SecondaryMatchProtocol.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.
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/// @file   protocols/enzdes/SecondaryMatchProtocol.hh
///
/// @brief
/// @author Florian Richter


#ifndef INCLUDED_protocols_enzdes_SecondaryMatchProtocol_hh
#define INCLUDED_protocols_enzdes_SecondaryMatchProtocol_hh


#include <protocols/enzdes/EnzdesBaseProtocol.hh>
// AUTO-REMOVED #include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>

#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/conformation/Residue.fwd.hh>

#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.fwd.hh>
#include <utility/vector1.hh>



namespace protocols{
namespace enzdes{

class SecondaryMatchProtocol;
typedef utility::pointer::owning_ptr< SecondaryMatchProtocol > SecondaryMatchProtocolOP;
typedef utility::pointer::owning_ptr< SecondaryMatchProtocol const > SecondaryMatchProtocolCOP;
typedef utility::pointer::access_ptr< SecondaryMatchProtocol const > SecondaryMatchProtocolCAP;

class PoseFoundResiduesCombination;

typedef utility::pointer::owning_ptr< PoseFoundResiduesCombination > PoseFoundResiduesCombinationOP;



class SecondaryMatchProtocol : public protocols::enzdes::EnzdesBaseProtocol
{

public:

  SecondaryMatchProtocol();
  ~SecondaryMatchProtocol();

  void apply( core::pose::Pose & start_pose);

  virtual std::string get_name() const;

  core::Size
  residues_compatible(
    core::conformation::ResidueCOP res1,
    core::conformation::ResidueCOP res2
  ) const;


  bool
  do_matching(
    core::pose::Pose & start_pose
  );

  void
  set_trial_positions(
    utility::vector1< core::Size > const & trial_pos ){
    trial_positions_ = trial_pos; }


protected:

  void
  add_enz_cst_interaction_to_pose(
    core::pose::Pose & pose,
    toolbox::match_enzdes_util::EnzConstraintParametersCOP params,
    toolbox::match_enzdes_util::EnzCstTemplateResCOP missing_template,
    toolbox::match_enzdes_util::EnzCstTemplateResCOP present_template,
    toolbox::match_enzdes_util::EnzConstraintIOCOP cstio
  );

  void
  find_all_allowed_positions(
    core::pose::Pose const & pose
  );

  bool
  generate_and_dump_pose_found_residues_combinations( core::pose::PoseCOP ref_poseCOP );


  bool
  restype_possible_at_position(
    core::pose::Pose const & pose,
    core::chemical::ResidueTypeCOP restype,
    core::conformation::ResidueCOP target_residue,
    core::Size const trial_pos
  );

  void
  determine_found_residues_compatibility( core::pose::PoseCOP ref_poseCOP );


private:
  utility::vector1< utility::vector1< core::conformation::ResidueOP > > found_resis_;

  std::map< core::conformation::ResidueCOP, std::map< core::conformation::ResidueCOP, core::Size > > found_res_compatibility_;
  bool found_res_compatibility_determined_;

  utility::vector1< core::Size >trial_positions_;
  core::scoring::ScoreFunctionOP reduced_scofx_;
  core::Size cut1_, cut2_, cut3_, cut4_;
  utility::vector1< toolbox::match_enzdes_util::EnzConstraintParametersCOP > match_params_;

}; //class SecondaryMatchProtocol


/// @brief helper class to process and output the different found poses
class PoseFoundResiduesCombination : public utility::pointer::ReferenceCount
{
public:
  virtual ~PoseFoundResiduesCombination();
  PoseFoundResiduesCombination(
    core::pose::PoseCOP ref_pose_in,
    SecondaryMatchProtocolCAP seqmatch_in
  );

  void
  add_residue( core::conformation::ResidueOP res_in );

  bool
  construct_and_dump_outpose( utility::vector1< toolbox::match_enzdes_util::EnzConstraintParametersCOP > match_params );

private:

  //the reference pose for this class
  core::pose::PoseCOP ref_pose_;

  //the residues that need to be put into the ref pose
  utility::vector1< core::conformation::ResidueCOP > combine_resis_;

  //the secondary match protocol that a particular instance comes from
  SecondaryMatchProtocolCAP secmatch_prot_;

}; //PoseFoundResidueCombination


} //namespace enzdes
} //namespace protocols


#endif // INCLUDED_protocols_enzdes_EnzdesFixBBProtocol_HH