ResidueBurialFeatures.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.
// (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/ResidueBurialFeatures.cc
/// @brief  report residue burial to features statistics scientific benchmark
/// @author Matthew O'Meara (mattjomeara@gmail.com)

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

// Project Headers
#include <core/id/AtomID_Map.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/TwelveANeighborGraph.hh>
#include <core/scoring/nv/NVscore.hh>
#include <core/types.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>

// Numeric Headers
#include <numeric/xyzVector.hh>

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

#include <core/scoring/methods/EnergyMethodOptions.fwd.hh>


namespace protocols{
namespace features{

using std::string;
using core::Size;
using core::Real;
using core::pose::Pose;
using core::conformation::Residue;
using core::id::AtomID_Map;
using core::scoring::calc_per_atom_sasa;
using core::scoring::EnergyMap;
using core::scoring::ScoreFunctionOP;
using core::scoring::TenANeighborGraph;
using core::scoring::TwelveANeighborGraph;
using core::scoring::neigh_vect_raw;
using core::scoring::methods::EnergyMethodOptions;
using core::scoring::nv::NVscore;
using utility::sql_database::sessionOP;
using utility::vector1;
using cppdb::statement;

ResidueBurialFeatures::ResidueBurialFeatures() :
  nv_score_(new NVscore())
{}

ResidueBurialFeatures::ResidueBurialFeatures(ResidueBurialFeatures const & src) :
  FeaturesReporter(),
  nv_score_(src.nv_score_)
{}

ResidueBurialFeatures::~ResidueBurialFeatures(){}

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

void
ResidueBurialFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  write_residue_burial_table_schema(db_session);
}

void
ResidueBurialFeatures::write_residue_burial_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 ten_a_neighbors("ten_a_neighbors", new DbInteger());
  Column twelve_a_neighbors("twelve_a_neighbors", new DbInteger());
  Column neigh_vect_raw("neigh_vect_raw", new DbReal());
  Column sasa_r100("sasa_r100", new DbReal());
  Column sasa_r140("sasa_r140", new DbReal());
  Column sasa_r200("sasa_r200", 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("residue_burial", primary_key);
  table.add_foreign_key(foreign_key);
  table.add_column(ten_a_neighbors);
  table.add_column(twelve_a_neighbors);
  table.add_column(neigh_vect_raw);
  table.add_column(sasa_r100);
  table.add_column(sasa_r140);
  table.add_column(sasa_r200);

  table.write(db_session);
}

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

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

  TenANeighborGraph const & tenA( pose.energies().tenA_neighbor_graph() );
  TwelveANeighborGraph const & twelveA( pose.energies().twelveA_neighbor_graph() );

  Real const probe_radius_s(1.0);
  AtomID_Map< Real > atom_sasa_s;
  vector1< Real > residue_sasa_s;
  calc_per_atom_sasa( pose, atom_sasa_s, residue_sasa_s, probe_radius_s);

  Real const probe_radius_m(1.4);
  AtomID_Map< Real > atom_sasa_m;
  vector1< Real > residue_sasa_m;
  calc_per_atom_sasa( pose, atom_sasa_m, residue_sasa_m, probe_radius_m);

  Real const probe_radius_l(2.0);
  AtomID_Map< Real > atom_sasa_l;
  vector1< Real > residue_sasa_l;
  calc_per_atom_sasa( pose, atom_sasa_l, residue_sasa_l, probe_radius_l);

  std::string statement_string = "INSERT INTO residue_burial (struct_id, resNum, ten_a_neighbors, twelve_a_neighbors, neigh_vect_raw, sasa_r100, sasa_r140, sasa_r200) VALUES (?,?,?,?,?,?,?,?);";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));

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

    Size const ten_a_neighbors(tenA.get_node(resNum)->num_neighbors_counting_self_static());
    Size const twelve_a_neighbors(twelveA.get_node(resNum)->num_neighbors_counting_self_static());

    EnergyMap nv_emap;
    nv_score_->residue_energy(res, pose, nv_emap);

    stmt.bind(1,struct_id);
    stmt.bind(2,resNum);
    stmt.bind(3,ten_a_neighbors);
    stmt.bind(4,twelve_a_neighbors);
    stmt.bind(5,nv_emap[neigh_vect_raw]);
    stmt.bind(6,residue_sasa_s[resNum]);
    stmt.bind(7,residue_sasa_m[resNum]);
    stmt.bind(8,residue_sasa_l[resNum]);
    basic::database::safely_write_to_database(stmt);
  }
  return 0;
}

} // namespace
} // namespace