PoseBalls.hh

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// 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.
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/// @file   core/scoring/packing/PoseBalls.hh
/// @brief
/// @author

#ifndef INCLUDED_core_scoring_packing_PoseBalls_hh
#define INCLUDED_core_scoring_packing_PoseBalls_hh


#include <core/pose/Pose.fwd.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/scoring/packing/Ball.hh>

#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace packing {

class PoseBalls : public utility::pointer::ReferenceCount {
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~PoseBalls();

  // hmode = 0 --> no hydrogens
  // hmode = 1 --> polar H's
  // hmode = 2 --> all H's
  // in all cases, H area is added to the "parent" atom
  PoseBalls( core::pose::Pose const & pose, core::Size Hmode = 0, bool ignore_water = true );

  inline core::Size const & nballs() const {
    return nballs_;
  }

  inline core::Size const & id_to_index( core::id::AtomID const & aid ) const {
    return id_to_index_[aid];
  }

  inline core::id::AtomID const & index_to_id( core::Size const & index ) const {
    return index_to_id_[index];
  }

  inline Ball const & ball( core::Size const & index ) const {
    return balls_[index];
  }

  inline Ball const & ball( core::id::AtomID const & id ) const {
    return balls_[ id_to_index_[id] ];
  }

  inline Ball & ball( core::Size const & index ) { return balls_[index];  }
  inline Ball & ball( core::id::AtomID const & id ) { return balls_[ id_to_index_[id] ];  }

  inline std::string const & atom_name( core::Size const & index ) const {
    return atom_name_[index];
  }

  inline core::Size const & atom_num( core::Size const & index ) const {
    return atom_num_[index];
  }

  inline core::Size const & atom_type( core::Size const & index ) const {
    return atom_type_[index];
  }

  inline std::string const & res_name( core::Size const & index ) const {
    return res_name_[index];
  }

  inline core::Size const & res_num( core::Size const & index ) const {
    return res_num_[index];
  }

  void reset_surf() {
    surf_.resize(nballs_);
    for( core::Size i = 1; i <= nballs_; i++ ) {
      surf_[i].resize(20);
      for( core::Size j = 1; j <= 20; j++ ) surf_[i][j] = 0.0;
    }
  }

  inline void set_surf( core::Size const & index, core::Size const & ialpha, Real const & val ) {
    surf_[ atom_parent_[index] ][ialpha] += val; // usually parent is self
    // surf_[ index ][ialpha] += val; // usually parent is self // for testing
  }

  inline Real const & surf( core::Size const & index, core::Size const & ialpha ) {
    return surf_[index][ialpha];
  }

  inline utility::vector1<Ball> const & balls() const {
    return balls_;
  }

  inline utility::vector1<core::id::AtomID> const & atomids() const {
    return index_to_id_;
  }

  inline char const & secstruct( core::Size const & i ) const {
    return secstruct_[i];
  }
  inline core::Real const & smooth_nb( core::Size const & i ) const {
    return smooth_nb_[i];
  }
  inline core::Real const & bfac( core::Size const & i ) const {
    return bfac_[i];
  }
  inline bool havesurf( core::Size const & i ) const {
    return atom_parent_[i] == i;
  }

  inline bool is_heavy( core::Size const & i ) const {
    return is_heavy_[i];
  }

  inline uint nbhist( core::Size atype, core::Size bin ) {
    return nbhist_[atype][bin];
  }

  void output_pdb( std::ostream & out ) const;

   void compute_smooth_nb();

private:

  // core::pose::Pose pose_;
  core::Size nballs_;
  core::id::AtomID_Map<Size> id_to_index_;
  utility::vector1<core::id::AtomID> index_to_id_;
  utility::vector1<Ball> balls_;
  utility::vector1<std::string> atom_name_;
  utility::vector1<core::Size>  atom_num_;
  utility::vector1<std::string> res_name_;
  utility::vector1<core::Size>  res_num_;
  utility::vector1<core::Size>  atom_type_;
  utility::vector1<core::Size>  atom_parent_;
  utility::vector1<core::Real>  smooth_nb_;
  utility::vector1<core::Real>  bfac_;
  utility::vector1<bool> is_heavy_;
  utility::vector1<char> secstruct_;
  utility::vector1<utility::vector1<Real> > surf_;
  utility::vector1<utility::vector1<uint> > nbhist_;

};

template< class T >
void
initialize_AtomID_Map( core::id::AtomID_Map<T> & map, PoseBalls const & pb ) {
  for( Size i = 1; i <= pb.nballs(); i++ ) {
    Size res_num = pb.res_num(i);
    Size atom_num = pb.atom_num(i);
    map.resize( std::max(map.size(),res_num) );
    map.resize( res_num, std::max(map.n_atom(res_num),atom_num) );
  }
}


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


#endif // INCLUDED_core_scoring_packing_PoseBalls_HHBalls_HH