ChargeGrid.hh

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/// @file   src/protocols/qsar/scoring_grid/ChargeGrid.hh
/// @author Sam DeLuca
/// @brief This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857.  doi:10.1021/jm00145a002

#ifndef INCLUDED_protocols_qsar_scoring_grid_ChargeGrid_HH
#define INCLUDED_protocols_qsar_scoring_grid_ChargeGrid_HH

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

namespace protocols {
namespace qsar {
namespace scoring_grid {

/// @brief a very light representation of an atom that is just a charge and a cartesian space position
struct ChargeAtom
{
  ChargeAtom(core::Vector const &  in_xyz, core::Real const & in_charge, core::Size const & nc)
  {
    xyz = in_xyz;
    charge = in_charge;
    neighbor_count = nc;

  }

  ChargeAtom()
  {
    charge = 0.0;
    neighbor_count = 0;
  }

  utility::json_spirit::Value serialize();

  void deserialize(utility::json_spirit::mObject data);

  core::Vector xyz;
  core::Real charge;
  core::Size neighbor_count;
};


class ChargeGrid : public SingleGrid
{
public:
  ChargeGrid();
  ChargeGrid(core::Real charge);
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center, core::Size const & ligand_chain_id_to_exclude);
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center);
  virtual void refresh(core::pose::Pose const & pose, core::Vector const & center, utility::vector1<core::Size> ligand_chain_ids_to_exclude);
  /// @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);
  void parse_my_tag(utility::tag::TagPtr const tag);
    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);

private:

  /// @brief calculate nominal depth based on atom count within 4 Angstroms. See
  /// Table 2 of the 1985 Goodford Paper
  core::Real nominal_depth(core::Size const & n_atoms) const;

  core::Real charge_charge_electrostatic(core::pose::Pose const & pose, ChargeAtom const & atom_q, ChargeAtom const & atom_p) const;

  void setup_charge_atoms(core::pose::Pose const & pose);

private:

  core::Real zeta_;
  core::Real epsilon_;
  core::Real indirect_numerator_; // (zeta - epsilon) / (zeta + epsilon)
  core::Real epsilon_0_;
  std::list<ChargeAtom> charge_atom_list_;

};


}
}
}



#endif /* CHARGEGRID_HH_ */