APBSWrapper.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   core/scoring/ABPSWrapper.fwd.hh
/// @brief  APBSWrapper class declaration
/// @author Sachko Honda (honda@apl.washington.edu)

#ifndef INCLUDED_core_scoring_APBSWrapper_HH
#define INCLUDED_core_scoring_APBSWrapper_HH

#include <core/scoring/APBSWrapper.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>

// Utility headers
#include <numeric/xyzVector.hh>

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <vector>
#include <string>
#include <map>

namespace core {
namespace scoring {

///-------------------------------------------------------------------------------------
/// APBS wrapper
//--------------------------------------------------------------------------------------
class APBSWrapper : public utility::pointer::ReferenceCount {

  PQROP pqr;
  APBSConfigOP config;
  APBSResultOP result;
public:
  APBSWrapper(pose::Pose const & pose,
        std::map<std::string, bool> const & charged_residues,
              int dbg, bool calcenergy);
  virtual ~APBSWrapper();
  APBSResultCOP exec();
private:
  // Count the number of non-virtual atoms
  int count_atoms( pose::Pose const & pose ) const;
};
///-------------------------------------------------------------------------------------
/// PQR
//--------------------------------------------------------------------------------------
class PQR : public utility::pointer::ReferenceCount {
public:
  PQR(pose::Pose const &pose, int natoms, std::map<std::string, bool> const & charged_residues);
  virtual ~PQR();
  inline int get_natoms() { return natoms_; }
  static std::string const chains;
  int natoms_;
  std::vector<double> x, y, z, charge, radius;
};
///-------------------------------------------------------------------------------------
/// APBSResult
//--------------------------------------------------------------------------------------
class  APBSResult  : public utility::pointer::ReferenceCount {
public:
  APBSResult(int nsims, int natoms, int grid_dimes[3],
             int calcforce, int calcenergy,
             int write_pot, int write_charge, int write_smol,
             int write_kappa, int write_diel, int write_atompot ) ;
  virtual ~APBSResult();

  std::vector<double> esEnergy;
  std::vector<double> npEnergy;
  std::vector<double> dx;
  std::vector<double> dy;
  std::vector<double> dz;
  std::vector<double> qfx;
  std::vector<double> qfy;
  std::vector<double> qfz;
  std::vector<double> ibx;
  std::vector<double> iby;
  std::vector<double> ibz;
  std::vector<double> npx;
  std::vector<double> npy;
  std::vector<double> npz;
  std::vector<double> dbx;
  std::vector<double> dby;
  std::vector<double> dbz;
  int nwrites;
  double grid_meta[13];
  std::vector< std::vector<double> > grid_data;
};
///-------------------------------------------------------------------------------------
/// APBSConfig
//--------------------------------------------------------------------------------------
class APBSConfig : public utility::pointer::ReferenceCount{

public:

  ///---------------------------------------------------------
  /// I_PARAM
  ///---------------------------------------------------------
  class I_PARAM : public utility::pointer::ReferenceCount 
  {    
    mutable int array[25];
  public:
    int sim_type; // 0=mg-manual, 1=mg-auto, 2=mg-parallel
    int nlev;
    int grid_centering_mode; // 0=use ccener[0-2], 1=mol 1
    int coarse_centering_mode; // 0=use ccener[0-2], 1=mol 1
    int fine_centering_mode;// 0=use ccener[0-2], 1=mol 1
    int chgm; // 0=sp10, 1=sp12, 2=sp14
    int pbe_mode; // 0=lpbe, 1=npbe, 2=lrpbe, 3=nrpbe, 4=smpbe
    int bcfl; //0=zero, 1=sdh, 2=mdh, 4=focus
    int srfm; //0=mol, 1=smol, 2=sp12, 3=sp14
    int calcforce; // 0=no, 1=yes
    int calcenergy; // 0=no, 1=yes
    int write_pot;
    int write_charge;
    int write_smol;
    int write_kappa;
    int write_diel;
    int write_atompot;
    int use_pot;
    int iparam19;
    int apol_calcforce;
    int apol_calcenergy;
    int nions;
    int use_charge;
    int use_kappa;
    int use_diel;
  
    I_PARAM();
    ~I_PARAM();
    int * raw_array();
  }; 

  ///---------------------------------------------------------
  /// R_PARAM
  ///---------------------------------------------------------
  class R_PARAM : public utility::pointer::ReferenceCount
  {
    mutable double array[9];
  public:
    double pdie, nsdie, srad, swin, temp, sdens, gamma, smpbe_vol, smpbe_size;
    R_PARAM();
    ~R_PARAM();
    double * raw_array();
  };

  APBSConfig(pose::Pose const & pose, int natoms, int dbg, bool calcenergy);
  virtual ~APBSConfig();
  
  // APBS debug level
  int dbg;
  
  // Number of simulations
  int nsims;
  
  // Number of atoms
  int natoms;

  // Grid generation parameters:
  double cfac;
  double fadd;
  double space;

  // APBS config parameters
  double grid[3];  // For manual & energy
  int dime[3];
  int pdime[3];  // Non 1 for parallel
  double glen[3]; // manual only
  double center[3]; // manual only
  double cglen[3];
  double fglen[3];
  double ccenter[3];
  double fcenter[3];
  
  double ionq[4], ionc[4], ionr[4];
  double ofrac; // parallel only 
  I_PARAM i_param;
  R_PARAM r_param;

  bool calcenergy;  // calculate energy?

}; // end of APBSConfig

} // scoring
} // core
#endif