ResidueFeatures.cc

Go to the documentation of this file.

// -*- 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/ResidueFeatures.cc
/// @brief  report residue features to features Statistics Scientific Benchmark
/// @author Matthew O'Meara

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

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

// Project Headers
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>

//Basic Headers
#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>
#include <basic/database/schema_generator/Constraint.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>

#include <basic/database/insert_statement_generator/InsertGenerator.hh>
#include <basic/database/insert_statement_generator/RowData.hh>

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

// External Headers
#include <cppdb/frontend.h>

// C++ Headers
//#include <cmath>

namespace protocols{
namespace features{

static basic::Tracer TR("protocols.features.ResidueFeatures");

using std::string;
using core::Size;
using core::Real;
using core::pose::Pose;
using core::conformation::Residue;
using utility::vector1;
using utility::sql_database::sessionOP;
using cppdb::statement;
using basic::database::insert_statement_generator::InsertGenerator;
using basic::database::insert_statement_generator::RowDataBaseOP;
using basic::database::insert_statement_generator::RowData;

ResidueFeatures::ResidueFeatures() {}

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

ResidueFeatures::~ResidueFeatures()
{}

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

void
ResidueFeatures::write_schema_to_db(utility::sql_database::sessionOP db_session) const{
  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID(), false);
  Column resNum("resNum", new DbInteger(), false);
  Column name3("name3", new DbText(), false);
  Column res_type("res_type", new DbText(), false);

  utility::vector1<Column> residues_pkey_cols;
  residues_pkey_cols.push_back(struct_id);
  residues_pkey_cols.push_back(resNum);

  Schema residues("residues", PrimaryKey(residues_pkey_cols));
  residues.add_column(struct_id);
  residues.add_column(resNum);
  residues.add_column(name3);
  residues.add_column(res_type);
  residues.add_foreign_key(ForeignKey(struct_id, "structures", "struct_id", true));

  //TODO add constraint resNum > 0

  residues.write(db_session);

}

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

Size
ResidueFeatures::report_features(
  Pose const & pose,
  vector1< bool > const & relevant_residues,
  boost::uuids::uuid const struct_id,
  sessionOP db_session
){
  insert_residue_rows(pose, relevant_residues, struct_id, db_session);
  return 0;
}


void
ResidueFeatures::insert_residue_rows(
  Pose const & pose,
  vector1< bool > const & relevant_residues,
  boost::uuids::uuid const struct_id,
  sessionOP db_session
){


  InsertGenerator residues_insert("residues");
  residues_insert.add_column("struct_id");
  residues_insert.add_column("resNum");
  residues_insert.add_column("name3");
  residues_insert.add_column("res_type");

  RowDataBaseOP struct_id_data = new RowData<boost::uuids::uuid>("struct_id",struct_id);

  for(Size resNum=1; resNum <= pose.total_residue(); ++resNum){
    if(!relevant_residues[resNum]) continue;
    Residue res = pose.residue(resNum);

    string const name3( res.name3() );
    string const res_type( res.name() );

    RowDataBaseOP resnum_data = new RowData<Size>("resNum",resNum);
    RowDataBaseOP name3_data = new RowData<string>("name3",name3);
    RowDataBaseOP res_type_data = new RowData<string>("res_type",res_type);

    residues_insert.add_row(utility::tools::make_vector(struct_id_data,resnum_data,name3_data,res_type_data));

  }

  residues_insert.write_to_database(db_session);
}

void
ResidueFeatures::delete_record(
  boost::uuids::uuid struct_id,
  sessionOP db_session) {

  delete_records_from_table("residues", struct_id, db_session);
}



} // namesapce
} // namespace