MembEtable.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file
/// @brief
/// @author Patrick Barth

#ifndef INCLUDED_core_scoring_etable_MembEtable_hh
#define INCLUDED_core_scoring_etable_MembEtable_hh

// Unit Headers
#include <core/scoring/etable/Etable.fwd.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/memb_etable/MembEtable.fwd.hh>

// Package Headers
#include <core/scoring/etable/EtableOptions.hh>

#include <core/chemical/AtomTypeSet.hh>
#include <utility/pointer/access_ptr.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
//#include <ObjexxFCL/FArray5D.hh>

#include <utility/pointer/ReferenceCount.hh>

// C++ Headers
//#include <iosfwd>
//#include <list>
//#include <string>


namespace core {
namespace scoring {
namespace etable {


/// jk Class definition for Etable
class MembEtable : public Etable {

public:
  typedef Etable Etable;

  ///  constructor
  MembEtable(
    chemical::AtomTypeSetCAP atom_set_in, // like etable namespace
    EtableOptions const & options,
    std::string const alternate_parameter_set = ""
  );

  //pba needed ?
  void copy_from( Etable const * source );

  /// const access to the arrays
/*  ObjexxFCL::FArray3D< Real > const &
  ljatr() const
  {
    return ljatr_;
  }

  ObjexxFCL::FArray3D< Real > const &
  ljrep() const
  {
    return ljrep_;
  }
*/
  ObjexxFCL::FArray3D< Real > const &
  solv1() const
  {
    return solv1_;
  }

  ObjexxFCL::FArray3D< Real > const &
  solv2() const
  {
    return solv2_;
  }

  //pba
  ObjexxFCL::FArray3D< Real > const &
  memb_solv1() const
  {
    return memb_solv1_;
  }

  //pba
  ObjexxFCL::FArray3D< Real > const &
  memb_solv2() const
  {
    return memb_solv2_;
  }

  /// const access to the deriv arrays
/*  ObjexxFCL::FArray3D< Real > const &
  dljatr() const
  {
    return dljatr_;
  }

  ObjexxFCL::FArray3D< Real > const &
  dljrep() const
  {
    return dljrep_;
  }
*/
  /// @brief return the solvation derivative table for the desolvation of atom1 by atom2
  ObjexxFCL::FArray3D< Real > const &
  dsolv1() const
  {
    return dsolv1_;
  }

  /// @brief return the solvation derivative table that combines atom1 and atom2's desolvations
  ObjexxFCL::FArray3D< Real > const &
  dsolv2() const
  {
    return dsolv2_;
  }

  /// pba @brief return the solvation derivative table for the desolvation of atom1 by atom2
  ObjexxFCL::FArray3D< Real > const &
  memb_dsolv1() const
  {
    return memb_dsolv1_;
  }

  /// pba @brief return the solvation derivative table that combines atom1 and atom2's desolvations
  ObjexxFCL::FArray3D< Real > const &
  memb_dsolv2() const
  {
    return memb_dsolv2_;
  }

  Real
  max_dis() const
  {
    return max_dis_;
  }

  Real
  get_safe_max_dis2() const
  {
    return safe_max_dis2;
  }

  int
  get_bins_per_A2() const
  {
    return bins_per_A2;
  }

  chemical::AtomTypeSetCAP
  atom_set() const
  {
    return atom_set_;
  }

  Real
  hydrogen_interaction_cutoff2() const
  {
    return hydrogen_interaction_cutoff2_;
  }

  ///
  Real
  nblist_dis2_cutoff_XX() const
  {
    return nblist_dis2_cutoff_XX_;
  }

  ///
  Real
  nblist_dis2_cutoff_XH() const
  {
    return nblist_dis2_cutoff_XH_;
  }

  ///
  Real
  nblist_dis2_cutoff_HH() const
  {
    return nblist_dis2_cutoff_HH_;
  }

  /// @brief Returns the maximum lj radius for any non-hydrogen
  /// atom as defined by the atom-type-set used to create this Etable.
  Real
  max_non_hydrogen_lj_radius() const;

  /// @brief Returns the maximum lj radius for any hydrogen atom as
  /// defined by the input atom-type-set used to create this Etable.
  Real
  max_hydrogen_lj_radius() const;

  /// set these up in the ctor
  inline
  Real
  lj_radius( int const i ) const
  {
    return lj_radius_[i];
  }
/*
  ///
  Real
  lj_wdepth( int const i ) const
  {
    return lj_wdepth_[i];
  }
*/
  ///
  Real
  lk_dgfree( int const i ) const
  {
    return lk_dgfree_[i];
  }

  ///
  Real
  lk_volume( int const i ) const
  {
    return lk_volume_[i];
  }

  ///
  Real
  lk_lambda( int const i ) const
  {
    return lk_lambda_[i];
  }

  //pba
  Real
  memb_lk_dgfree( int const i ) const
  {
    return memb_lk_dgfree_[i];
  }

  //pba
  /*Real
  lk_dgrefce( int const i ) const
  {
    return lk_dgrefce_[i];
  }*/

  ObjexxFCL::FArray1D< Real > const &
  lk_dgrefce() const
  {
    return lk_dgrefce_;
  }

  //pba
  /*Real
  memb_lk_dgrefce( int const i ) const
  {
    return memb_lk_dgrefce_[i];
  }*/

  ObjexxFCL::FArray1D< Real > const &
  memb_lk_dgrefce() const
  {
    return memb_lk_dgrefce_;
  }

private:

  void
  output_etable(
    ObjexxFCL::FArray3D<Real> & etable,
    std::string label,
    std::ostream & out
  );

  void
  input_etable(
    ObjexxFCL::FArray3D<Real> & etable,
    const std::string label,
    std::istream & in
  );

private:

  chemical::AtomTypeSetCAP atom_set_;

  // parameters:
  int const n_atomtypes;

  // from options
  Real const max_dis_;
  int const bins_per_A2;
  Real const Wradius; // global mod to radii
  Real const lj_switch_dis2sigma; // actual value used for switch
  Real const max_dis2;
  int const etable_disbins;

  // hard-coded for now
  bool const lj_use_lj_deriv_slope;
  Real const lj_slope_intercept;
  bool const lj_use_hbond_radii;
  Real const lj_hbond_dis;
  Real const lj_hbond_hdis;
  Real const lj_hbond_accOch_dis;
  Real const lj_hbond_accOch_hdis;
  bool const lj_use_water_radii;
  Real const lj_water_dis;
  Real const lj_water_hdis;
  Real const lk_min_dis2sigma;
  Real const min_dis;
  Real const min_dis2; // was double
  bool const add_long_range_damping;
  Real const long_range_damping_length;
  Real const epsilon;
  Real const safe_max_dis2;
  Real hydrogen_interaction_cutoff2_;
  Real const nblist_dis2_cutoff_XX_;
  Real const nblist_dis2_cutoff_XH_;
  Real const nblist_dis2_cutoff_HH_;
  Real max_non_hydrogen_lj_radius_;
  Real max_hydrogen_lj_radius_;

  // these three derived from other data
/*  Real lj_switch_sigma2dis;
  Real lj_switch_value2wdepth;
  Real lj_switch_slope_sigma2wdepth;*/

  //
  utility::vector1< Real > lj_radius_;
  /*utility::vector1< Real > lj_wdepth_;*/
  utility::vector1< Real > lk_dgfree_;
  utility::vector1< Real > lk_volume_;
  utility::vector1< Real > lk_lambda_;
  utility::vector1< Real > memb_lk_dgfree_; //pba
  //utility::vector1< Real > lk_dgrefce_;     //pba
  //utility::vector1< Real > memb_lk_dgrefce_;   //pba
  ObjexxFCL::FArray1D< Real > lk_dgrefce_;
  ObjexxFCL::FArray1D< Real > memb_lk_dgrefce_;

  // the etables themselves
/*  ObjexxFCL::FArray3D< Real > ljatr_;
  ObjexxFCL::FArray3D< Real > ljrep_;*/
  ObjexxFCL::FArray3D< Real > solv1_;
  ObjexxFCL::FArray3D< Real > solv2_;
/*  ObjexxFCL::FArray3D< Real > dljatr_;
  ObjexxFCL::FArray3D< Real > dljrep_;*/
  ObjexxFCL::FArray3D< Real > dsolv1_;
  ObjexxFCL::FArray3D< Real > dsolv2_;
  ObjexxFCL::FArray3D< Real > memb_solv1_; //pba
  ObjexxFCL::FArray3D< Real > memb_solv2_; //pba
  ObjexxFCL::FArray3D< Real > memb_dsolv2_; //pba
  ObjexxFCL::FArray3D< Real > memb_dsolv1_; //pba

  // private methods

  // get the AtomType object corresponding to a give type index
  chemical::AtomType const &
  atom_type( int const type )
  {
    return (*atom_set_)[ type ];
  }

  void smooth_etables();
  void modify_pot();
  void make_pairenergy_table();

  // helper functions
  void
  precalc_etable_coefficients(
    ObjexxFCL::FArray2< Real > & lj_sigma,
    /*ObjexxFCL::FArray2< Real > & lj_r6_coeff,
    ObjexxFCL::FArray2< Real > & lj_r12_coeff,
    ObjexxFCL::FArray2< Real > & lj_switch_intercept,
    ObjexxFCL::FArray2< Real > & lj_switch_slope,*/
    ObjexxFCL::FArray1< Real > & lk_inv_lambda2,
    ObjexxFCL::FArray2< Real > & lk_coeff,
    ObjexxFCL::FArray2< Real > & memb_lk_coeff, //pba
    ObjexxFCL::FArray2< Real > & lk_min_dis2sigma_value,
    ObjexxFCL::FArray2< Real > & memb_lk_min_dis2sigma_value //pba
  );

  void
  calc_etable_value(
    Real & dis2,
    int & atype1,
    int & atype2,
/*    Real & atrE,
    Real & d_atrE,
    Real & repE,
    Real & d_repE,*/
    Real & solvE1,
    Real & solvE2,
    Real & dsolvE1,
    Real & dsolvE2,
    ObjexxFCL::FArray2< Real > & lj_sigma,
    /*ObjexxFCL::FArray2< Real > & lj_r6_coeff,
    ObjexxFCL::FArray2< Real > & lj_r12_coeff,
    ObjexxFCL::FArray2< Real > & lj_switch_intercept,
    ObjexxFCL::FArray2< Real > & lj_switch_slope,*/
    ObjexxFCL::FArray1< Real > & lk_inv_lambda2,
    ObjexxFCL::FArray2< Real > & lk_coeff,
    ObjexxFCL::FArray2< Real > & lk_min_dis2sigma_value,
    Real & memb_solvE1, //pba
    Real & memb_solvE2,
    ObjexxFCL::FArray2< Real > & memb_lk_coeff,
    ObjexxFCL::FArray2< Real > & memb_lk_min_dis2sigma_value,
    Real & memb_dsolvE1,
    Real & memb_dsolvE2
  );

/*  void
  zero_hydrogen_and_water_ljatr();*/

};

} // etable
} // scoring
} // core

#endif