PoseBallsLite.cc

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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/packing/PoseBallsLite.cc
/// @brief
/// @author

#include <core/scoring/packing/PoseBallsLite.hh>
// AUTO-REMOVED #include <core/scoring/packstat/AtomRadiusMap.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/Tracer.hh>
#include <core/pose/util.hh>

#include <map>

// ObjexxFCL headers
#include <ObjexxFCL/string.functions.hh>
// AUTO-REMOVED #include <ObjexxFCL/format.hh>

#include <core/chemical/AtomType.hh>
#include <utility/vector1.hh>

//Auto Headers
#include <core/pose/util.tmpl.hh>

namespace core {
namespace scoring {
namespace packing {

/// @details Auto-generated virtual destructor
PoseBallsLite::~PoseBallsLite() {}

using namespace ObjexxFCL;

static basic::Tracer TR("core.scoring.packing.PoseBallsLite");

inline core::Real sqr ( core::Real x ) {
  return x*x;
}

// smoothed neighbor is between 9 and 11 A
inline core::Real sigmoidish_neighbor( core::Real sqdist ) {
  if( sqdist > 121.0 ) {
    return 0.0;
  } else if( sqdist < 81.0 ) {
    return 1.0;
  } else {
    Real dist = sqrt( sqdist );
    return sqr(1.0 - sqr( (dist - 9.0) / (11.0 - 9.0) ) );
  }
}

/// @details Remove spaces from given string.
inline std::string strip_whitespace( std::string const & name )
{
  std::string trimmed_name( name );
  left_justify( trimmed_name ); trim( trimmed_name ); // simpler way to dothis?
  return trimmed_name;
}



PoseBallsLite::PoseBallsLite(
  core::pose::Pose const & pose,
  core::Size Hmode,
  bool /*ignore_water*/
)
{
  using namespace numeric;

  // std::cerr << "PoseBallsLite.cc:67 (" << pose.total_residue() << ")" << std::endl;

  // initialize index and vars
  core::Size index = 0;
  Size num_unrec = 0;
  if( pose.pdb_info() ) num_unrec = pose.pdb_info()->get_num_unrecognized_atoms();
  balls_      .reserve( pose.total_residue()*5 + num_unrec );
  index_to_id_.reserve( pose.total_residue()*5 + num_unrec );
  core::pose::initialize_atomid_map( id_to_index_, pose );
  id_to_index_.resize( pose.total_residue() + num_unrec );

// std::cerr << "PoseBallsLite.cc:85 (" << ")" << std::endl;

  // add atoms in pose
  core::Size skippedH = 0;
  for( core::Size ir = 1; ir <= pose.total_residue(); ++ir ) {
    for( core::Size ia = 1; ia <= pose.residue(ir).natoms(); ++ia ) {
// std::cerr << "PoseBallsLite.cc:91 (" << ")" << std::endl;
      if( pose.residue(ir).is_virtual(ia) ) continue;
      if ( Hmode == 0 ) { // no H's
        if( pose.residue(ir).atom_type(ia).is_hydrogen() ) {
          skippedH++;
          continue;
        }
      } else if( Hmode == 1 ) { // polar H's only
        if( pose.residue(ir).atom_type(ia).is_hydrogen() &&
           !pose.residue(ir).atom_type(ia).is_polar_hydrogen() ) {
            skippedH++;
            continue;
          }
      } else if( Hmode == 2 ) {
        ; // all Hs
      }
      atom_num_.push_back(ia);
      res_num_.push_back(ir);

// std::cerr << "PoseBallsLite.cc:107 (" << ")" << std::endl;
      core::id::AtomID aid(ia,ir);
      id_to_index_[ aid ] = ++index;
      index_to_id_.push_back( aid );
      balls_.push_back( Ball( pose.xyz(aid), pose.residue(ir).atom_type(ia).lj_radius() ) );
    }
  }
// std::cerr << "PoseBallsLite.cc:134 (" << ")" << std::endl;

  nballs_ = index;
}


} // namespace packing
} // namespace scoring
} // namespace core