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

#include <AntibodyDatabaseManager.hh>

Inheritance diagram for protocols::antibody::AntibodyDatabaseManager:

Public Member Functions
	AntibodyDatabaseManager (AntibodyInfoCOP ab_info, bool force_north_paper_db=false)

	~AntibodyDatabaseManager () override

	AntibodyDatabaseManager (AntibodyDatabaseManager const &src)

AntibodyDatabaseManagerOP	clone () const

void	set_outlier_use (bool use_outliers)
	Set to parse outliers for both sequence and structural data. Default False. More...

CDRDBPoseSet	load_cdr_poses (AntibodyCDRSetOptions const &options, core::pose::Pose const &pose, core::Size overhang=3)
	Load CDRs from options of all cdrs.. More...

core::pose::PoseOP	load_cdr_pose (CDRDBPose &db_pose)
	Load a single pose into the db_pose using the given struct_id. If failure, it is nullptr. More...

utility::vector1< bool >	load_cdr_design_data (design::AntibodyCDRSeqDesignOptions const &options, core::pose::Pose const &pose, std::map< core::Size, AAProbabilities > &prob_set, core::Size const cutoff)
	Load CDRs from single cdr options. More...

utility::vector1< bool >	load_cdr_design_data_for_cdrs (utility::vector1< bool > const &cdrs, core::pose::Pose const &pose, std::map< core::Size, AAProbabilities > &prob_set, core::Size const cutoff)

CDRDBSequenceSet	load_cdr_sequences (utility::vector1< bool > const &cdrs, core::pose::Pose const &pose, bool match_on_length=false)
	Load a set of CDR sequences from the database. More...

utility::vector1< CDRDBSequence >	load_cdr_sequences_for_cdr_length (CDRNameEnum const cdr, core::Size const length)

utility::vector1< CDRDBSequence >	load_cdr_sequences_for_cdr_cluster (CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster)

void	ignore_light_chain (bool const ignore_light_chain)

template<typename T >
bool	has_vec_inconsistency (vector1< T > const &include, vector1< T > const &exclude) const

Private Member Functions
utility::vector1< CDRDBSequence >	load_cdr_sequences_for_cdr (CDRNameEnum const cdr, core::Size const length, clusters::CDRClusterEnum const cluster, bool load_on_length)

void	create_database_session (std::string const &database_path)
	Create the actual sessionOP. More...

void	check_for_graft_instruction_inconsistencies (AntibodyCDRSetOptions const &options)
	Checks to make sure the instructions make sense before trying to create the statement for the db.. More...

template<typename T >
bool	has_vec_inconsistency (utility::vector1< T > const &include, utility::vector1< T > const &leave_out) const
	Checks for inconsistency in include_only and leave_out string vectors from GraftInstructions. More...

void	bind_vec_constraint (utility::vector1< std::string > const &vec, cppdb::statement &select_statement, core::Size &col) const
	Bind the values in the vector to the select statement. More...

utility::vector1< std::string >	get_cluster_string_vec (utility::vector1< clusters::CDRClusterEnum > const &clusters)

utility::vector1< core::Size >	get_cluster_totals (bool use_outliers) const
	Does the work. Not pretty. More...

utility::vector1< core::Size >	get_cluster_totals () const
	Main function called - deals with outliers vs H3_outliers. More...

std::string	get_ands (std::string name, core::Size n) const

void	load_structure_loading_info ()
	Loads a text file with structures to SKIP from the database or are OK to load. More...

Private Attributes
std::string	db_path_

utility::sql_database::sessionOP	db_session_

AntibodyInfoCOP	ab_info_

bool	use_outliers_

bool	use_h3_graft_outliers_

bool	use_only_H3_kinked_

bool	high_mem_mode_ = false

core::Size	cdr_cache_limit_ = 300

bool	ignore_light_chain_ = false

utility::vector1< std::string >	loadable_structure_tags_

utility::vector1< std::string >	skip_structure_tags_

Detailed Description

Class responsible for loading information from the AntibodyDatabase.

Constructor & Destructor Documentation

◆ AntibodyDatabaseManager() [1/2]

protocols::antibody::AntibodyDatabaseManager::AntibodyDatabaseManager	(	AntibodyInfoCOP	ab_info,
		bool	force_north_paper_db = `false`
	)

References cdr_cache_limit_, create_database_session(), db_session_, high_mem_mode_, protocols::antibody::TR(), use_h3_graft_outliers_, use_only_H3_kinked_, and use_outliers_.

◆ ~AntibodyDatabaseManager()

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

overridedefault

◆ AntibodyDatabaseManager() [2/2]

protocols::antibody::AntibodyDatabaseManager::AntibodyDatabaseManager ( AntibodyDatabaseManager const & src )

References ab_info_, and db_session_.

Member Function Documentation

◆ bind_vec_constraint()

void protocols::antibody::AntibodyDatabaseManager::bind_vec_constraint	(	utility::vector1< std::string > const &	vec,
		cppdb::statement &	select_statement,
		core::Size &	col
	)		const

private

Bind the values in the vector to the select statement.

Referenced by load_cdr_poses().

◆ check_for_graft_instruction_inconsistencies()

void protocols::antibody::AntibodyDatabaseManager::check_for_graft_instruction_inconsistencies ( AntibodyCDRSetOptions const & options )

private

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

References protocols::antibody::CDRNameEnum_total, and has_vec_inconsistency().

Referenced by load_cdr_poses().

◆ clone()

AntibodyDatabaseManagerOP protocols::antibody::AntibodyDatabaseManager::clone ( ) const

◆ create_database_session()

void protocols::antibody::AntibodyDatabaseManager::create_database_session ( std::string const & database_path )

private

Create the actual sessionOP.

References db_path_, db_session_, and protocols::antibody::TR().

Referenced by AntibodyDatabaseManager().

◆ get_ands()

std::string protocols::antibody::AntibodyDatabaseManager::get_ands	(	std::string	name,
		core::Size	n
	)		const

private

References core::conformation::membrane::out.

◆ get_cluster_string_vec()

vector1< std::string > protocols::antibody::AntibodyDatabaseManager::get_cluster_string_vec ( utility::vector1< clusters::CDRClusterEnum > const & clusters )

private

References ab_info_.

Referenced by load_cdr_poses().

◆ get_cluster_totals() [1/2]

utility::vector1< core::Size > protocols::antibody::AntibodyDatabaseManager::get_cluster_totals ( ) const

private

Main function called - deals with outliers vs H3_outliers.

References ab_info_, protocols::antibody::clusters::CDRClusterEnum_stop, protocols::antibody::h3, use_h3_graft_outliers_, and use_outliers_.

Referenced by load_cdr_poses().

◆ get_cluster_totals() [2/2]

utility::vector1< core::Size > protocols::antibody::AntibodyDatabaseManager::get_cluster_totals ( bool use_outliers ) const

private

Does the work. Not pretty.

References ab_info_, protocols::antibody::clusters::CDRClusterEnum_total, db_session_, protocols::antibody::lambda, and protocols::antibody::unknown.

◆ has_vec_inconsistency() [1/2]

template<typename T >

bool protocols::antibody::AntibodyDatabaseManager::has_vec_inconsistency	(	utility::vector1< T > const &	include,
		utility::vector1< T > const &	leave_out
	)		const

private

Checks for inconsistency in include_only and leave_out string vectors from GraftInstructions.

Referenced by check_for_graft_instruction_inconsistencies().

◆ has_vec_inconsistency() [2/2]

template<typename T >

bool protocols::antibody::AntibodyDatabaseManager::has_vec_inconsistency	(	vector1< T > const &	include,
		vector1< T > const &	exclude
	)		const

◆ ignore_light_chain()

void protocols::antibody::AntibodyDatabaseManager::ignore_light_chain ( bool const ignore_light_chain )

inline

References ignore_light_chain_.

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply(), protocols::antibody::design::get_cluster_profile_probability_data(), and protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data().

◆ load_cdr_design_data()

vector1< bool > protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data	(	design::AntibodyCDRSeqDesignOptions const &	options,
		core::pose::Pose const &	pose,
		std::map< core::Size, AAProbabilities > &	prob_set,
		core::Size const	cutoff
	)

Load CDRs from single cdr options.

Will attempt to use Pose Datacache for identification of CDR clusters first.

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.

Will attempt to use Pose Datacache for identification of CDR clusters first.

References protocols::antibody::CDRNameEnum_total, load_cdr_design_data_for_cdrs(), protocols::antibody::design::seq_design_profiles, and protocols::antibody::TR().

Referenced by protocols::antibody::design::get_cluster_profile_probability_data().

◆ load_cdr_design_data_for_cdrs()

vector1< bool > protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs	(	utility::vector1< bool > const &	cdrs,
		core::pose::Pose const &	pose,
		std::map< core::Size, AAProbabilities > &	prob_set,
		core::Size const	cutoff
	)

References core::chemical::aa_from_oneletter_code(), ab_info_, protocols::antibody::CDRNameEnum_total, core::pose::Pose::data(), db_session_, protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), core::enzymes::NA, protocols::antibody::North, protocols::simple_moves::bb_sampler::probability, protocols::antibody::TR(), and use_outliers_.

Referenced by protocols::antibody::design::get_cluster_profile_probability_data(), and load_cdr_design_data().

◆ load_cdr_pose()

core::pose::PoseOP protocols::antibody::AntibodyDatabaseManager::load_cdr_pose ( CDRDBPose & db_pose )

Load a single pose into the db_pose using the given struct_id. If failure, it is nullptr.

References db_session_, protocols::features::ProteinSilentReport::load_pose(), protocols::antibody::CDRDBPose::pdb, protocols::antibody::CDRDBPose::struct_id, protocols::antibody::CDRDBPose::structure_length, and protocols::antibody::TR().

◆ load_cdr_poses()

CDRDBPoseSet protocols::antibody::AntibodyDatabaseManager::load_cdr_poses	(	AntibodyCDRSetOptions const &	options,
		core::pose::Pose const &	pose,
		core::Size	overhang = `3`
	)

Load CDRs from options of all cdrs..

Will attempt to use Pose Datacache for identification of CDR clusters first.

◆ load_cdr_sequences()

CDRDBSequenceSet protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences	(	utility::vector1< bool > const &	cdrs,
		core::pose::Pose const &	pose,
		bool	match_on_length = `false`
	)

Load a set of CDR sequences from the database.

References ab_info_, core::pose::Pose::data(), protocols::antibody::clusters::BasicCDRClusterSet::get_cluster(), protocols::antibody::h4, protocols::antibody::l4, load_cdr_sequences_for_cdr(), core::enzymes::NA, protocols::antibody::North, and protocols::antibody::TR().

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply(), and protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data().

◆ load_cdr_sequences_for_cdr()

utility::vector1< CDRDBSequence > protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr	(	CDRNameEnum const	cdr,
		core::Size const	length,
		clusters::CDRClusterEnum const	cluster,
		bool	load_on_length
	)

private

References ab_info_, db_session_, protocols::antibody::h3, ignore_light_chain_, protocols::antibody::is_H3_rama_kinked(), protocols::antibody::lambda, core::scoring::rama, protocols::antibody::TR(), protocols::antibody::unknown, use_h3_graft_outliers_, use_only_H3_kinked_, and use_outliers_.

Referenced by load_cdr_sequences(), load_cdr_sequences_for_cdr_cluster(), and load_cdr_sequences_for_cdr_length().

◆ load_cdr_sequences_for_cdr_cluster()

utility::vector1< CDRDBSequence > protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr_cluster	(	CDRNameEnum const	cdr,
		clusters::CDRClusterEnum const	cluster
	)

References load_cdr_sequences_for_cdr().

◆ load_cdr_sequences_for_cdr_length()

utility::vector1< CDRDBSequence > protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences_for_cdr_length	(	CDRNameEnum const	cdr,
		core::Size const	length
	)