GeometricSolvationFeatures.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/GeometricSolvationFeatures.cc
/// @brief  report geometric solvation energy for each polar site to a features database
/// @author Matthew O'Meara

// Unit Headers
#include <protocols/features/GeometricSolvationFeatures.hh>

//External
#include <boost/uuid/uuid.hpp>
#include <boost/uuid/uuid_io.hpp>

// Platform Headers
#include <core/pose/Pose.hh>
#include <core/scoring/geometric_solvation/ExactOccludedHbondSolEnergy.hh>
#include <core/types.hh>

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

// Basic Headers
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/database/sql_utils.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>
// AUTO-REMOVED #include <cppdb/errors.h>

// C++ Headers
#include <string>

namespace protocols{
namespace features{

using std::string;
using core::Size;
using core::Real;
using core::pose::Pose;
using core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy;
using utility::vector1;
using utility::sql_database::sessionOP;
using cppdb::statement;
using cppdb::result;

GeometricSolvationFeatures::GeometricSolvationFeatures() :
  geo_sol_energy_(ExactOccludedHbondSolEnergy())
{

  //I would like to simply assert that this has been called, but that
  //currently is not possible.
  //geo_sol_energy_.setup_for_scoring(pose, scfxn_);

}

GeometricSolvationFeatures::GeometricSolvationFeatures(
  GeometricSolvationFeatures const & src ) :
  FeaturesReporter(),
  geo_sol_energy_(src.geo_sol_energy_)
{}

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

void
GeometricSolvationFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  write_geometric_solvation_table_schema(db_session);
}

void
GeometricSolvationFeatures::write_geometric_solvation_table_schema(
  sessionOP db_session
) const {
  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID());
  Column hbond_site_id("hbond_site_id", new DbInteger());
  Column geometric_solvation_exact("geometric_solvation_exact", new DbReal());

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

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

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

  table.write(db_session);
}

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

Size
GeometricSolvationFeatures::report_features(
  Pose const & pose,
  vector1< bool > const &,
  boost::uuids::uuid struct_id,
  sessionOP db_session
){

  std::string select_string =
    "SELECT\n"
    " site.site_id,\n"
    " site.resNum,\n"
    " site.atmNum\n"
    "FROM\n"
    " hbond_sites as site\n"
    "WHERE\n"
    " site.struct_id = ?;";
  statement select_statement(basic::database::safely_prepare_statement(select_string,db_session));
  select_statement.bind(1,struct_id);
  result res(basic::database::safely_read_from_database(select_statement));

  while(res.next()){
    Size site_id, resNum, atmNum;
    res >> site_id >> resNum >> atmNum;

    Real const geometric_solvation_exact(
      geo_sol_energy_.compute_polar_group_sol_energy(
      pose,
      pose.residue(resNum),
      atmNum));

    std::string insert_string = "INSERT INTO geometric_solvation (struct_id, hbond_site_id, geometric_solvation_exact) VALUES (?,?,?)";
    statement insert_statement(basic::database::safely_prepare_statement(insert_string,db_session));
    insert_statement.bind(1,struct_id);
    insert_statement.bind(2,site_id);
    insert_statement.bind(3,geometric_solvation_exact);
    basic::database::safely_write_to_database(insert_statement);
  }

  // locate the polar sites from the hbond_sites table

  return 0;
}

} //namesapce
} //namespace