Motif.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 Motif.hh
/// @brief Header for interaction motif between residues
/// @author havranek, sthyme (sthyme@gmail.com)

#ifndef INCLUDED_protocols_motifs_Motif_hh
#define INCLUDED_protocols_motifs_Motif_hh

// Unit Headers
#include <protocols/motifs/Motif.fwd.hh>

// Package Headers

// Project Headers
#include <core/conformation/Atom.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>

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

// C++ Headers
#include <iosfwd>
#include <map>
#include <string>

#include <utility/vector1.hh>


namespace protocols {
namespace motifs {

class Motif : public utility::pointer::ReferenceCount
{

static std::map < std::string, utility::vector1 < std::string > > motifAtomIDs;
static std::map < std::string, utility::vector1 < std::string > > basebaseAtomIDs;

public:
  // This is a 'by hand' way to associate a jump with the coordinate system-forming
  // atoms.
  Motif(
    std::string const resname1,
    std::string const res1_atom1,
    std::string const res1_atom2,
    std::string const res1_atom3,
    std::string const resname2,
    std::string const res2_atom1,
    std::string const res2_atom2,
    std::string const res2_atom3,
    core::kinematics::Jump const & orientation
  );

  // This constructor gets the jump for you - PDB numbering + chain id
  Motif(
    core::pose::Pose const & pose,
    Size const pdb_residue_position_1,
    char const pdb_chain_id1,
    std::string const res1_atom1,
    std::string const res1_atom2,
    std::string const res1_atom3,
    Size const pdb_residue_position_2,
    char const pdb_chain_id2,
    std::string const res2_atom1,
    std::string const res2_atom2,
    std::string const res2_atom3
  );

  // This constructor gets the jump for you - Rosetta numbering
  Motif(
    core::pose::Pose const & pose,
    Size const pdb_residue_position_1,
    std::string const res1_atom1,
    std::string const res1_atom2,
    std::string const res1_atom3,
    Size const pdb_residue_position_2,
    std::string const res2_atom1,
    std::string const res2_atom2,
    std::string const res2_atom3
  );

  // This constructor forms a motif using preset atom types from a static map
  Motif(
    core::conformation::Residue const & res1,
    core::conformation::Residue const & res2
  );

  // Ligand motif constructor: This constructor gets the jump for you - Rosetta numbering
  Motif(
    core::conformation::Residue const & res1,
    core::conformation::Residue const & res2,
    utility::vector1< Size >  const res2_atoms
  );

// Ligand motif search constructor: No residues, just atom names and a jump
  Motif(
    std::string const resname1,
    std::string const res1_atom1,
    std::string const res1_atom2,
    std::string const res1_atom3,
    std::string const res2_atom1,
    std::string const res2_atom2,
    std::string const res2_atom3,
    core::kinematics::Jump const & orientation
  );

  // Copy constructor
  Motif(
    Motif const & src
  );

  // Clone method
  MotifOP
  clone() const;

  // Destructor
  virtual ~Motif();

  // Residue check_res is res1 of motif
  virtual bool
  forward_check(
    core::conformation::Residue const & check_res
  ) const;

  // Residue check_res is res2 of motif
  virtual bool
  backward_check(
    core::conformation::Residue const & check_res
  ) const;

  // Position in pose is same type as motif
  virtual bool
  apply_check(
    core::pose::Pose const & pose,
    Size const pos
  ) const;

  // Make atom integers for this motif, unused as of now, may want in future
  //virtual void
  //generate_atom_ints();

  virtual core::pack::rotamer_set::RotamerSetOP
  build_rotamers(
    core::pose::Pose & pose,
    Size const rotamer_build_position,
    bool use_forward,
    Size const ex_,
    bool res2 = false
  ) const;

  // Build a rotamer library using this motif and one given position to serve as the start
  // point for the motif.  The third, optional argument is the position at which to build
  // the rotamers.  If neglected, finds the closest position in the pose and uses that.
  virtual core::pack::rotamer_set::RotamerSetOP
  build_inverted_rotamers(
    core::pose::Pose & pose,
    Size const motif_anchor_position,
    bool use_forward,
    Size rotamer_build_position = 0
  ) const;

  // The place_residue function moves the mobile residue based on motif geometry
  virtual void
  place_residue(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool one_three = true
  ) const;

  virtual void
  place_atoms(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    utility::vector1< std::string > const & atoms,
    bool one_three = true
  ) const;

  virtual void
  place_atom(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    core::conformation::Atom & atm,
    bool one_three = true,
    std::string const atomtype = "C1*"
  ) const;

  virtual void
  place_residue_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    bool one_three = true
  ) const;

  virtual void
  place_atom_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    core::conformation::Atom & atm,
    bool one_three = true,
    std::string const atomtype = "C1*"
  ) const;

  virtual void
  place_atoms_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    utility::vector1< std::string > const & atoms,
    bool one_three = true
  ) const;

  // Ligand motifs place_residue
  virtual void
  place_residue(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    bool one_three = true
  ) const;

  // Ligand motifs place_atoms
  virtual void
  place_atoms(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    utility::vector1< Size > const & atoms,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    bool one_three = true
  ) const;

  // Ligand motifs place_atom
  virtual void
  place_atom(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    core::conformation::Atom & atm,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    Size const & atomtype,
    bool one_three = true
  ) const;

  // Ligand motifs place_residue_
  virtual void
  place_residue_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    bool one_three = true
  ) const;

  // Ligand motifs place_atom_
  virtual void
  place_atom_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    core::conformation::Atom & atm,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    Size const & atomtype,
    bool one_three = true
  ) const;

  // Ligand motifs place_atoms_
  virtual void
  place_atoms_(
    core::conformation::Residue const & fixed,
    core::conformation::Residue & mobile,
    bool forward,
    utility::vector1< Size > const & atoms,
    Size const & res2_atom1_index_in,
    Size const & res2_atom2_index_in,
    Size const & res2_atom3_index_in,
    bool one_three = true
  ) const;

  // For output
  virtual void
  print(
    std::ostream & os
  ) const;

  // For output
  virtual
  std::string print() const;

  // Overloaded operator for output
  friend std::ostream & operator <<(
    std::ostream & os,
    Motif const & mot
  );

  // Stores remark, havranek uses
  void
  store_remark(
    std::string const & remark_in
  );

  // Stores path of motif for future output if motif was read from pdb
  void
  store_path(
    std::string const & path_in
  );

  // Accessors
  std::string const & restype_name1() const { return restype_name1_; }
  std::string const & res1_atom1_name() const { return res1_atom1_name_; }
  std::string const & res1_atom2_name() const { return res1_atom2_name_; }
  std::string const & res1_atom3_name() const { return res1_atom3_name_; }
  int const & res1_atom1_int() const { return res1_atom1_int_; }
  int const & res1_atom2_int() const { return res1_atom2_int_; }
  int const & res1_atom3_int() const { return res1_atom3_int_; }
  Size const & res1_atom1_index() const { return res1_atom1_index_; }
  Size const & res1_atom2_index() const { return res1_atom2_index_; }
  Size const & res1_atom3_index() const { return res1_atom3_index_; }
  std::string const & restype_name2() const { return restype_name2_; }
  std::string const & res2_atom1_name() const { return res2_atom1_name_; }
  std::string const & res2_atom2_name() const { return res2_atom2_name_; }
  std::string const & res2_atom3_name() const { return res2_atom3_name_; }
  int const & res2_atom1_int() const { return res2_atom1_int_; }
  int const & res2_atom2_int() const { return res2_atom2_int_; }
  int const & res2_atom3_int() const { return res2_atom3_int_; }
  Size const & res2_atom1_index() const { return res2_atom1_index_; }
  Size const & res2_atom2_index() const { return res2_atom2_index_; }
  Size const & res2_atom3_index() const { return res2_atom3_index_; }
  core::kinematics::Jump const & forward_jump() const { return forward_jump_; }
  core::kinematics::Jump const & backward_jump() const { return backward_jump_; }
  bool has_remark() const { return has_remark_;}
  bool has_path() const { return has_path_;}
  std::string const & remark() const { return remark_;}
  std::string const & path() const { return path_;}

private:
  // names (name3) of the residues in motif and each of the 6 motif atoms
  std::string restype_name1_;
  std::string res1_atom1_name_;
  std::string res1_atom2_name_;
  std::string res1_atom3_name_;
  int res1_atom1_int_;
  int res1_atom2_int_;
  int res1_atom3_int_;
  Size res1_atom1_index_;
  Size res1_atom2_index_;
  Size res1_atom3_index_;
  std::string restype_name2_;
  std::string res2_atom1_name_;
  std::string res2_atom2_name_;
  std::string res2_atom3_name_;
  int res2_atom1_int_;
  int res2_atom2_int_;
  int res2_atom3_int_;
  Size res2_atom1_index_;
  Size res2_atom2_index_;
  Size res2_atom3_index_;
  // Jumps associated with the motif
  core::kinematics::Jump forward_jump_;
  core::kinematics::Jump backward_jump_;
  // Associated information for future output
  std::string remark_;
  std::string path_;
  bool has_remark_;
  bool has_path_;

};

} // namespace motifs
} // namespace protocols

#endif // INCLUDED_protocols_motifs_Motif