SingleLigandRotamerLibrary.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file   core/scoring/dunbrack/SingleLigandRotamerLibrary.hh
///
/// @brief
/// @author Ian W. Davis


#ifndef INCLUDED_core_pack_dunbrack_SingleLigandRotamerLibrary_hh
#define INCLUDED_core_pack_dunbrack_SingleLigandRotamerLibrary_hh

#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/conformation/Residue.hh>

#include <utility/vector1.hh>


namespace core {
namespace pack {
namespace dunbrack {


class SingleLigandRotamerLibrary; // fwd declaration
typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary > SingleLigandRotamerLibraryOP;
typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary const > SingleLigandRotamerLibraryCOP;
typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary > SingleLigandRotamerLibraryAP;
typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary const > SingleLigandRotamerLibraryCAP;

///@brief A fixed library of conformations for some residue type (doesn't have to be a ligand).
///@details Reads residue conformations in PDB format separated by mandatory TER records.
/// "Included" from a residue .params file with the PDB_ROTAMERS keyword.
class SingleLigandRotamerLibrary : public SingleResidueRotamerLibrary
{
  //typedef utility::vector1< core::Size > Fragment; // a list of atom indices (variable len)
  //typedef utility::vector1< Fragment > Fragments;
  //typedef utility::vector1< core::Size > Automorphism; // a remapping of atom indices (fixed len)
  //typedef utility::vector1< Automorphism > Automorphisms;

public:

  SingleLigandRotamerLibrary();

  virtual ~SingleLigandRotamerLibrary();

  /// @brief explicit constructor
  SingleLigandRotamerLibrary(
    utility::vector1< conformation::ResidueOP > & rotamers_in,
    Real ref_E_in
  );
  /// @brief Reads conformers from PDB-format file (must be separated by TER records!)
  virtual
  void
  init_from_file(
    std::string const & filename,
    chemical::ResidueTypeCOP restype
  );

  /// @brief Adheres to the contract from SingleLigandRotamerLibrary
  virtual
  Real
  rotamer_energy_deriv(
    conformation::Residue const & rsd,
    RotamerLibraryScratchSpace & scratch
  ) const;

  /// @brief Adheres to the contract from SingleLigandRotamerLibrary
  virtual
  Real
  rotamer_energy(
    conformation::Residue const & rsd,
    RotamerLibraryScratchSpace & scratch
  ) const;

  virtual
  Real
  best_rotamer_energy(
    conformation::Residue const & rsd,
    bool curr_rotamer_only,
    RotamerLibraryScratchSpace & scratch
  ) const;

  virtual
  void
  assign_random_rotamer_with_bias(
    conformation::Residue const &,// rsd,
    RotamerLibraryScratchSpace &,// scratch,
    numeric::random::RandomGenerator &,// RG,
    ChiVector &,// new_chi_angles,
    bool //perturb_from_rotamer_center
  ) const {} // stubbed out for the moment.

  /// @brief Adheres to the contract from SingleLigandRotamerLibrary
  virtual
  void
  fill_rotamer_vector(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    pack::task::PackerTask const & task,
    graph::GraphCOP,
    chemical::ResidueTypeCOP concrete_residue,
    conformation::Residue const& existing_residue,
    utility::vector1< utility::vector1< Real > > const & extra_chi_steps,
    bool buried,
    RotamerVector & rotamers
  ) const;

  //XRW_B_T1
  /*
  /// @brief Adheres to the contract from SingleLigandRotamerLibrary
  virtual
  SingleResidueRotamerLibraryOP
  coarsify(coarse::Translator const &map) const;
  */
  //XRW_E_T1

  /// @brief Adheres to the contract from SingleLigandRotamerLibrary
  virtual
  void
  write_to_file( utility::io::ozstream &out ) const;

  Real
  get_reference_energy() const{
    return ref_energy_;
  }

  void set_reference_energy( Real ref_E_in){
    ref_energy_ = ref_E_in;
  }

  void set_rotamers( utility::vector1< conformation::ResidueOP > & rotamers_in ){
    rotamers_ = rotamers_in;
  }

  utility::vector1< conformation::ResidueOP > const &
  get_rotamers() const {
    return rotamers_;
  }



private:

  /// @brief Fills in missing hydrogens/virtual atoms from library load
  ///
  /// @details "missing" is the vector for atoms missing for the current "rsd"
  //           "missed" is the vector annotating which atoms have already been filled (for diagnostic output tracking)
  void
  fill_missing_atoms( utility::vector1< bool > missing, conformation::ResidueOP rsd, utility::vector1< bool > & missed ) const;

  // Breaking the ligand into rigid fragments that would supply (putative) pharamacophores
  // to superimpose on was a nice idea, but it breaks the packer assumption that nbr_atom doesn't move.

  //void find_fragments(chemical::ResidueTypeCOP restype);
  //void list_automorphisms(chemical::ResidueTypeCOP restype);
  //void unique_auto_for_frags();

  //void superimpose(
  //  conformation::Residue const & existing,
  //  conformation::Residue & conformer,
  //  Fragment const & frag,
  //  Automorphism const & morph
  //) const;

private:

  utility::vector1< conformation::ResidueOP > rotamers_;

  // A baseline reference energy applied to *all* conformers in this library,
  // like amino acid reference energies.
  Real ref_energy_;

  // Breaking the ligand into rigid fragments that would supply (putative) pharamacophores
  // to superimpose on was a nice idea, but it breaks the packer assumption that nbr_atom doesn't move.

  /// A ligand with N torsions decomposes into N+1 rigid fragments,
  /// or fewer if some consist of 2 atoms or less.
  /// Each fragement can be used for superimposing on, possibly in multiple ways.
  //Fragments rigid_frags_;
  /// All the automorphisms for the ligand as a whole, shared among frags (below).
  //Automorphisms automorphs_;
  /// A subset of automorphs_ that reflects the *unique* automorphisms within
  /// a particular rigid fragment.  These represent different ways of
  /// superimposing two structures using the atoms from that fragment.
  //utility::vector1< utility::vector1 < Automorphism * > > frag_automorphs_;
  /// Total number of automorphisms in frag_automorphs_ -- number of possible ways to superimpose
  //Size total_superpos_;

}; // SingleLigandRotamerLibrary


} // namespace dunbrack
} // namespace scoring
} // namespace core

#endif // INCLUDED_core_pack_dunbrack_SingleLigandRotamerLibrary_HH