SeqprofConsensusOperation.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 protocols/toolbox/task_operations/SeqprofConsensus.hh
/// @brief set every position to be designable to residues observed in sequence profile
/// @author Florian Richter, floric@u.washington.edu, april 2011

#ifndef INCLUDED_protocols_toolbox_task_operations_SeqprofConsensusOperation_hh
#define INCLUDED_protocols_toolbox_task_operations_SeqprofConsensusOperation_hh

// unit headers
#include <protocols/toolbox/task_operations/SeqprofConsensusOperation.fwd.hh>

//package headers
#include <core/pack/task/operation/TaskOperation.hh>

//project headers
#include <core/chemical/AA.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/sequence/SequenceProfile.fwd.hh>
#include <core/types.hh>
#include <core/io/ddg/PositionDdGInfo.fwd.hh>

// Utility Headers
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.hh>

// AUTO-REMOVED #include <iostream>

#include <map>


using namespace core::pack::task;

namespace protocols{
namespace toolbox{
namespace task_operations{

class SeqprofConsensusOperation : public core::pack::task::operation::TaskOperation {
public:

  typedef std::string String;
  typedef core::Real Real;
  typedef core::pose::Pose Pose;
  typedef core::pack::task::PackerTask PackerTask;
  typedef core::pack::task::operation::TaskOperation TaskOperation;
  typedef core::pack::task::operation::TaskOperationOP TaskOperationOP;
  typedef TaskOperation parent;
  typedef utility::tag::TagPtr TagPtr;


public:

  /// @brief default constructor
  SeqprofConsensusOperation();

  /// @brief destructor
   ~SeqprofConsensusOperation();

  /// @brief make clone
  virtual TaskOperationOP clone() const;

public:

  void parse_tag( TagPtr tag );

  /// @brief apply
  virtual void apply( Pose const & pose, PackerTask & task ) const;

  core::sequence::SequenceProfileCOP
  seqprof() const;

  void
  set_ignore_pose_profile_length_mismatch( bool const setting ) {
    ignore_pose_profile_length_mismatch_ = setting; }

  /// @brief Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first
  void
  set_seqprof( core::sequence::SequenceProfileCOP seqprof, bool reweight = false );

private:

  std::string seqprof_filename_;
  /// @details Stored as a per-position probability weighted value
  core::sequence::SequenceProfileCOP seqprof_;
  /// @brief mininum probability that an aa must have in the sequence profile to be considered
  core::Real min_aa_probability_;
  /// @brief whether probability of a given aa to be included needs to be higher than the probability of the aa in the input pose
  bool prob_larger_current_;

  /// @default false. if true, every pose seqpos that is bigger
  /// than the size of the sequence_profile will be set to repacking
  /// allows using this taskop in situations where one wants to
  /// do consensus design on one chain of a protein/protein interface
  bool ignore_pose_profile_length_mismatch_;

};

/// @brief a Task operation that will check whether the amino acid at a
/// position is conserved in the sequence profile and has an unfavorable
/// ddG when mutated to ala. all positions that match this criterion will
/// get set to repacking.
/// @details wt ala positions are set to repacking based on seqprof criterion
/// only.
/// If the input pose contains a forbidden (i.e. non wildtype ) residue
/// at an untouchable position, the residue currently in the pose is
/// also allowed.
class RestrictConservedLowDdgOperation : public SeqprofConsensusOperation {

public:
  typedef SeqprofConsensusOperation Parent;

  RestrictConservedLowDdgOperation();

  ~RestrictConservedLowDdgOperation();

  virtual TaskOperationOP clone() const;

  void parse_tag( TagPtr tag );

  virtual void apply( Pose const & pose, PackerTask & task ) const;

  /// @brief returns true if seqpos has a sequence profile
  /// frequency > conservation_cutoff_ and an X->A ddG of >
  /// ddG_cutoff_
  bool
  position_untouchable(
    core::Size seqpos,
    core::chemical::AA seqprof_wt
  ) const;

  //convenience function that returns the wild type residue
  //in the pssm file at seqpos
  core::chemical::AA
  seqprof_wt_aa( core::Size seqpos ) const;

  /// @brief convenience function to query
  /// what the ddG is for a to ala mutation
  /// at a certain position
  core::Real
  position_ala_ddG( core::Size seqpos ) const;

  bool
  verbose() const {
    return verbose_;}

private:
  std::string ddG_predictions_filename_;
  std::map< core::Size, core::io::PositionDdGInfo::PositionDdGInfoOP > position_ddGs_;
  core::Real conservation_cutoff_; //how freqeunt a residue must be in the sequence profile to count as conserved
  core::Real ddG_cutoff_; //how favorable the ddG at a position has to be for the residue to be considered untouchable
  bool verbose_; //spit out information about untouchable residues

};


} // TaskOperations
} // toolbox
} // protocols
#endif