MatchPositionModifiers.hh

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// (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
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/// @file   protocols/match/MatchPositionModifiers.hh
/// @brief  header file for MatchPositionModifiers
/// @author Florian Richter (floric@u.washington.edu ), may 2010

#ifndef INCLUDED_protocols_match_MatchPositionModifiers_hh
#define INCLUDED_protocols_match_MatchPositionModifiers_hh

// unit headers
#include <protocols/match/MatchPositionModifiers.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>

//package headers
#include <protocols/match/MatcherTask.fwd.hh>

//project headers
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>

// utility headers
#include <utility/vector1.hh>

// C++ headers
#include <set>

namespace protocols {
namespace match {

/// @brief "factory" function to create the match position modifiers
MatchPositionModifierCOP
create_match_position_modifier(
  std::string const mpm_name,
  core::Size geom_cst,
  utility::vector1< std::string > const & input_tokens );

/// @brief base class for objects that modify the match positions based
/// on some criterion
class MatchPositionModifier : public utility::pointer::ReferenceCount {

public:
  MatchPositionModifier();

  virtual ~MatchPositionModifier();

  /// @brief the positions in the vector1< Size > that is returned
  /// by this function will replace the match positions in the MatcherTask.
  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const = 0;

};

/// @brief removes positions at which the pose does not have the
/// desired secondary structure
class SecondaryStructureMPM : public MatchPositionModifier {

public:
  SecondaryStructureMPM( utility::vector1< std::string > const & input_tokens );

  ~SecondaryStructureMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;

private:

  std::set< char > desired_ss_chars_;
  utility::vector1< std::string > ss_motifs_;

};

/// @brief removes positions whose numer of neighbors
/// below a 10A cutoff is not within the desired range.
/// if either min_neighbors_ or max_neighbors_ are unspecified (0),
/// this means that they won't be taken into account, i.e.
/// if min is 5 and max is 0, every position that has
/// more than 4 neighbors will be allowed.
/// also offers the possibility of combining the num neighbors
/// cutoff with the angle between the CA->CB vector of the residue
/// and the CA->protein_center_of_mass vector, for example to
/// only allow positions that point inward
class NumNeighborsMPM : public MatchPositionModifier {

public:
  NumNeighborsMPM( utility::vector1< std::string > const & input_tokens );

  ~NumNeighborsMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;

  bool
  passes_com_vector_criterion(
    core::Size seqpos,
    core::pose::Pose const & pose,
    core::Vector const & com
  ) const;

private:

  core::Size min_neighbors_, max_neighbors_;

  bool com_vector_criterion_;  //whether to use center of mass vector
  bool both_criteria_needed_to_pass_;  //if fullfilling the com vector criterion and the num neighbors criterion is necessary for a position to pass
  core::Real min_com_vector_ang_cos_, max_com_vector_ang_cos_;

};


/// @brief removes positions at which the bfactors for
/// c-alpha atoms are above a desired cutoff. bfactors
/// stored in the pose pdbinfo are taken.
/// if relative bfactors are used, all bfactors are divided
/// by the largest observed bfactor
class BfactorMPM : public MatchPositionModifier {

public:
  BfactorMPM( utility::vector1< std::string > const & input_tokens );

  ~BfactorMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;

  utility::vector1< core::Real >
  get_ca_bfactors( core::pose::Pose const & pose ) const;

private:

  bool use_relative_bfactors_;
  mutable bool all_bfactors_zero_; //safeguard against pdbs that had their bfactors wiped
  core::Real max_bfactor_;

};

/// @brief MPM that returns a vector of all protein positions in the pose
/// i.e. allowing matching everywhere
class AddAllPositionsMPM : public MatchPositionModifier {

public:
  AddAllPositionsMPM();

  ~AddAllPositionsMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;


private:

};

/// @brief added by olga and flo 1/2011
/// class to exclude positions at the n and c termini of proteins from matching
class RemoveNorCTermMPM : public MatchPositionModifier {

public:

  RemoveNorCTermMPM( utility::vector1< std::string > const & input_tokens );

  ~RemoveNorCTermMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;


private:
  core::Size cterm_length_, nterm_length_;

};

/// @brief mpm that will get a task operation as specified in the tag
/// from the TaskOperationFactory, apply the task operation to the pose
/// and every residue that is then set to designing in the task will be
/// a match position
class TaskOperationMPM : public MatchPositionModifier {

public:

  TaskOperationMPM(
    core::Size geom_cst,
    utility::vector1< std::string > const & input_tokens
  );

  ~TaskOperationMPM();

  virtual
  utility::vector1< core::Size >
  modified_match_positions(
    utility::vector1< core::Size > const & original_positions,
    core::pose::Pose const & match_pose,
    protocols::match::MatcherTaskCOP mtask
  ) const;


private:
  core::Size which_geom_cst_;
  core::pack::task::operation::TaskOperationOP task_op_;
};


}
}

#endif