ChargeChargeFeatures.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/ChargeChargeFeatures.cc
/// @brief  report geometric solvation energy for each polar site to a features database
/// @author Joseph S Harrison

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

// Platform Headers
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Residue.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>

// Numeric Headers
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/sphericalVector.hh>
#include <core/kinematics/Stub.hh>
#include <numeric/constants.hh>

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

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

// Boost Headers
#include <boost/uuid/uuid_io.hpp>

// C++ Headers
#include <string>
#include <sstream>

namespace protocols{
namespace features{

using std::string;
using std::stringstream;
using std::endl;
using core::Size;
using core::Real;
using core::Vector;
using core::Length;
using core::Angle;
using core::Distance;
using core::PointPosition;
using core::kinematics::Stub;
using core::chemical::aa_asp;
using core::chemical::aa_glu;
using core::chemical::aa_lys;
using core::chemical::aa_his;
using core::chemical::aa_arg;
using core::conformation::Residue;
using core::pose::Pose;
using numeric::dihedral_radians;
using numeric::sphericalVector;
using numeric::xyz_to_spherical;
using numeric::constants::r::pi;
using numeric::constants::r::pi_over_2;
using numeric::constants::r::pi_over_180;
using utility::vector1;
using utility::sql_database::sessionOP;
using cppdb::statement;
using cppdb::result;
using boost::uuids::uuid;

ChargeChargeFeatures::ChargeChargeFeatures() :
  FeaturesReporter(),
  distance_cutoff_(8)
{}

ChargeChargeFeatures::ChargeChargeFeatures(
  Length distance_cutoff) :
  FeaturesReporter(),
  distance_cutoff_(distance_cutoff)
{}

ChargeChargeFeatures::ChargeChargeFeatures(
  ChargeChargeFeatures const & src ) :
  FeaturesReporter(),
  distance_cutoff_(src.distance_cutoff_)
{}

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

void
ChargeChargeFeatures::write_schema_to_db(
  sessionOP db_session
) const {

  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID(), false);
  Column q1_site_id("q1_site_id", new DbInteger(), false);
  Column q2_site_id("q2_site_id", new DbInteger(), false);
  Column q1_charge("q1_charge", new DbInteger(), false);
  Column q2_charge("q2_charge", new DbInteger(), false);
  Column B1q1q2_angle("B1q1q2_angle", new DbReal(), false);
  Column B2q2q1_angle("B2q2q1_angle", new DbReal(), false);
  Column q1q2_distance("q1q2_distance", new DbReal(), false);
  Column B1q1_torsion("B1q1_torsion", new DbReal(), false);
  Column B2q2_torsion("B2q2_torsion", new DbReal(), false);

  utility::vector1<Column> pkeys;
  pkeys.push_back(struct_id);
  pkeys.push_back(q1_site_id);
  pkeys.push_back(q2_site_id);


  utility::vector1<Column> fkey_site1_cols;
  fkey_site1_cols.push_back(struct_id);
  fkey_site1_cols.push_back(q1_site_id);

  utility::vector1<std::string> fkey_site1_reference_cols;
  fkey_site1_reference_cols.push_back("struct_id");
  fkey_site1_reference_cols.push_back("site_id");

  utility::vector1<Column> fkey_site2_cols;
  fkey_site2_cols.push_back(struct_id);
  fkey_site2_cols.push_back(q2_site_id);

  utility::vector1<std::string> fkey_site2_reference_cols;
  fkey_site2_reference_cols.push_back("struct_id");
  fkey_site2_reference_cols.push_back("site_id");

  Schema charge_charge_pairs("charge_charge_pairs", PrimaryKey(pkeys));
  charge_charge_pairs.add_column(struct_id);
  charge_charge_pairs.add_column(q1_site_id);
  charge_charge_pairs.add_column(q2_site_id);
  charge_charge_pairs.add_column(q1_charge);
  charge_charge_pairs.add_column(q2_charge);
  charge_charge_pairs.add_column(B1q1q2_angle);
  charge_charge_pairs.add_column(B2q2q1_angle);
  charge_charge_pairs.add_column(q1q2_distance);
  charge_charge_pairs.add_column(B1q1_torsion);
  charge_charge_pairs.add_column(B2q2_torsion);
  charge_charge_pairs.add_foreign_key(
    ForeignKey(fkey_site1_cols, "hbond_sites", fkey_site1_reference_cols, true));
  charge_charge_pairs.add_foreign_key(
    ForeignKey(fkey_site2_cols, "hbond_sites", fkey_site2_reference_cols, true));

  charge_charge_pairs.write(db_session);
}

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

Size
ChargeChargeFeatures::report_features(
  Pose const &,
  vector1< bool > const &,
  uuid struct_id,
  sessionOP db_session
){

  // locate candidate polar sites from the hbond_sites table

  // Note: these are all pairs of potential salt bridge sites, not
  // just the ones involved in hydrogen bonds
  std::string hbond_string =
    "SELECT\n"
    " q1.site_id AS q1_id,\n"
    " q2.site_id AS q2_id,\n"
    " CASE q1.is_donor WHEN 1 THEN 1 ELSE -1 END AS q1_charge,\n"
    " CASE q2.is_donor WHEN 1 THEN 1 ELSE -1 END AS q2_charge,\n"
    " q1_xyz.atm_x AS q1_x, q1_xyz.atm_y AS q1_y, q1_xyz.atm_z AS q1_z,\n"
    " q2_xyz.atm_x AS q2_x, q2_xyz.atm_y AS q2_y, q2_xyz.atm_z AS q2_z,\n"
    " q1_xyz.base_x AS B1_x, q1_xyz.base_y AS B1_y, q1_xyz.base_z AS B1_z,\n"
    " q2_xyz.base_x AS B2_x, q2_xyz.base_y AS B2_y, q2_xyz.base_z AS B2_z,\n"
    " q1_xyz.bbase_x AS C1_x, q1_xyz.bbase_y AS C1_y, q1_xyz.bbase_z AS C1_z,\n"
    " q2_xyz.bbase_x AS C2_x, q2_xyz.bbase_y AS C2_y, q2_xyz.bbase_z AS C2_z\n"
    "FROM\n"
    " hbond_sites AS q1,\n"
    " hbond_sites AS q2,\n"
    " hbond_site_atoms AS q1_xyz,\n"
    " hbond_site_atoms AS q2_xyz\n"
    "WHERE\n"
    " q1.struct_id = ? AND q2.struct_id = ? AND\n"
    " q1.resNum < q2.resNum AND\n"
    " (q1.HBChemType = 'hbacc_CXL' OR\n"
    " q1.HBChemType = 'hbacc_IMD' OR q1.HBChemType = 'hbacc_IME' OR q1.HBChemType = 'hbdon_IMD' OR q1.HBChemType = 'hbdon_IME' OR\n"
    " q1.HBChemType = 'hbdon_AMO' OR\n"
    " q1.HBChemType = 'hbdon_GDE' OR q1.HBChemType = 'hbdon_GDH' ) AND\n"
    " (q2.HBChemType = 'hbacc_CXL' OR\n"
    " q2.HBChemType = 'hbacc_IMD' OR q2.HBChemType = 'hbacc_IME' OR q2.HBChemType = 'hbdon_IMD' OR q2.HBChemType = 'hbdon_IME' OR\n"
    " q2.HBChemType = 'hbdon_AMO' OR\n"
    " q2.HBChemType = 'hbdon_GDE' OR q2.HBChemType = 'hbdon_GDH' ) AND\n"
    " q1_xyz.struct_id = q1.struct_id AND\n"
    " q2_xyz.struct_id = q2.struct_id AND\n"
    " q1_xyz.site_id = q1.site_id AND\n"
    " q2_xyz.site_id = q2.site_id;\n";

  statement hbond_stmt(basic::database::safely_prepare_statement(hbond_string,db_session));
  hbond_stmt.bind(1,struct_id);
  hbond_stmt.bind(2,struct_id);

  result res(basic::database::safely_read_from_database(hbond_stmt));
  Size q1_site_id, q2_site_id;
  int q1_charge;
  int q2_charge;
  Length q1_x, q1_y, q1_z;
  Length q2_x, q2_y, q2_z;
  Length B1_x, B1_y, B1_z;
  Length B2_x, B2_y, B2_z;
  Length C1_x, C1_y, C1_z;
  Length C2_x, C2_y, C2_z;

  std::string charge_charge_string = "INSERT INTO charge_charge_pairs (struct_id, q1_site_id, q2_site_id, q1_charge, q2_charge, B1q1q2_angle, B2q2q1_angle, q1q2_distance, B1q1_torsion, B2q2_torsion) VALUES (?,?,?,?,?,?,?,?,?,?);";
  statement charge_charge_statement(basic::database::safely_prepare_statement(charge_charge_string,db_session));


  while(res.next()){
    res >> q1_site_id >> q2_site_id;
    res >> q1_charge >> q2_charge;
    res >> q1_x >> q1_y >> q1_z;
    res >> q2_x >> q2_y >> q2_z;
    res >> B1_x >> B1_y >> B1_z;
    res >> B2_x >> B2_y >> B2_z;
    res >> C1_x >> C1_y >> C1_z;
    res >> C2_x >> C2_y >> C2_z;

    PointPosition const q1(q1_x, q1_y, q1_z);
    PointPosition const q2(q2_x, q2_y, q2_z);
    PointPosition const B1(B1_x, B1_y, B1_z);
    PointPosition const B2(B2_x, B2_y, B2_z);
    PointPosition const C1(C1_x, C1_y, C1_z);
    PointPosition const C2(C2_x, C2_y, C2_z);

    Angle const B1q1q2_angle(angle_of(B1, q1, q2));
    Angle const B2q2q1_angle(angle_of(B2, q2, q1));
    Distance const q1q2_distance = q1.distance(q2);
    Angle const B1q1_torsion(dihedral_radians(C1, B1, q1, q2));
    Angle const B2q2_torsion(dihedral_radians(C2, B2, q2, q1));


    if(q1q2_distance > distance_cutoff_){
      continue;
    }



    charge_charge_statement.bind(1,struct_id);
    charge_charge_statement.bind(2,q1_site_id);
    charge_charge_statement.bind(3,q2_site_id);
    charge_charge_statement.bind(4,q1_charge);
    charge_charge_statement.bind(5,q2_charge);
    charge_charge_statement.bind(6,B1q1q2_angle);
    charge_charge_statement.bind(7,B2q2q1_angle);
    charge_charge_statement.bind(8,q1q2_distance);
    charge_charge_statement.bind(9,B1q1_torsion);
    charge_charge_statement.bind(10,B2q2_torsion);
    basic::database::safely_write_to_database(charge_charge_statement);

  }

  return 0;
}

} //namesapce
} //namespace