LoopAnchorFeatures.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/features/LoopAnchorFeatures.hh
/// @brief  report comments stored with each pose
/// @author Matthew O'Meara

#ifndef INCLUDED_protocols_features_LoopAnchorFeatures_hh
#define INCLUDED_protocols_features_LoopAnchorFeatures_hh

// Unit Headers
#include <protocols/features/FeaturesReporter.hh>
#include <protocols/features/LoopAnchorFeatures.fwd.hh>

//External
#include <boost/uuid/uuid.hpp>
#include <cppdb/frontend.h>

// Utility Headers
#include <numeric/HomogeneousTransform.fwd.hh>

namespace protocols{
namespace features{

class LoopAnchorFeatures : public FeaturesReporter {
public:
  LoopAnchorFeatures();

  LoopAnchorFeatures(LoopAnchorFeatures const & );

  virtual ~LoopAnchorFeatures();

  ///@brief return string with class name
  std::string
  type_name() const;

  ///@brief generate the table schemas and write them to the database
  void
  write_schema_to_db(
    utility::sql_database::sessionOP db_session) const;

private:
  ///@brief generate the loop_anchors table schema
  void
  write_loop_anchors_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the loop_anchor_transforms table schema
  void
  write_loop_anchor_transforms_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the loop_anchor_transforms_three_res table schema
  void
  write_loop_anchor_transforms_three_res_table_schema(
    utility::sql_database::sessionOP db_session) const;

public:
  ///@brief return the set of features reporters that are required to
  ///also already be extracted by the time this one is used.
  utility::vector1<std::string>
  features_reporter_dependencies() const;

  void
  parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & /*data*/,
    protocols::filters::Filters_map const & /*filters*/,
    protocols::moves::Movers_map const & /*movers*/,
    core::pose::Pose const & /*pose*/);

  ///@brief collect all the feature data for the pose
  core::Size
  report_features(
    core::pose::Pose const & pose,
    utility::vector1< bool > const & /*relevant_residues*/,
    boost::uuids::uuid struct_id,
    utility::sql_database::sessionOP db_session);

    void
    set_use_relevant_residues_as_loop_length( bool const use_relevant_residues_as_loop_length );
    
    void
    set_use_single_residue_to_define_anchor_transfrom( bool const use_single_residue_to_define_anchor_transfrom );

private:

  utility::vector1<Size> start_residue(Size resNo);
  utility::vector1<Size> end_residue(Size resNo);
  utility::vector1<Size> atoms();
  
  core::Size min_loop_length( utility::vector1< bool > const & relevant_residue );
  core::Size max_loop_length( utility::vector1< bool > const & relevant_residue );
  core::Size determine_correct_length( utility::vector1< bool > const & relevant_residue, Size default_length );
  
  numeric::HomogeneousTransform<core::Real>
  compute_anchor_transform(
    core::pose::Pose const & pose,
    utility::vector1<core::Size> const & residue_begin,
    utility::vector1<core::Size> const & residue_end,
    utility::vector1<core::Size> const & atoms);
  
  void
  compute_transform_and_write_to_db(
    boost::uuids::uuid struct_id,
    core::Size begin,
    core::Size end,
    core::pose::Pose const & pose,
    cppdb::statement & stmt);
  
  core::Real
  compute_atom_angles(
    core::pose::Pose const & pose,
    utility::vector1<core::Size> const & residues,
    utility::vector1<core::Size> const & atoms);
private:

  bool use_relevant_residues_as_loop_length_;
  bool use_single_residue_to_define_anchor_transfrom_;
  core::Size min_loop_length_;
  core::Size max_loop_length_;

};

} // features namespace
} // protocols namespace

#endif //INCLUDED_protocols_features_LoopAnchorFeatures_hh