ContinuousRotamerSet.hh

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/// @file   core/pack/RotamerSet/ContinuousRotamerSet.hh
/// @brief  Declaration for the class which desribes rotamers statistically instead of as discrete samples
///         For use in stochastic packing (see Feng & Dokholyan, 2006)
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)


#ifndef INCLUDED_core_pack_rotamer_set_ContinuousRotamerSet_HH
#define INCLUDED_core_pack_rotamer_set_ContinuousRotamerSet_HH

// Unit Headers
#include <core/pack/rotamer_set/ContinuousRotamerSet.fwd.hh>

// Package Headers
// AUTO-REMOVED #include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/task/PackerTask.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <core/chemical/AA.hh>
//#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

#include <core/chemical/ResidueType.fwd.hh>
#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>


namespace core {
namespace pack {
namespace rotamer_set {


class ContinuousRotamerSet : public utility::pointer::ReferenceCount
{
private: // typedefs
  typedef utility::pointer::ReferenceCount parent;
  typedef utility::vector1< dunbrack::DunbrackRotamerSampleData >  RotamersForAA;

public:
  ContinuousRotamerSet();
  virtual ~ContinuousRotamerSet();

  void build_rotamers(
    pose::Pose const & pose,
    Size resid,
    task::PackerTask const & task
  );

  Size
  get_n_residue_types() const;

  //Size
  //get_residue_type_begin( Size which_restype ) const;

  Size
  get_n_sampling_rotamers_for_rotblock( Size which_restype ) const;

  Size
  get_n_baserotamers_for_rotblock( Size which_restype ) const;

  /// @brief Rotamers i to i+j of all the same residue type are grouped together.
  /// This function returns the index of the residue type in a contiguous block
  /// of rotamers.  E.g. rotamers 100 to 120 might all be lysine rotamers, and might
  /// be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99.
  /// If new lysine rotamers are appended to the end of the rotamer set, they are
  /// considered to be in a separate residue type block.  Lysine rotamers 200 to 210 might
  /// be block 15 while lysine rotamers 100 to 120 are still block 7.
  Size
  get_rotblock_index_for_sampling_rotamer( Size which_rotamer ) const;

  Size
  num_base_rotamers_total() const;

  Size
  num_sampling_rotamers_total() const;

  Size
  sampling_id_for_current_rotamer() const;

  utility::vector1< Vector > const &
  current_rotamer_coords() const;
  
  Size resid() const;

  chemical::ResidueTypeCOP
  restype_for_rotblock( Size rotblock ) const;

  dunbrack::DunbrackRotamerSampleData const &
  baserotamer_data( Size aa_ind, Size rotid_for_aa ) const;

  Size
  pick_baserotamer_from_rotblock( Size aa_ind, Real rand_btw_0_and_1 ) const;

private:
  void determine_rotcounts_for_restype( Size );

private:

  Size resid_; //which residue is this?

  Size input_rotamer_samplingrot_index_;
  Size input_rotamer_rotblock_;
  utility::vector1< Vector > input_rotamer_coords_;

  Size n_restypes_; // aka n_rotblocks
  utility::vector1< chemical::AA >              aa_for_rotblock_;
  utility::vector1< chemical::ResidueTypeCOP >  restype_for_rotblock_;

  Size n_baserots_total_; // excluding proton chis, how many dihedral angle bins are there?
  utility::vector1< Size >          n_baserotamers_for_rotblock_;
  utility::vector1< Size >          baserots_offsets_;
  utility::vector1< Size >          aa_block_for_baserotamer_;

  Size n_samplingrots_total_; // // how many rotamers above the 98% probability threshold?
  utility::vector1< Size >          n_samplingrots_for_rotblock_; //top 98% by prob * nproton_chi_extra
  utility::vector1< Size >          samplingrot_offsets_;
  utility::vector1< Size >          aa_block_for_samplingrotamer_;

  utility::vector1< RotamersForAA > samples_;

};

class ContinuousRotamerSets : public utility::pointer::ReferenceCount
{
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~ContinuousRotamerSets();
  ContinuousRotamerSets(
    pose::Pose const & pose,
    task::PackerTask const & task
  );

  Size nmoltenres() const;
  Size total_residue() const;

  Size resid_2_moltenresid( Size ) const;
  Size moltenresid_2_resid( Size ) const;

  ContinuousRotamerSet const &
  rotamer_set_for_moltenres( Size ) const;

  ContinuousRotamerSet const &
  rotamer_set_for_res( Size ) const;

  Size
  n_sample_rotamers() const;

  Size
  moltenres_for_sample_rot( Size sample_rotno );

  Size
  full_sample_rot_index_2_moltenres_sample_rot_index( Size sample_rotno ) const;

private:
  Size total_residue_;
  Size nmoltenres_;
  utility::vector1< Size > moltenresid_2_resid_;
  utility::vector1< Size > resid_2_moltenresid_;
  utility::vector1< ContinuousRotamerSet > rotamer_sets_;
  Size n_sample_rotamers_;
  utility::vector1< Size > moltenres_for_sample_rot_;
  utility::vector1< Size > moltenres_sample_rot_offset_;
};


} // namespace rotamer_set
} // namespace pack
} // namespace core


#endif // INCLUDED_core_pack_RotamerSet_RotamerSet_HH