RNA_LowResolutionPotential.hh

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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/methods/RNA_LowResolutionPotential.hh
/// @brief  Statistically derived rotamer pair potential class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay

#ifndef INCLUDED_core_scoring_rna_RNA_LowResolutionPotential_hh
#define INCLUDED_core_scoring_rna_RNA_LowResolutionPotential_hh

#include <core/types.hh>

// Unit headers
#include <core/scoring/rna/RNA_LowResolutionPotential.fwd.hh>
#include <core/scoring/rna/RNA_RawBaseBaseInfo.hh>

// Package headers
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>

// Project headers
#include <core/id/AtomID.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>

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

#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/FArray4D.hh>
#include <ObjexxFCL/FArray5D.hh>





namespace core {
namespace scoring {
namespace rna {

////////////////////////////////////////////////////////////////////////////////////////////////////

class RNA_LowResolutionPotential : public utility::pointer::ReferenceCount {

public:
  RNA_LowResolutionPotential();

  ///
  void
  update_rna_centroid_info(
    pose::Pose & pose
  ) const;

  void
  update_rna_base_base_interactions(
    pose::Pose & pose
  ) const;

  void
  update_rna_base_pair_list(
    pose::Pose & pose
  ) const;

  void
  finalize( pose::Pose & pose ) const;

  Real
  rna_base_backbone_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    Vector const & centroid1,
    Vector const & centroid2,
    core::kinematics::Stub const & stub1,
    core::kinematics::Stub const & stub2) const;

  Real
  rna_backbone_backbone_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2) const;

  Real
  rna_repulsive_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2) const;

  // void initialize_atom_numbers_for_backbone_score_calculations( pose::Pose & pose ) const; // Deprecated.Commenting out to make Python bindings compile.

  Real
  get_rna_stack_score(
    Distance const x, // used in fading
    Distance const y, // used in fading
    Distance const z, // used in fading
    Real & deriv_x = dummy_deriv,
    Real & deriv_y = dummy_deriv,
    Real & deriv_z = dummy_deriv ) const;

  void
  eval_atom_derivative_base_base(
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    scoring::EnergyMap const & weights,
    Vector & F1,
    Vector & F2 ) const;

  void
  eval_atom_derivative_rna_base_backbone(
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    Vector & F1,
    Vector & F2 ) const;

  void
  eval_atom_derivative_rna_backbone_backbone(
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    Vector & F1,
    Vector & F2 ) const;

  void
  eval_atom_derivative_rna_repulsive(
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    Vector & F1,
    Vector & F2 ) const;

  bool
  check_clear_for_stacking(
   pose::Pose & pose,
   Size const & i,
   int const & sign ) const;

  bool
  check_forming_base_pair(
    pose::Pose & pose,
    Size const & i,
    Size const & j ) const;

  void
  eval_rna_base_pair_energy(
    rna::RNA_RawBaseBaseInfo & rna_raw_base_base_info,
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    Vector const & centroid1,
    Vector const & centroid2,
    core::kinematics::Stub const & stub1,
    core::kinematics::Stub const & stub2) const;

  void
  more_precise_base_pair_classification( bool const & value ){ more_precise_base_pair_classification_ = value; }

private:

  void
  eval_rna_base_pair_energy_one_way(
    rna::RNA_RawBaseBaseInfo & rna_raw_base_base_info,
    conformation::Residue const & res_i,
    conformation::Residue const & res_j,
    pose::Pose const & pose,
    Vector const & centroid1,
    Vector const & centroid2,
    core::kinematics::Stub const & stub1,
    core::kinematics::Stub const & stub2) const;

  Real
  rna_base_backbone_pair_energy_one_way(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    Vector const & centroid1,
    core::kinematics::Stub const & stub1) const;

  Size
  find_backbone_oxygen_atom(
     ObjexxFCL::FArray2D< Size > const & atom_number_for_backbone_score_calculations,
     Size const & i,
     Size const & atom_num_i ) const;


  Size
  find_backbone_oxygen_atom(
     Size const & atom_num_i ) const;

private:

  void initialize_rna_basepair_xy();
  void initialize_rna_axis();
  void initialize_rna_stagger();
  void initialize_RNA_backbone_oxygen_atoms();
  void initialize_atom_numbers_for_backbone_score_calculations();
  void initialize_rna_base_backbone_xy();
  void initialize_rna_backbone_backbone_weights();
  void initialize_rna_backbone_backbone();
  void initialize_rna_repulsive_weights();
  void initialize_more_precise_base_pair_cutoffs();

  void
  fill_atom_numbers_for_backbone_oxygens( core::chemical::ResidueTypeSetCAP & rsd_set, core::chemical::AA const & aa );

  bool
  check_atom_numbers_for_backbone_oxygens( core::chemical::ResidueTypeSetCAP & rsd_set, core::chemical::AA const & aa ) const;


  Real get_rna_axis_score(
   Real const cos_theta,
   Real & deriv = dummy_deriv) const;

  Real get_rna_stagger_score( Distance const height, Real & deriv = dummy_deriv ) const;

  Real get_rna_basepair_xy(
    Distance const x,
    Distance const y,
    Distance const z, // z is used for fading.
    Real const cos_theta,
    conformation::Residue const & res_i,
    conformation::Residue const & res_j,
    bool const deriv_check = true,
    Real & deriv_x = dummy_deriv,
    Real & deriv_y = dummy_deriv,
    Real & deriv_z = dummy_deriv ) const;

  Real
  get_rna_backbone_backbone_score(
    Distance const & r,
    Size const & atom_num_j_bin,
    Real & deriv = dummy_deriv ) const;

  Real
  get_rna_repulsive_score(
   Distance const & r,
   Size const & atom_num_j_bin,
   Real & deriv = dummy_deriv ) const;


  Real
  rna_backbone_backbone_pair_energy_one_way(
      conformation::Residue const & rsd1,
      conformation::Residue const & rsd2
 ) const;

  Real
  rna_repulsive_pair_energy_one_way(
      conformation::Residue const & rsd1,
      conformation::Residue const & rsd2 ) const;

  Real
  get_rna_base_backbone_xy(
    Distance const x,
    Distance const y,
    Distance const z,
    conformation::Residue const & res_i,
    Size const & atom_num_j_bin,
    bool const deriv_check = false,
    Real & deriv_x = dummy_deriv,
    Real & deriv_y = dummy_deriv,
    Real & deriv_z = dummy_deriv  ) const;

  Real
  get_rna_backbone_backbone_xy( Distance const x,
                           Distance const y,
                           conformation::Residue const & res_i,
                           Size const & atom_num_j_bin ) const;

  bool
  check_for_base_neighbor(
    conformation::Residue const & rsd1,
    Vector const & heavy_atom_j,
    Real & atom_cutoff_weight) const;

  void
  setup_precise_zeta_cutoffs( chemical::AA const & na_rad,
                              std::string const & hoogsteen_cutoff_atom,
                              std::string const & sugar_cutoff_atom
                              );

  void
  get_zeta_cutoff(
                  conformation::Residue const & res_i,
                  Real & zeta_hoogsteen_cutoff,
                  Real & zeta_sugar_cutoff
                  ) const;

private: // data

  // Knowledge-based statistics -- read in from files?
  ObjexxFCL::FArray5D< Real > rna_basepair_xy_;
  ObjexxFCL::FArray1D< Real > rna_stagger_;
  ObjexxFCL::FArray1D< Real > rna_axis_;

  utility::vector1< std::string > RNA_backbone_oxygen_atoms_;
  utility::vector1< Size > atom_numbers_for_backbone_score_calculations_;

  ObjexxFCL::FArray4D< Real > rna_base_backbone_xy_;

  ObjexxFCL::FArray1D< Real > rna_backbone_backbone_weight_;
  ObjexxFCL::FArray1D< Real > rna_backbone_backbone_potential_;

  ObjexxFCL::FArray1D< Real > rna_repulsive_weight_;

  ObjexxFCL::FArray1D< Real > zeta_hoogsteen_cutoff_precise_;
  ObjexxFCL::FArray1D< Real > zeta_sugar_cutoff_precise_;

  //Some parameters for scoring.
  Distance const rna_basepair_radius_cutoff_;
  Distance const rna_basepair_stagger_cutoff_;
  Real const rna_basepair_radius_cutoff2_;
  Distance const basepair_xy_bin_width_;
  Size const basepair_xy_num_bins_;
  Size const basepair_xy_table_size_;
  Distance const basepair_xy_z_fade_zone_;

  Distance const base_stack_min_height_;
  Distance const base_stack_max_height_;
  Distance const base_stack_radius_;
  Real const base_stack_radius2_;
  Distance const base_stack_z_fade_zone_;
  Distance const base_stack_rho_fade_zone_;

  Real const axis_bin_width_;
  Size const axis_num_bins_;

  Size const stagger_num_bins_;
  Distance const stagger_bin_width_;
  Distance const stagger_distance_cutoff_;

  Distance const base_backbone_bin_width_;
  Size const base_backbone_num_bins_;
  Size const base_backbone_table_size_;

  Distance const base_backbone_distance_cutoff_;
  Distance const base_backbone_z_cutoff_;
  Distance const base_backbone_rho_cutoff_;
  Distance const base_backbone_atom_dist_cutoff_;
  Distance const base_backbone_z_fade_zone_;
  Distance const base_backbone_rho_fade_zone_;
  bool const base_backbone_check_atom_neighbor_;

  Real const backbone_backbone_bin_width_;
  Real const backbone_backbone_distance_cutoff_;
  Size const backbone_backbone_num_bins_;

  Real const rna_repulsive_max_penalty_;
  Real const rna_repulsive_screen_scale_;
  Real const rna_repulsive_distance_cutoff_;
  Real const rna_repulse_all_;

  Size const num_RNA_base_pair_orientations_;
  Size const num_RNA_backbone_oxygen_atoms_;
  Size const num_RNA_res_types_;

  Size o2star_index_within_special_backbone_atoms_;
  Size o2p_index_within_special_backbone_atoms_;

  bool const interpolate_;
  bool const fade_;

  bool const rna_verbose_;

  bool more_precise_base_pair_classification_;

public:
  // This must be public for PyRosetta.  It's quite silly.
  static Real dummy_deriv;

};

} // ns rna
} // ns scoring
} // ns core

#endif