematical functions for assigning values to the grid go here
  void set_sphere(core::Vector const & coords, core::Real radius, core::Real value);
  void set_ring(
      core::Vector const & coords,
      core::Real inner_radius,
      core::Real outer_radius,
      core::Real value
  );
  void diffuse_ring(core::Vector const & coords, core::Real radius, core::Real width, core::Real magnitude);
  void set_distance_sphere( core::Vector const & coords,core::Real cutoff);
  void set_point(core::Vector const & coords, core::Real value);
  void set_distance_sphere_for_atom(core::Real const & atom_shell, core::Vector const & coords,core::Real cutoff);
  void set_score_sphere_for_atom(numeric::interpolation::spline::InterpolatorOP lj_spline,core::Vector const & coords, core::Real cutoff);
  /// @fill the entire grid with some value
  void fill_with_value(core::Real);
private:
  core::grid::CartGrid<core::Real> grid_;
  std::string type_;
  core::Vector center_;
  char chain_;

};


}
}
}

#endif /* GRIDBASE_HH_ */