Rosetta  2021.16
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util.cc File Reference
#include <core/types.hh>
#include <protocols/features/util.hh>
#include <protocols/features/FeaturesReporter.hh>
#include <protocols/features/ProtocolFeatures.hh>
#include <protocols/features/BatchFeatures.hh>
#include <basic/mpi/MessageListenerFactory.hh>
#include <basic/mpi/MessageListener.hh>
#include <basic/mpi/DbMoverMessageListener.hh>
#include <basic/mpi/util.hh>
#include <basic/mpi/mpi_enums.hh>
#include <basic/database/schema_generator/Schema.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/DbDataType.hh>
#include <basic/Tracer.hh>
#include <basic/database/sql_utils.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/string_util.hh>
#include <utility/mpi_util.hh>
#include <utility/exit.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/Binary_Util.hh>
#include <cppdb/frontend.h>
#include <cppdb/errors.h>
#include <core/conformation/Residue.hh>
#include <string>
#include <sstream>
#include <utility>
#include <iostream>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::features
 

Functions

static Tracer protocols::features::TR ("protocols.features.util")
 
void protocols::features::set_protocol_and_batch_id (core::Size protocol_id, core::Size batch_id, string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
 write the given protocol and batch ids to the database. The protocol and batches features reporters will check for an existing entry with the same key, and write if one does not exist. Not recommended for parallel use as it is subject to race conditions (due to the nature of 'insert or ignore' type database writing) More...
 
pair< core::Size, core::Sizeprotocols::features::get_protocol_and_batch_id (string const &batch_name, string const &batch_description, utility::vector1< FeaturesReporterOP > features_reporters, sessionOP db_session)
 Get the protocol and batch ids or create them if they don't yet exist. For MPI protocols, only allow the head node to create protocol or batch ids and have the other nodes ask the head node for the info. More...
 
void protocols::features::write_features_reporters_table (utility::vector1< FeaturesReporterOP > features_reporters, utility::sql_database::sessionOP db_session)
 
void protocols::features::write_batch_reports_table (utility::vector1< FeaturesReporterOP > features_reporters, core::Size batch_id, utility::sql_database::sessionOP db_session)
 write the linking table between features reporters and batches. This happens here so that the protocol/batch id framework can be used to prevent duplicate key entries. This function gets called when the batch id is written. More...
 
pair< core::Size, core::Sizeprotocols::features::deserialize_db_listener_data (string data)
 
string protocols::features::serialize_ids (int protocol_id, string batch_name, core::Size batch_id)
 
Size protocols::features::get_batch_id (StructureID struct_id, sessionOP db_session)
 
utility::vector1< StructureID > protocols::features::struct_ids_from_tag (sessionOP db_session, string const &tag)
 
std::string protocols::features::serialize_residue_xyz_coords (core::conformation::Residue const &residue)
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
protocols::features::deserialize_xyz_coords (std::string const &data, core::Size natoms)
 
std::string protocols::features::get_question_mark_string (core::Size const n)
 Returns (?,?,?) With question marks of length n to help create database query. More...
 

Variables

Size protocols::features::static_protocol_id_ = 0
 
bool protocols::features::protocol_table_initialized_ = false
 
map< string, core::Sizeprotocols::features::static_batch_id_map_