ProteinRMSDFeatures.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/ProteinRMSDFeatures.cc
/// @brief  report the root mean squared deviation between two poses
/// @author Matthew O'Meara (mattjomeara@gmail.com)

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

// Project Headers
#include <core/pose/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

// Platform Headers
#include <basic/Tracer.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <protocols/rosetta_scripts/util.hh>

// Utility Headers
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>

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

// Boost Headers
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

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

#include <utility/vector0.hh>


namespace protocols{
namespace features{

using std::string;
using std::list;
using std::endl;
using core::Size;
using core::import_pose::pose_from_pdb;
using core::pose::Pose;
using core::pose::PoseCOP;
using core::pose::PoseOP;
using protocols::filters::Filters_map;
using protocols::moves::DataMap;
using protocols::moves::Movers_map;
using protocols::rosetta_scripts::saved_reference_pose;
using utility::vector1;
using utility::sql_database::sessionOP;
using utility::tag::TagPtr;
using cppdb::statement;

static basic::Tracer tr("protocols.features.ProteinRMSDFeatures");

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


PoseCOP
ProteinRMSDFeatures::reference_pose() const {
  return reference_pose_;
}

void
ProteinRMSDFeatures::reference_pose(
  PoseCOP pose
) {
  reference_pose_ = pose;
}

ProteinRMSDFeatures::ProteinRMSDFeatures(
  PoseCOP reference_pose ) :
  reference_pose_(reference_pose)
{}

void
ProteinRMSDFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  write_protein_rmsd_table_schema(db_session);
}

void
ProteinRMSDFeatures::write_protein_rmsd_table_schema(
  sessionOP db_session
) const {
  using namespace basic::database::schema_generator;

  Column struct_id("struct_id", new DbUUID());
  Column reference_tag("reference_tag", new DbText(255));
  Column protein_CA("protein_CA", new DbReal());
  Column protein_CA_or_CB("protein_CA_or_CB", new DbReal());
  Column protein_backbone("protein_backbone", new DbReal());
  Column protein_backbone_including_O("protein_backbone_including_O", new DbReal());
  Column protein_backbone_sidechain_heavyatom("protein_backbone_sidechain_heavyatom", new DbReal());
  Column heavyatom("heavyatom", new DbReal());
  Column nbr_atom("nbr_atom", new DbReal());
  Column all_atom("all_atom", new DbReal());

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

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

  Schema table("protein_rmsd", primary_key);
  table.add_foreign_key(foreign_key);
  table.add_column(reference_tag);
  table.add_column(protein_CA);
  table.add_column(protein_CA_or_CB);
  table.add_column(protein_backbone);
  table.add_column(protein_backbone_including_O);
  table.add_column(protein_backbone_sidechain_heavyatom);
  table.add_column(heavyatom);
  table.add_column(nbr_atom);
  table.add_column(all_atom);

  table.write(db_session);
}

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

void
ProteinRMSDFeatures::parse_my_tag(
  TagPtr const tag,
  DataMap & data,
  Filters_map const & /*filters*/,
  Movers_map const & /*movers*/,
  Pose const & pose
) {
  runtime_assert(tag->getOption<string>("name") == type_name());

  if(tag->hasOption("reference_name")){
    // Use with SavePoseMover
    // WARNING! reference_pose is not initialized until apply time
    reference_pose(saved_reference_pose(tag, data));
  } else {
    using namespace basic::options;
    if (option[OptionKeys::in::file::native].user()) {
      PoseOP ref_pose = new core::pose::Pose();
      string native_pdb_fname(option[OptionKeys::in::file::native]());
      pose_from_pdb(*ref_pose, native_pdb_fname);
      tr << "Adding features reporter '" << type_name() << "' referencing '"
        << " the -in:file:native='" << native_pdb_fname << "'" << endl;
      reference_pose(ref_pose);
    } else {
      tr << "Setting '" << type_name() << "' to reference the starting structure." << endl;
      reference_pose(new Pose(pose));
    }
  }
}

Size
ProteinRMSDFeatures::report_features(
  Pose const & pose,
  vector1< bool > const & relevant_residues,
  boost::uuids::uuid struct_id,
  sessionOP db_session
){
  using namespace core::scoring;

  if(!reference_pose_ || !reference_pose_->total_residue()){
    utility_exit_with_message("No reference pose has been initialized.");
    return 0;
  }

  list< Size > subset_residues;
  for(Size i = 1; i <= relevant_residues.size(); ++i){
    if(relevant_residues[i]) subset_residues.push_back(i);
  }

  std::string statement_string = "INSERT INTO protein_rmsd (struct_id, reference_tag, protein_CA, protein_CA_or_CB, protein_backbone, protein_backbone_including_O, protein_backbone_sidechain_heavyatom, heavyatom, nbr_atom, all_atom) VALUES (?,?,?,?,?,?,?,?,?,?);";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));

  stmt.bind(1,struct_id);
  stmt.bind(2,find_tag(*reference_pose_));
  stmt.bind(3,rmsd_with_super(*reference_pose_, pose, subset_residues, is_protein_CA));
  stmt.bind(4,rmsd_with_super(*reference_pose_, pose, subset_residues, is_protein_CA_or_CB));
  stmt.bind(5,rmsd_with_super(*reference_pose_, pose, subset_residues, is_protein_backbone));
  stmt.bind(6,rmsd_with_super(*reference_pose_, pose, subset_residues, is_protein_backbone_including_O));
  stmt.bind(7,rmsd_with_super(*reference_pose_, pose, subset_residues, is_protein_sidechain_heavyatom));
  stmt.bind(8,rmsd_with_super(*reference_pose_, pose, subset_residues, is_heavyatom));
  stmt.bind(9,rmsd_with_super(*reference_pose_, pose, subset_residues, is_nbr_atom));
  stmt.bind(10,all_atom_rmsd(*reference_pose_, pose, subset_residues));

  basic::database::safely_write_to_database(stmt);

  return 0;
}

} //namesapce
} //namespace