RadiusOfGyrationFeatures.cc

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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.
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// (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/features/RadiusOfGyrationFeatures.cc
/// @brief  report the radius of gyration to features Statistics Scientific Benchmark
/// @author Matthew O'Meara (mattjomeara@gmail.com)

// Unit Headers
#include <protocols/features/RadiusOfGyrationFeatures.hh>
#include <core/scoring/methods/RG_Energy_Fast.hh>

// Project Headers
#include <core/types.hh>
#include <basic/database/sql_utils.hh>

// Utility Headers
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/vector1.hh>

#include <basic/database/schema_generator/PrimaryKey.hh>
#include <basic/database/schema_generator/ForeignKey.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/Schema.hh>

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

namespace protocols{
namespace features{

using std::string;
using core::Size;
using core::pose::Pose;
using core::scoring::methods::RG_Energy_Fast;
using utility::vector1;
using utility::sql_database::sessionOP;
using cppdb::statement;

RadiusOfGyrationFeatures::RadiusOfGyrationFeatures(){}

RadiusOfGyrationFeatures::RadiusOfGyrationFeatures( RadiusOfGyrationFeatures const & ) :
  FeaturesReporter()
{}

RadiusOfGyrationFeatures::~RadiusOfGyrationFeatures(){}

string
RadiusOfGyrationFeatures::type_name() const { return "RadiusOfGyrationFeatures"; }

void
RadiusOfGyrationFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  write_radius_of_gyration_table_schema(db_session);
}

void
RadiusOfGyrationFeatures::write_radius_of_gyration_table_schema(
  sessionOP db_session
) const {
  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID());
  Column radius_of_gyration("radius_of_gyration", new DbReal());

  Columns primary_key_columns;
  primary_key_columns.push_back(struct_id);
  PrimaryKey primary_key(primary_key_columns);

  Columns foreign_key_columns;
  foreign_key_columns.push_back(struct_id);
  vector1< std::string > reference_columns;
  reference_columns.push_back("struct_id");
  ForeignKey foreign_key(foreign_key_columns, "structures", reference_columns, true);

  Schema table("radius_of_gyration", primary_key);
  table.add_foreign_key(foreign_key);
  table.add_column(radius_of_gyration);

  table.write(db_session);
}

utility::vector1<std::string>
RadiusOfGyrationFeatures::features_reporter_dependencies() const {
  utility::vector1<std::string> dependencies;
  dependencies.push_back("StructureFeatures");
  return dependencies;
}

Size
RadiusOfGyrationFeatures::report_features(
  Pose const & pose,
  vector1< bool > const & relevant_residues,
  boost::uuids::uuid struct_id,
  sessionOP db_session
){
  RG_Energy_Fast rg;

  std::string statement_string =  "INSERT INTO radius_of_gyration (struct_id, radius_of_gyration) VALUES (?,?);";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  stmt.bind(1,struct_id);
  stmt.bind(2,rg.calculate_rg_score(pose, relevant_residues));
  basic::database::safely_write_to_database(stmt);
  return 0;
}

} // features namesapce
} // protocols namespace