ProteinBackboneTorsionAngleFeatures.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/ProteinBackboneTorsionAngleFeatures.cc
/// @brief  report Backbone Torsional Angle features
/// @author Matthew O'Meara (mattjomeara@gmail.com)

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

// Project Headers
#include <core/conformation/Residue.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/vector1.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>


// Platform Headers
#include <core/pose/Pose.hh>

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

namespace protocols{
namespace features{

using std::string;
using cppdb::statement;
using core::Size;
using core::Real;
using core::conformation::Residue;
using core::pose::Pose;
using utility::vector1;
using utility::sql_database::sessionOP;


ProteinBackboneTorsionAngleFeatures::ProteinBackboneTorsionAngleFeatures(){}

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

ProteinBackboneTorsionAngleFeatures::~ProteinBackboneTorsionAngleFeatures(){}

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

void
ProteinBackboneTorsionAngleFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  write_protein_backbone_torsion_angles_table_schema(db_session);
}

void
ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(
  sessionOP db_session
) const {
  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID());
  Column resNum("resNum", new DbInteger());
  Column phi("phi", new DbReal());
  Column psi("psi", new DbReal());
  Column omega("omega", new DbReal());


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

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

  Schema table("protein_backbone_torsion_angles", primary_key);
  table.add_foreign_key(foreign_key);
  table.add_column(phi);
  table.add_column(psi);
  table.add_column(omega);

  table.write(db_session);
}

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

Size
ProteinBackboneTorsionAngleFeatures::report_features(
  Pose const & pose,
  vector1< bool > const & relevant_residues,
  boost::uuids::uuid const struct_id,
  sessionOP db_session
){
  std::string statement_string ="INSERT INTO protein_backbone_torsion_angles (struct_id, resNum, phi, psi, omega) VALUES (?,?,?,?,?)";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  for (Size i = 1; i <= pose.total_residue(); ++i) {
    if(!relevant_residues[i]) continue;

    Residue const & resi = pose.residue(i);
    if(!resi.is_protein()) continue;


    Real phi  (resi.mainchain_torsion(1));
    Real psi  (resi.mainchain_torsion(2));
    Real omega(resi.mainchain_torsion(3));

    stmt.bind(1,struct_id);
    stmt.bind(2,i);
    stmt.bind(3,phi);
    stmt.bind(4,psi);
    stmt.bind(5,omega);
    basic::database::safely_write_to_database(stmt);

  }
  return 0;
}

} // namesapce
} // namespace