PoseCommentsFeatures.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/PoseCommentsFeatures.cc
/// @brief  report comments stored with each pose
/// @author Matthew O'Meara

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

// Project Headers
#include <core/pose/util.hh>

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

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

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

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

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

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

namespace protocols{
namespace features{

using std::string;
using std::map;
using core::Size;
using core::Real;
using core::pose::Pose;
using core::pose::get_all_comments;
using core::pose::add_comment;
using core::conformation::Residue;
using core::chemical::num_canonical_aas;
using basic::database::table_exists;
using utility::sql_database::sessionOP;
using utility::vector1;
using cppdb::statement;
using cppdb::result;
using basic::database::insert_statement_generator::InsertGenerator;
using basic::database::insert_statement_generator::RowDataBaseOP;
using basic::database::insert_statement_generator::RowData;

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

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

  //******pose_comments******//
  Column struct_id("struct_id", new DbUUID(), false);
  Column comment_key("comment_key", new DbTextKey(), false);
  Column value("value", new DbText(), false);

  utility::vector1<Column> pkey_cols;
  pkey_cols.push_back(struct_id);
  pkey_cols.push_back(comment_key);

  Schema pose_comments("pose_comments", PrimaryKey(pkey_cols));
  pose_comments.add_column(struct_id);
  pose_comments.add_column(comment_key);
  pose_comments.add_column(value);

  pose_comments.add_foreign_key(ForeignKey(struct_id, "structures", "struct_id", true));
  pose_comments.write(db_session);

}

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


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

  InsertGenerator pose_comments_insert("pose_comments");
  pose_comments_insert.add_column("struct_id");
  pose_comments_insert.add_column("comment_key");
  pose_comments_insert.add_column("value");


  typedef map< string, string >::value_type kv_pair;

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

  foreach(kv_pair const & kv, get_all_comments(pose)){

    RowDataBaseOP comment_key_data =new RowData<string>("comment_key",kv.first);
    RowDataBaseOP value_data = new RowData<string>("value",kv.second);

    pose_comments_insert.add_row(utility::tools::make_vector(struct_id_data,comment_key_data,value_data));
  }

  pose_comments_insert.write_to_database(db_session);

  return 0;
}

void PoseCommentsFeatures::delete_record(
  boost::uuids::uuid struct_id,
  utility::sql_database::sessionOP db_session
) {

  std::string statement_string = "DELETE FROM pose_comments where struct_id = ?;";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  stmt.bind(1,struct_id);
  basic::database::safely_write_to_database(stmt);

}

void
PoseCommentsFeatures::load_into_pose(
  sessionOP db_session,
  boost::uuids::uuid struct_id,
  Pose & pose){

  if(!table_exists(db_session, "pose_comments")) return;


  std::string statement_string =
    "SELECT\n"
    " comment_key,\n"
    " value\n"
    "FROM\n"
    " pose_comments\n"
    "WHERE\n"
    " pose_comments.struct_id = ?;";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  stmt.bind(1,struct_id);

  result res(basic::database::safely_read_from_database(stmt));

  while(res.next()){
    string key, value;
    res >> key >> value;
    add_comment(pose, key, value);
  }
}

} //namesapce
} //namespace