protocols::antibody::design::AntibodyDatabaseManager Class Reference

Class responsible for loading information from the AntibodyDatabase. More...

#include <AntibodyDatabaseManager.hh>

Public Member Functions
	AntibodyDatabaseManager ()
	AntibodyDatabaseManager (std::string const database_path)
virtual	~AntibodyDatabaseManager ()
std::pair< CDRSet, CDRClusterMap >	load_cdrs_for_grafting (AntibodyInfoCOP ab_info, GraftInstructions &instructions, PDBMap &pdbmap, core::Size overhang=3)
	Load data needed for GraftDesigner - CDR structures + their corresponding cluster. More...
vector1< CDRNameEnum >	load_cdr_design_data (AntibodyInfoCOP ab_info, core::pose::Pose const &pose, std::map< core::Size, AAProbabilities > &prob_set, core::Size const cutoff, DesignInstructions &instructions)
	Load probability data for CDR Design. Returns CDRs where data could not be loaded. Cutoff indicates number of total sequences needed to use the data. More...

Private Member Functions
void	start_database_session (std::string const database_path)
	Gets database session. More...
void	check_for_graft_instruction_inconsistencies (AntibodyInfoCOP ab_info, GraftInstructions &instructions)
	Checks to make sure the instructions make sense before trying to create the statement for the db.. More...

Private Attributes
std::string	db_path_
utility::sql_database::sessionOP	db_session_

Detailed Description

Class responsible for loading information from the AntibodyDatabase.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDatabaseManager::AntibodyDatabaseManager

(

)

References basic::options::OptionKeys::antibody::design::antibody_database, basic::database::full_name(), and basic::options::option.

protocols::antibody::design::AntibodyDatabaseManager::AntibodyDatabaseManager

(

std::string const

database_path

)

protocols::antibody::design::AntibodyDatabaseManager::~AntibodyDatabaseManager ( )

virtual

Member Function Documentation

void protocols::antibody::design::AntibodyDatabaseManager::check_for_graft_instruction_inconsistencies ( AntibodyInfoCOP  ab_info, GraftInstructions &  instructions  )

private

Checks to make sure the instructions make sense before trying to create the statement for the db..

References protocols::antibody::CDRNameEnum_total, and utility_exit_with_message.

vector1< CDRNameEnum > protocols::antibody::design::AntibodyDatabaseManager::load_cdr_design_data	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose const &	pose,
		std::map< core::Size, AAProbabilities > &	prob_set,
		core::Size const	cutoff,
		DesignInstructions &	instructions
	)

Load probability data for CDR Design. Returns CDRs where data could not be loaded. Cutoff indicates number of total sequences needed to use the data.

References core::chemical::aa_from_oneletter_code(), protocols::antibody::CDRNameEnum_total, cluster, design, NA, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and protocols::antibody::TR.

Referenced by protocols::antibody::design::AntibodySeqDesignMover::setup_probability_data().

std::pair< CDRSet, CDRClusterMap > protocols::antibody::design::AntibodyDatabaseManager::load_cdrs_for_grafting	(	AntibodyInfoCOP	ab_info,
		GraftInstructions &	instructions,
		PDBMap &	pdbmap,
		core::Size	overhang = 3
	)

Load data needed for GraftDesigner - CDR structures + their corresponding cluster.

References protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_is_present(), protocols::antibody::CDRNameEnum_total, cluster, core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), protocols::features::get_question_mark_string(), protocols::antibody::h3, protocols::features::ProteinSilentReport::load_pose(), NA, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), t, tag, tags, core::pose::Pose::total_residue(), protocols::antibody::TR, type, and utility_exit_with_message.

void protocols::antibody::design::AntibodyDatabaseManager::start_database_session ( std::string const  database_path )

private

Gets database session.

References basic::database::get_db_session().

Member Data Documentation

std::string protocols::antibody::design::AntibodyDatabaseManager::db_path_

private

utility::sql_database::sessionOP protocols::antibody::design::AntibodyDatabaseManager::db_session_

private

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The documentation for this class was generated from the following files:

• src/protocols/antibody/design/AntibodyDatabaseManager.hh
• src/protocols/antibody/design/AntibodyDatabaseManager.cc