GeometrySecMatchRPE.hh

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/// @file   protocols/match/downstream/GeometrySecMatchRPE.hh
/// @brief
/// @author Florian Richter, floric@u.washington.edu, june 09


#ifndef INCLUDED_protocols_match_downstream_GeometrySecMatchRPE_hh
#define INCLUDED_protocols_match_downstream_GeometrySecMatchRPE_hh

// Unit headers
#include <protocols/match/downstream/GeometrySecMatchRPE.fwd.hh>

// Package headers
#include <protocols/match/downstream/SecMatchResiduePairEvaluator.hh>
#include <protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.fwd.hh>

// Project headers
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>

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

// C++ headers
// AUTO-REMOVED #include <list>
// AUTO-REMOVED #include <string>

#include <core/chemical/ResidueType.fwd.hh>
#include <utility/vector1_bool.hh>


namespace protocols {
namespace match {
namespace downstream {



/// @brief helper class for GeometrySec
/// abstract base class for distance, angle, and dihedral derived classes
class AtomGeometrySecMatchRPE : public SecMatchResiduePairEvaluator
{

public:

  typedef std::pair< core::Size, core::Size > SizePair;

  typedef core::Real Real;

  AtomGeometrySecMatchRPE( protocols::toolbox::match_enzdes_util::GeomSampleInfo const & gsi );

  ~AtomGeometrySecMatchRPE();

  virtual
  bool
  evaluate_residues(
    core::conformation::Residue const & candidate_res,
    core::conformation::Residue const & target_res
  ) const = 0;

  virtual
  bool
  require_all_target_residue_atom_coordinates() const;

  virtual
  bool
  require_target_atom_coordinate( Size target_atom_id ) const;


  /// @brief determines if the passed in value is between lowval and highval
  bool
  check_value(
    core::Real value
  ) const;

  utility::vector1< SizePair > const &
  at_inds() const {
    return at_inds_; }

  void
  add_at_ind(
    core::Size which_cst_res,
    core::Size atom_ind_in_res
  );

  core::Real
  lowval() const {
    return lowval_;
  }

  core::Real
  highval() const {
    return highval_;
  }

  virtual
  std::string
  print(
    core::chemical::ResidueTypeCOP candidate_restype,
    core::chemical::ResidueTypeCOP target_restype
  ) const = 0;


protected:

  void
  clear_at_inds();

  void
  set_lowval( core::Real lowval );

  void
  set_highval( core::Real highval );

private:

  Real lowval_;
  Real highval_;
  utility::vector1< SizePair > at_inds_;

};

/// @brief RPE to figure out if two atoms are within a given distance
/// atoms need to be set through the parent class add_at_ind function
class AtomDistanceSecMatchRPE : public AtomGeometrySecMatchRPE
{

public:

  /// @brief the constructor for this rpe sets the lowval and highval to
  /// the squared values of the initial values, that should make distance
  /// evaluation faster
  AtomDistanceSecMatchRPE( protocols::toolbox::match_enzdes_util::GeomSampleInfo const & gsi );

  virtual
  bool
  evaluate_residues(
    core::conformation::Residue const & candidate_res,
    core::conformation::Residue const & target_res
  ) const;

  virtual
  bool
  require_candidate_residue_atoms_to_lie_near_target_atom( Size target_atom_id ) const;

  virtual
  utility::vector1< Size >
  candidate_res_atoms_reqd_near_target_atom(
    Size target_atom_id
  ) const;

  virtual
  Real
  max_separation_dist_to_target_atom( Size target_atom_id ) const;

  virtual
  std::string
  print(
    core::chemical::ResidueTypeCOP candidate_restype,
    core::chemical::ResidueTypeCOP target_restype
  ) const;

};

/// @brief RPE to figure out if three atoms are within a given angle
/// atoms need to be set through the parent class add_at_ind function
class AtomAngleSecMatchRPE : public AtomGeometrySecMatchRPE
{

public:

  AtomAngleSecMatchRPE( protocols::toolbox::match_enzdes_util::GeomSampleInfo const & gsi );

  virtual
  bool
  evaluate_residues(
    core::conformation::Residue const & candidate_res,
    core::conformation::Residue const & target_res
  ) const;

  virtual
  std::string
  print(
    core::chemical::ResidueTypeCOP candidate_restype,
    core::chemical::ResidueTypeCOP target_restype
  ) const;

};


/// @brief RPE to figure out if four atoms are within a given dihedral angle
/// atoms need to be set through the parent class add_at_ind function
/// also checks whether a dihedral is periodic, i.e. multiple minima
class AtomDihedralSecMatchRPE : public AtomGeometrySecMatchRPE
{

public:

  AtomDihedralSecMatchRPE( protocols::toolbox::match_enzdes_util::GeomSampleInfo const & gsi );

  virtual
  bool
  evaluate_residues(
    core::conformation::Residue const & candidate_res,
    core::conformation::Residue const & target_res
  ) const;

  virtual
  std::string
  print(
    core::chemical::ResidueTypeCOP candidate_restype,
    core::chemical::ResidueTypeCOP target_restype
  ) const;

private:

  bool check_periodicity_;

  Real periodicity_;
  Real offset_;
};


/// @brief holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence
/// when an instance of this class is asked to evaluate two residues.
class GeometrySecMatchRPE : public SecMatchResiduePairEvaluator
{

public:

  /// @brief convenience constructor from mcfi
  /// the downstream_inds and upstream_inds vector must
  /// contain atoms D1(U1), D2(U2), and D3(U3), respectively,
  /// in that order
  GeometrySecMatchRPE(
    protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo const & mcfi,
    utility::vector1< core::Size > const & downstream_inds,
    utility::vector1< core::Size > const & upstream_inds
  );

  /// @brief empty constructor
  GeometrySecMatchRPE(){}

  /// @brief performs a logical AND for all of the AtomGeometry evaluators.
  virtual
  bool
  evaluate_residues(
    core::conformation::Residue const & candidate_res,
    core::conformation::Residue const & target_res
  ) const;

  void
  add_atomgeom_evaluator(
    AtomGeometrySecMatchRPECOP evaluator
  );

  virtual
  bool
  require_all_target_residue_atom_coordinates() const;

  virtual
  bool
  require_target_atom_coordinate( Size target_atom_id ) const;

  virtual
  bool
  require_candidate_residue_atoms_to_lie_near_target_atom( Size target_atom_id ) const;

  virtual
  utility::vector1< Size >
  candidate_res_atoms_reqd_near_target_atom(
    Size target_atom_id
  ) const;

  virtual
  Real
  max_separation_dist_to_target_atom( Size target_atom_id ) const;

  utility::vector1< AtomGeometrySecMatchRPECOP > const &
  atom_geom_rpes() const {
    return atom_geom_rpes_;
  }

private:

  utility::vector1< AtomGeometrySecMatchRPECOP > atom_geom_rpes_;

};

}
}
}

#endif