surf_vol.cc

Go to the documentation of this file.

// -*- 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/packing/surf_vol.cc
/// @brief  Packing Score
/// @author Will Sheffler

//Unit headers
#include <core/scoring/packing/surf_vol.hh>

//Package headers

// AUTO-REMOVED #include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/id/AtomID_Map.Pose.hh>
#include <basic/options/option.hh>

#include <basic/prof.hh>

//numeric headers
#include <numeric/numeric.functions.hh>
#include <numeric/xyzMatrix.hh>
// AUTO-REMOVED #include <numeric/xyz.functions.hh>

//utility headers
#include <utility/vector1.hh>
#include <utility/exit.hh>
#ifdef  __native_client__ 
#define WIN32
#endif

#ifndef WIN32
#include <pstream.h>
#endif

//C++ headers
#include <iostream>
#include <iomanip>

// option key includes

#include <basic/options/keys/holes.OptionKeys.gen.hh>

#include <core/chemical/ResidueType.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/packing/PoseBalls.hh>
#include <core/scoring/packing/PoseBallsLite.hh>






namespace core {
namespace scoring {
namespace packing {



Real
get_surf_tot(
  pose::Pose const & pose,
  core::Real const   probe_radius
) {
  using namespace core;

  Real tot_surf = 0;

#ifndef WIN32
  PROF_START( basic::DALPHABALL );
  PoseBallsLite pb(pose);

  std::string cmd = basic::options::option[ basic::options::OptionKeys::holes::dalphaball ]();
  redi::pstream proc( cmd + " totalsurf" );
  // proc.precision(20);
  proc << "NPOINTS" << std::endl << pb.nballs() << std::endl << "COORDS" << std::endl;
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    Ball b(pb.ball(i));
    proc << b.x() << " " << b.y() << " " << b.z() << " " << b.r() + probe_radius << " " << std::endl;
  }
  // no weights in surf_vol mode
  proc << "END" << std::endl << redi::peof;

  proc >> tot_surf;
  // std::string s;
  // proc >> s; std::cerr << s << std::endl;
  // proc >> s; std::cerr << s << std::endl;
  // proc >> s; std::cerr << s << std::endl;
  // proc >> s; std::cerr << s << std::endl;
  // Size index;
  // Real s,v;
  // for( Size i = 1; i <= pb.nballs(); i++ ) {
  //  proc >> index >> s >> v;
  //  if( i != index ) {
  //    std::cerr << "DALPHABALL output indicies not matching! " << i << "!=" << index << std::endl;
  //    std::exit(-1);
  //  }
  //  tot_surf += s;
  // }

  PROF_STOP( basic::DALPHABALL );

#endif

  return tot_surf;
}


SurfVol
get_surf_vol(
  pose::Pose const & pose,
  core::Real const   probe_radius
) {
  using namespace core;

  SurfVol result;

#ifndef WIN32


  PoseBallsLite pb(pose);

  initialize_AtomID_Map<Real>(result.surf,pb);
  initialize_AtomID_Map<Real>(result.vol ,pb);

  PROF_START( basic::DALPHABALL );

  std::string cmd = basic::options::option[ basic::options::OptionKeys::holes::dalphaball ]();
  redi::pstream proc( cmd + " surf_vol" );
  // proc.precision(20);
  proc << "NPOINTS" << std::endl << pb.nballs() << std::endl << "COORDS" << std::endl;
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    Ball b(pb.ball(i));
    proc << b.x() << " " << b.y() << " " << b.z() << " " << b.r() + probe_radius << " " << std::endl;
  }
  // no weights in surf_vol mode
  proc << "END" << std::endl << redi::peof;

  result.tot_surf = 0.0;
  result.tot_vol  = 0.0;
  Size index;
  Real s,v;
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    proc >> index >> s >> v;
    if( i != index ) {
      std::cerr << "DALPHABALL output indicies not matching! " << i << "!=" << index << std::endl;
      std::exit(-1);
    }
    result.surf[ pb.index_to_id(i) ] = s;
    result.vol [ pb.index_to_id(i) ] = v;
    result.tot_surf += s;
    result.tot_vol  += v;
  }

  PROF_STOP( basic::DALPHABALL );

#endif

  return result;
}


SurfVolDeriv
get_surf_vol_deriv(
  pose::Pose const & pose,
  core::Real const   probe_radius
) {
  using namespace core;

  SurfVolDeriv result;

#ifndef WIN32

  PROF_START( basic::DALPHABALL );

  PoseBalls pb(pose);

  initialize_AtomID_Map<Real>(result.surf,pb);
  initialize_AtomID_Map<Real>(result.vol ,pb);
  initialize_AtomID_Map<numeric::xyzVector<Real> >(result.dsurf,pb);
  initialize_AtomID_Map<numeric::xyzVector<Real> >(result.dvol ,pb);

  std::string cmd = basic::options::option[ basic::options::OptionKeys::holes::dalphaball ]();
  redi::pstream proc( cmd + " surf_vol_deriv" );
  proc.precision(20);
  proc << "NPOINTS" << std::endl << pb.nballs() << std::endl << "COORDS" << std::endl;
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    Ball b(pb.ball(i));
    proc << b.x() << " " << b.y() << " " << b.z() << " " << b.r() + probe_radius << " " << std::endl;
  }
  // no weights in surf_vol mode
  proc << "END" << std::endl << redi::peof;

  result.tot_surf = 0.0;
  result.tot_vol  = 0.0;
  Size index;
  Real s,v,dsx,dsy,dsz,dvx,dvy,dvz;
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    proc >> index >> s >> v >> dsx >> dsy >> dsz >> dvx >> dvy >> dvz;
    if( i != index ) {
      std::cerr << "DALPHABALL output indicies not matching! " << i << "!=" << index << std::endl;
      std::exit(-1);
    }
    result.surf[ pb.index_to_id(i) ] = s;
    result.vol [ pb.index_to_id(i) ] = v;
    result.dsurf[ pb.index_to_id(i) ] = numeric::xyzVector<Real>(dsx,dsy,dsz);
    result.dvol [ pb.index_to_id(i) ] = numeric::xyzVector<Real>(dvx,dvy,dvz);
    result.tot_surf += s;
    result.tot_vol  += v;
  }

  PROF_STOP( basic::DALPHABALL );

#endif

  return result;
}


}
}
}