The core of the fragment picking machinery. More...

#include <FragmentPicker.hh>

Inheritance diagram for protocols::frag_picker::FragmentPicker:

Public Member Functions
	FragmentPicker ()

	FragmentPicker (std::string fragment_score_manager_type)

	~FragmentPicker () override

FragmentPickerCOP	get_self_ptr () const

FragmentPickerOP	get_self_ptr ()

FragmentPickerCAP	get_self_weak_ptr () const

FragmentPickerAP	get_self_weak_ptr ()

void	parse_command_line ()

void	set_max_threads (core::Size const setting)
	Set the number of threads to use. More...

void	keep_all_protocol ()
	Picks fragments and saves them into proper files - independently for each query position. More...

void	bounded_protocol ()
	Picks fragments and saves them into proper files - uses bounded queue. More...

void	quota_protocol ()

void	fragment_contacts (core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set)

scores::FragmentScoreManagerOP	get_score_manager (core::Size index=1)
	returns a pointer to a scoring manager More...

void	nonlocal_pairs_at_position (core::Size const position, core::Size const &fragment_size, utility::vector1< bool > const &skip, utility::vector1< Candidates > const &fragment_set, utility::vector1< nonlocal::NonlocalPairOP > &pairs)

void	nonlocal_pairs (core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set)

void	read_vall (std::string const &fn)
	reads a vall file More...

void	read_vall (utility::vector1< std::string > const &fns)

void	set_vall (VallProviderOP vall_chunks)
	sets vall data More...

VallProviderOP	get_vall ()

void	set_frag_sizes (utility::vector1< core::Size > size, bool clear)
	Lets you set frag sizes outside the command line. More...

utility::vector1< core::Size >	get_frag_sizes () const
	getter for frag_sizes_ More...

void	set_n_frags (core::Size n_frags)
	Sets n_frags_. More...

core::Size	get_n_frags () const
	Gets n_frags_. More...

void	set_n_candidates (core::Size n_candidates)
	Sets n_candidates_. More...

core::Size	get_n_candidates () const
	Gets n_candidates_. More...

void	set_selector (FragmentSelectingRuleOP selector)
	Sets selector_. More...

void	set_query_sa (utility::vector1< core::Real > &query_sa)
	Sets the query surface area. More...

void	set_query_phi (utility::vector1< core::Real > &query_phi)
	Sets the query phi angles. More...

void	set_query_psi (utility::vector1< core::Real > &query_psi)
	Sets the query psi angles. More...

void	set_query_phi_conf (utility::vector1< core::Real > &query_phi_conf)
	Sets the query phi angle confidence. More...

void	set_query_psi_conf (utility::vector1< core::Real > &query_psi_conf)
	Sets the query psi angle confidence. More...

void	set_query_seq (core::sequence::SequenceProfileOP query_sequence)
	sets the query sequence More...

void	set_query_seq (std::string &query_sequence)
	sets the query sequence More...

std::string &	get_query_seq_string ()
	Returns the sequence we are picking fragments for (as a string) More...

core::sequence::SequenceProfileOP	get_query_seq ()

utility::vector1< core::Real > &	get_query_sa_prediction ()
	Returns the solvent accessibility prediction. More...

utility::vector1< core::Real > &	get_query_phi_prediction ()
	Returns the phi prediction. More...

utility::vector1< core::Real > &	get_query_psi_prediction ()
	Returns the psi prediction. More...

utility::vector1< core::Real > &	get_query_phi_prediction_conf ()
	Returns the phi prediction confidence. More...

utility::vector1< core::Real > &	get_query_psi_prediction_conf ()
	Returns the psi prediction confidence. More...

utility::vector1< core::Real > &	get_query_residue_depth ()
	Returns residue depth values. More...

void	set_query_profile (core::sequence::SequenceProfileOP profile)
	Sets the sequence object we are picking fragments for. More...

core::fragment::SecondaryStructureOP	get_query_ss (std::string prediction_name)
	Returns the query secondary structure as a SecondaryStructure object. More...

void	read_ss_files (utility::vector1< std::string > const &sec_str_input)
	Reads a bunch of ss predicitons from files and plugs them into the picker. More...

std::string &	get_query_ss_string (std::string prediction_name)
	Returns the query secondary structure as a string. More...

void	add_query_ss (std::string, std::string)
	Sets the query secondary structure. More...

core::Size	count_query_ss ()
	Sets the query secondary structure. More...

void	read_ss_file (std::string const &, std::string const &)
	Identifies if the ss file is psipred or talos, calls appropriate reader. More...

void	read_spine_x (std::string const &file_name)
	Reads spine-x phi, psi, and solvent accessibility predictions. More...

void	read_depth (std::string const &file_name)
	Reads DEPTH residue depth values. More...

core::Size	size_of_query ()

void	set_picked_positions (core::Size, core::Size)
	Asks the picker to pick fragments from a given range in a query sequence. More...

void	set_picked_positions (utility::vector1< core::Size >)
	Asks the picker to pick fragments for given positions in a query sequence. More...

utility::vector1< core::Size >	get_picked_positions () const
	returns vector of picked positions More...

void	pick_chunk_candidates (VallChunkOP chunk, basic::thread_manager::RosettaThreadAssignmentInfo const &assignments)
	picks fragment candidates. More...

void	pick_candidates ()

void	get_final_fragments (core::Size qPos, core::Size frag_size, Candidates &out)

void	get_final_fragments (core::Size qPos, Candidates &out)

void	pick_candidates (core::Size i_pos, core::Size frag_len)

core::Real	total_score (scores::FragmentScoreMapOP f, core::Size index=1)
	Calculates total score for a given vector of small scores (FragmentScoreMap object pointer) More...

void	save_candidates ()

void	save_fragments ()

core::Size	max_frag_len ()
	How long is the longest fragment? More...

void	show_scoring_methods (std::ostream &out, core::Size index=1)

void	add_scoring_method (scores::FragmentScoringMethodOP scoring_term, core::Real weight, core::Size index=1)
	adds a new scoring method to the scoring scheme More...

void	create_scores (std::string file_name)
	Creates scoring methods from score file, same as using frags::scoring::config command-line option. More...

utility::vector1< core::fragment::ConstantLengthFragSetOP >	getFragSet (int residueInPose_)

void	read_psipred_ss2 (std::string const &, std::string)
	Reads query secondary structure prediction from a PsiPred file. More...

void	read_talos_ss (std::string const &, std::string)
	Reads query secondary structure prediction from a Talos+ file. More...

void	parse_quota_command_line ()

void	set_up_quota_nnmake_style ()

void	set_up_ss_abego_quota ()

bool	is_valid_chunk (VallChunkOP chunk)

bool	is_valid_chunk (core::Size const frag_len, VallChunkOP chunk)

void	output_fragments (core::Size const fragment_size, utility::vector1< Candidates > const &final_fragments)

void	set_candidates_collector (core::Size frag_size, CandidatesCollectorOP sink, core::Size index=1)
	sets a collector where fragment candidates will be kept until final selection More...

CandidatesCollectorOP	get_candidates_collector (core::Size frag_size, core::Size index=1)
	returns a pointer to the candidates collector currently used More...

void	add_chunk_filter (VallChunkFilterOP filter)
	adds a chunk filter that will be used to screen chunks before they are cut into fragments More...

Public Attributes
utility::vector1< core::Size >	frag_sizes_

core::Size	n_candidates_

core::Size	n_frags_

std::string	prefix_

FragmentSelectingRuleOP	selector_

Static Public Attributes
static QuotaDebug	log_25_

static QuotaDebug	log_200_

Private Member Functions
void	output_pair_counts (core::Size const fragment_size, core::Size const neighbors, std::map< std::pair< core::Real, ContactType >, ContactCountsOP > contact_counts)

Private Attributes
core::Size	max_threads_ = 0
	Number of threads to use. Default value is zero, meaning use all available threads. Must be set to zero or one in single-threaded build. More...

core::Size	max_frag_size_

core::sequence::SequenceProfileOP	query_profile_

std::string	query_seq_as_string_

std::map< std::string, core::fragment::SecondaryStructureOP >	query_ss_profile_

std::map< std::string, std::string >	query_ss_as_string_

utility::vector1< core::Size >	query_positions_

VallProviderOP	chunks_

utility::vector1< VallChunkFilterOP >	filters_

CandidatesSink	candidates_sink_

utility::vector1< CandidatesSink >	candidates_sinks_

utility::vector1< scores::FragmentScoreManagerOP >	scores_

core::Size	contacts_min_seq_sep_

std::set< ContactType >	contact_types_

core::Real	contacts_dist_cutoff_squared_

utility::vector1< core::Real >	contacts_dist_cutoffs_squared_

SidechainContactDistCutoffOP	sidechain_contact_dist_cutoff_

core::Real	nonlocal_min_contacts_per_res_

utility::vector1< core::Real >	query_sa_prediction_

utility::vector1< core::Real >	query_phi_prediction_

utility::vector1< core::Real >	query_psi_prediction_

utility::vector1< core::Real >	query_phi_prediction_conf_

utility::vector1< core::Real >	query_psi_prediction_conf_

utility::vector1< core::Real >	query_residue_depth_

utility::vector1< utility::vector1< core::Real > >	atom_pair_constraint_contact_map_

Detailed Description

The core of the fragment picking machinery.

FragmentPicker class does:

know about query data: sequence, sequence profile, secondary structure. All other query data must be loaded directly to the relevant scoring methods
provide slots for 'plugable' parts of the machinery, like chunk filters, scoring methods and so on.
pick fragments

Constructor & Destructor Documentation

◆ FragmentPicker() [1/2]

protocols::frag_picker::FragmentPicker::FragmentPicker ( )

inline

References candidates_sinks_, contacts_dist_cutoff_squared_, contacts_min_seq_sep_, max_frag_size_, max_threads_, nonlocal_min_contacts_per_res_, prefix_, and scores_.

◆ FragmentPicker() [2/2]

protocols::frag_picker::FragmentPicker::FragmentPicker ( std::string fragment_score_manager_type )

inline

References candidates_sinks_, contacts_dist_cutoff_squared_, contacts_min_seq_sep_, max_frag_size_, max_threads_, nonlocal_min_contacts_per_res_, prefix_, and scores_.

◆ ~FragmentPicker()

protocols::frag_picker::FragmentPicker::~FragmentPicker ( )

overridedefault

Member Function Documentation

◆ add_chunk_filter()

void protocols::frag_picker::FragmentPicker::add_chunk_filter ( VallChunkFilterOP filter )

inline

adds a chunk filter that will be used to screen chunks before they are cut into fragments

References filters_.

◆ add_query_ss()

void protocols::frag_picker::FragmentPicker::add_query_ss	(	std::string	query_secondary,
		std::string	prediction_name
	)

Sets the query secondary structure.

◆ add_scoring_method()

void protocols::frag_picker::FragmentPicker::add_scoring_method	(	scores::FragmentScoringMethodOP	scoring_term,
		core::Real	weight,
		core::Size	index = `1`
	)

inline

adds a new scoring method to the scoring scheme

References scores_.

◆ bounded_protocol()

void protocols::frag_picker::FragmentPicker::bounded_protocol ( )

Picks fragments and saves them into proper files - uses bounded queue.

This protocol scores all vall data against all query positions and keeps a limited number of candidates per position using a bounded queue. When all candidates for all positions are scored, it selects final fragments.

References protocols::frag_picker::tr().

◆ count_query_ss()

core::Size protocols::frag_picker::FragmentPicker::count_query_ss ( )

inline

Sets the query secondary structure.

References query_ss_profile_.

◆ create_scores()

void protocols::frag_picker::FragmentPicker::create_scores ( std::string file_name )

inline

Creates scoring methods from score file, same as using frags::scoring::config command-line option.

References get_self_ptr(), and scores_.

◆ fragment_contacts()

void protocols::frag_picker::FragmentPicker::fragment_contacts	(	core::Size const	fragment_size,
		utility::vector1< Candidates > const &	fragment_set
	)

References protocols::frag_picker::CEN, protocols::frag_picker::contact_name(), core::kinematics::tree::distance_squared(), core::chemical::element::F, and protocols::forge::methods::replace().

◆ get_candidates_collector()

CandidatesCollectorOP protocols::frag_picker::FragmentPicker::get_candidates_collector	(	core::Size	frag_size,
		core::Size	index = `1`
	)

inline

returns a pointer to the candidates collector currently used

one may need this instance to access the candidates that have been found by the picker

References candidates_sink_, and candidates_sinks_.

◆ get_final_fragments() [1/2]

void protocols::frag_picker::FragmentPicker::get_final_fragments	(	core::Size	qPos,
		Candidates &	out
	)

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

◆ get_final_fragments() [2/2]

void protocols::frag_picker::FragmentPicker::get_final_fragments	(	core::Size	qPos,
		core::Size	frag_size,
		Candidates &	out
	)

References core::conformation::membrane::in, and core::conformation::membrane::out.

◆ get_frag_sizes()

utility::vector1< core::Size > protocols::frag_picker::FragmentPicker::get_frag_sizes ( ) const

getter for frag_sizes_

◆ get_n_candidates()

core::Size protocols::frag_picker::FragmentPicker::get_n_candidates ( ) const

Gets n_candidates_.

◆ get_n_frags()

core::Size protocols::frag_picker::FragmentPicker::get_n_frags ( ) const

Gets n_frags_.

◆ get_picked_positions()

utility::vector1< core::Size > protocols::frag_picker::FragmentPicker::get_picked_positions ( ) const

returns vector of picked positions

◆ get_query_phi_prediction()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_phi_prediction ( )

inline

Returns the phi prediction.

References query_phi_prediction_.

◆ get_query_phi_prediction_conf()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_phi_prediction_conf ( )

inline

Returns the phi prediction confidence.

References query_phi_prediction_conf_.

◆ get_query_psi_prediction()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_psi_prediction ( )

inline

Returns the psi prediction.

References query_psi_prediction_.

◆ get_query_psi_prediction_conf()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_psi_prediction_conf ( )

inline

Returns the psi prediction confidence.

References query_psi_prediction_conf_.

◆ get_query_residue_depth()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_residue_depth ( )

inline

Returns residue depth values.

References query_residue_depth_.

◆ get_query_sa_prediction()

utility::vector1<core::Real>& protocols::frag_picker::FragmentPicker::get_query_sa_prediction ( )

inline

Returns the solvent accessibility prediction.

References query_sa_prediction_.

◆ get_query_seq()

core::sequence::SequenceProfileOP protocols::frag_picker::FragmentPicker::get_query_seq ( )

inline

References query_profile_.

◆ get_query_seq_string()

std::string& protocols::frag_picker::FragmentPicker::get_query_seq_string ( )

inline

Returns the sequence we are picking fragments for (as a string)

References query_seq_as_string_.

◆ get_query_ss()

core::fragment::SecondaryStructureOP protocols::frag_picker::FragmentPicker::get_query_ss ( std::string prediction_name )

inline

Returns the query secondary structure as a SecondaryStructure object.

References query_ss_profile_.

◆ get_query_ss_string()

std::string& protocols::frag_picker::FragmentPicker::get_query_ss_string ( std::string prediction_name )

inline

Returns the query secondary structure as a string.

References query_ss_as_string_.

◆ get_score_manager()

scores::FragmentScoreManagerOP protocols::frag_picker::FragmentPicker::get_score_manager ( core::Size index = 1 )

inline

returns a pointer to a scoring manager

References scores_.

◆ get_self_ptr() [1/2]

FragmentPickerOP protocols::frag_picker::FragmentPicker::get_self_ptr ( )

inline

◆ get_self_ptr() [2/2]

FragmentPickerCOP protocols::frag_picker::FragmentPicker::get_self_ptr ( ) const

inline

Referenced by create_scores().

◆ get_self_weak_ptr() [1/2]

FragmentPickerAP protocols::frag_picker::FragmentPicker::get_self_weak_ptr ( )

inline

◆ get_self_weak_ptr() [2/2]

FragmentPickerCAP protocols::frag_picker::FragmentPicker::get_self_weak_ptr ( ) const

inline

◆ get_vall()

VallProviderOP protocols::frag_picker::FragmentPicker::get_vall ( )

inline

Returns: a pointer to Vall provider

References chunks_.

◆ getFragSet()

utility::vector1< ConstantLengthFragSetOP > protocols::frag_picker::FragmentPicker::getFragSet ( int residueInPose_ )

References protocols::cluster::calibur::aa, core::scoring::omega, and core::conformation::membrane::out.

◆ is_valid_chunk() [1/2]

bool protocols::frag_picker::FragmentPicker::is_valid_chunk	(	core::Size const	frag_len,
		VallChunkOP	chunk
	)

◆ is_valid_chunk() [2/2]

bool protocols::frag_picker::FragmentPicker::is_valid_chunk ( VallChunkOP chunk )

References protocols::frag_picker::tr().

◆ keep_all_protocol()

void protocols::frag_picker::FragmentPicker::keep_all_protocol ( )

Picks fragments and saves them into proper files - independently for each query position.

This protocol scores all vall data against a given position and keeps all the candidates unless they fail an energy filter When all candidates for a positions are scored, it selects fragments for the position and proceeds to the next position. Bounded queue is not used

References core::chemical::element::I, core::conformation::membrane::out, and protocols::frag_picker::tr().

◆ max_frag_len()

core::Size protocols::frag_picker::FragmentPicker::max_frag_len ( )

inline

How long is the longest fragment?

References frag_sizes_.

◆ nonlocal_pairs()

void protocols::frag_picker::FragmentPicker::nonlocal_pairs	(	core::Size const	fragment_size,
		utility::vector1< Candidates > const &	fragment_set
	)

◆ nonlocal_pairs_at_position()

void protocols::frag_picker::FragmentPicker::nonlocal_pairs_at_position	(	core::Size const	position,
		core::Size const &	fragment_size,
		utility::vector1< bool > const &	skip,
		utility::vector1< Candidates > const &	fragment_set,
		utility::vector1< nonlocal::NonlocalPairOP > &	pairs
	)

Note: Should be threadsafe.

References protocols::frag_picker::CEN, and core::scoring::pair.

Referenced by nonlocal_pairs().

◆ output_fragments()

void protocols::frag_picker::FragmentPicker::output_fragments	(	core::Size const	fragment_size,
		utility::vector1< Candidates > const &	final_fragments
	)

References core::chemical::element::I, and protocols::frag_picker::tr().

◆ output_pair_counts()

void protocols::frag_picker::FragmentPicker::output_pair_counts	(	core::Size const	fragment_size,
		core::Size const	neighbors,
		std::map< std::pair< core::Real, ContactType >, ContactCountsOP >	contact_counts
	)

private

References protocols::frag_picker::CEN, protocols::frag_picker::contact_name(), protocols::frag_picker::contact_type(), core::sequence::end, and protocols::forge::methods::replace().

◆ parse_command_line()

void protocols::frag_picker::FragmentPicker::parse_command_line ( )

References protocols::frag_picker::CEN, protocols::frag_picker::contact_type(), core::sequence::read_fasta_file(), and protocols::frag_picker::tr().

◆ parse_quota_command_line()

void protocols::frag_picker::FragmentPicker::parse_quota_command_line ( )

◆ pick_candidates() [1/2]

void protocols::frag_picker::FragmentPicker::pick_candidates ( )

References pick_chunk_candidates(), and protocols::frag_picker::tr().

◆ pick_candidates() [2/2]

void protocols::frag_picker::FragmentPicker::pick_candidates	(	core::Size	i_pos,
		core::Size	frag_len
	)

References protocols::frag_picker::tr().

◆ pick_chunk_candidates()

void protocols::frag_picker::FragmentPicker::pick_chunk_candidates	(	VallChunkOP	chunk,
		basic::thread_manager::RosettaThreadAssignmentInfo const &	assignments
	)

picks fragment candidates.

These basically become fragments if pass the final selection. Fragment candidates are stored in a container that a user must plug into the picker multi-threaded task

Referenced by pick_candidates().

◆ quota_protocol()

void protocols::frag_picker::FragmentPicker::quota_protocol ( )

References protocols::frag_picker::quota::QuotaSelector::select_fragments(), and protocols::frag_picker::tr().

◆ read_depth()

void protocols::frag_picker::FragmentPicker::read_depth ( std::string const & file_name )

Reads DEPTH residue depth values.

◆ read_psipred_ss2()

void protocols::frag_picker::FragmentPicker::read_psipred_ss2	(	std::string const &	file_name,
		std::string	prediction_name
	)

Reads query secondary structure prediction from a PsiPred file.

◆ read_spine_x()

void protocols::frag_picker::FragmentPicker::read_spine_x ( std::string const & file_name )

Reads spine-x phi, psi, and solvent accessibility predictions.

References protocols::frag_picker::sa_faraggi_max().

◆ read_ss_file()

void protocols::frag_picker::FragmentPicker::read_ss_file	(	std::string const &	file_name,
		std::string const &	prediction_name
	)

Identifies if the ss file is psipred or talos, calls appropriate reader.

References protocols::antibody::l1, protocols::antibody::l2, protocols::antibody::l3, and protocols::antibody::l4.

◆ read_ss_files()

void protocols::frag_picker::FragmentPicker::read_ss_files ( utility::vector1< std::string > const & sec_str_input )

Reads a bunch of ss predicitons from files and plugs them into the picker.

References protocols::frag_picker::tr().

◆ read_talos_ss()

void protocols::frag_picker::FragmentPicker::read_talos_ss	(	std::string const &	file_name,
		std::string	prediction_name
	)

Reads query secondary structure prediction from a Talos+ file.

◆ read_vall() [1/2]

void protocols::frag_picker::FragmentPicker::read_vall ( std::string const & fn )

reads a vall file

◆ read_vall() [2/2]

void protocols::frag_picker::FragmentPicker::read_vall ( utility::vector1< std::string > const & fns )

◆ save_candidates()

void protocols::frag_picker::FragmentPicker::save_candidates ( )

References core::chemical::element::I, core::conformation::membrane::out, and protocols::frag_picker::tr().

◆ save_fragments()

void protocols::frag_picker::FragmentPicker::save_fragments ( )

References core::conformation::membrane::in, core::conformation::membrane::out, and protocols::frag_picker::tr().

◆ set_candidates_collector()

void protocols::frag_picker::FragmentPicker::set_candidates_collector	(	core::Size	frag_size,
		CandidatesCollectorOP	sink,
		core::Size	index = `1`
	)

inline

sets a collector where fragment candidates will be kept until final selection

References candidates_sink_, and candidates_sinks_.

◆ set_frag_sizes()

void protocols::frag_picker::FragmentPicker::set_frag_sizes	(	utility::vector1< core::Size >	size,
		bool	clear
	)

Lets you set frag sizes outside the command line.

◆ set_max_threads()

void protocols::frag_picker::FragmentPicker::set_max_threads ( core::Size const setting )

Set the number of threads to use.

A value of zero means use all available threads.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

References core::id::to_string(), and protocols::frag_picker::tr().

◆ set_n_candidates()

void protocols::frag_picker::FragmentPicker::set_n_candidates ( core::Size n_candidates )

Sets n_candidates_.

◆ set_n_frags()

void protocols::frag_picker::FragmentPicker::set_n_frags ( core::Size n_frags )

Sets n_frags_.

◆ set_picked_positions() [1/2]

void protocols::frag_picker::FragmentPicker::set_picked_positions	(	core::Size	from,
		core::Size	to
	)

Asks the picker to pick fragments from a given range in a query sequence.

Referenced by set_query_profile().

◆ set_picked_positions() [2/2]

void protocols::frag_picker::FragmentPicker::set_picked_positions ( utility::vector1< core::Size > q_positions )

Asks the picker to pick fragments for given positions in a query sequence.

◆ set_query_phi()

void protocols::frag_picker::FragmentPicker::set_query_phi ( utility::vector1< core::Real > & query_phi )

Sets the query phi angles.

Directly sets the query phi angles instead of reading it from a file

◆ set_query_phi_conf()

void protocols::frag_picker::FragmentPicker::set_query_phi_conf ( utility::vector1< core::Real > & query_phi_conf )

Sets the query phi angle confidence.

Directly sets the query phi angle confidence instead of reading it from a file

◆ set_query_profile()

void protocols::frag_picker::FragmentPicker::set_query_profile ( core::sequence::SequenceProfileOP profile )

inline

Sets the sequence object we are picking fragments for.

References query_profile_, query_seq_as_string_, and set_picked_positions().

◆ set_query_psi()

void protocols::frag_picker::FragmentPicker::set_query_psi ( utility::vector1< core::Real > & query_psi )

Sets the query psi angles.

Directly sets the query psi angles isntead of reading it from a file

◆ set_query_psi_conf()

void protocols::frag_picker::FragmentPicker::set_query_psi_conf ( utility::vector1< core::Real > & query_psi_conf )

Sets the query psi angle confidence.

Directly sets the query psi angle confidence instead of reading it form a file

◆ set_query_sa()

void protocols::frag_picker::FragmentPicker::set_query_sa ( utility::vector1< core::Real > & query_sa )

Sets the query surface area.

Directly sets the query surface area instead of reading it from a file

◆ set_query_seq() [1/2]

void protocols::frag_picker::FragmentPicker::set_query_seq ( core::sequence::SequenceProfileOP query_sequence )

sets the query sequence

Well, it is a sequence profile, but the sequence can be extracted from it

◆ set_query_seq() [2/2]

void protocols::frag_picker::FragmentPicker::set_query_seq ( std::string & query_sequence )

sets the query sequence

References protocols::frag_picker::tr().

◆ set_selector()

void protocols::frag_picker::FragmentPicker::set_selector ( FragmentSelectingRuleOP selector )

inline

Sets selector_.

References selector_.

◆ set_up_quota_nnmake_style()

void protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style ( )

References core::sequence::end, protocols::frag_picker::quota::QuotaConfig::get_fraction(), protocols::frag_picker::quota::QuotaConfig::is_valid_quota_pool_name(), and protocols::frag_picker::tr().

◆ set_up_ss_abego_quota()

void protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota ( )

References protocols::frag_picker::quota::ABEGO_SS_Config::get_pool_bins(), protocols::frag_picker::quota::QuotaConfig::get_pool_name(), protocols::frag_picker::quota::ABEGO_SS_Config::n_columns(), protocols::frag_picker::quota::ABEGO_SS_Config::probability(), protocols::frag_picker::quota::ABEGO_SS_Config::size(), and protocols::frag_picker::tr().

◆ set_vall()

void protocols::frag_picker::FragmentPicker::set_vall ( VallProviderOP vall_chunks )

inline

sets vall data

References chunks_.

◆ show_scoring_methods()

void protocols::frag_picker::FragmentPicker::show_scoring_methods	(	std::ostream &	out,
		core::Size	index = `1`
	)

inline

References core::conformation::membrane::out, and scores_.

◆ size_of_query()

core::Size protocols::frag_picker::FragmentPicker::size_of_query ( )

inline

References query_profile_, and query_seq_as_string_.

◆ total_score()

core::Real protocols::frag_picker::FragmentPicker::total_score	(	scores::FragmentScoreMapOP	f,
		core::Size	index = `1`
	)

Calculates total score for a given vector of small scores (FragmentScoreMap object pointer)

FragmentScoreManager that is stored inside the picker is used for this calculation. It particular it provides weights

References protocols::analysis::total.

Member Data Documentation

◆ atom_pair_constraint_contact_map_

utility::vector1<utility::vector1<core::Real> > protocols::frag_picker::FragmentPicker::atom_pair_constraint_contact_map_

private

◆ candidates_sink_

CandidatesSink protocols::frag_picker::FragmentPicker::candidates_sink_

private

Referenced by get_candidates_collector(), and set_candidates_collector().

◆ candidates_sinks_

utility::vector1<CandidatesSink> protocols::frag_picker::FragmentPicker::candidates_sinks_

private

Referenced by FragmentPicker(), get_candidates_collector(), and set_candidates_collector().

◆ chunks_

VallProviderOP protocols::frag_picker::FragmentPicker::chunks_

private

Referenced by get_vall(), and set_vall().

◆ contact_types_

std::set<ContactType> protocols::frag_picker::FragmentPicker::contact_types_

private

◆ contacts_dist_cutoff_squared_

core::Real protocols::frag_picker::FragmentPicker::contacts_dist_cutoff_squared_

private

Referenced by FragmentPicker().

◆ contacts_dist_cutoffs_squared_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::contacts_dist_cutoffs_squared_

private

◆ contacts_min_seq_sep_

core::Size protocols::frag_picker::FragmentPicker::contacts_min_seq_sep_

private

Referenced by FragmentPicker().

◆ filters_

utility::vector1<VallChunkFilterOP> protocols::frag_picker::FragmentPicker::filters_

private

Referenced by add_chunk_filter().

◆ frag_sizes_

utility::vector1<core::Size> protocols::frag_picker::FragmentPicker::frag_sizes_

Referenced by max_frag_len().

◆ log_200_

QuotaDebug protocols::frag_picker::FragmentPicker::log_200_

static

Referenced by protocols::frag_picker::quota::QuotaSelector::select_fragments_25_200().

◆ log_25_

QuotaDebug protocols::frag_picker::FragmentPicker::log_25_

static

Referenced by protocols::frag_picker::quota::QuotaSelector::select_fragments_25_200().

◆ max_frag_size_

core::Size protocols::frag_picker::FragmentPicker::max_frag_size_

private

Referenced by FragmentPicker().

◆ max_threads_

core::Size protocols::frag_picker::FragmentPicker::max_threads_ = 0

private

Number of threads to use. Default value is zero, meaning use all available threads. Must be set to zero or one in single-threaded build.

Referenced by FragmentPicker().

◆ n_candidates_

core::Size protocols::frag_picker::FragmentPicker::n_candidates_

◆ n_frags_

core::Size protocols::frag_picker::FragmentPicker::n_frags_

◆ nonlocal_min_contacts_per_res_

core::Real protocols::frag_picker::FragmentPicker::nonlocal_min_contacts_per_res_

private

Referenced by FragmentPicker().

◆ prefix_

std::string protocols::frag_picker::FragmentPicker::prefix_

Referenced by FragmentPicker().

◆ query_phi_prediction_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_phi_prediction_

private

Referenced by get_query_phi_prediction().

◆ query_phi_prediction_conf_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_phi_prediction_conf_

private

Referenced by get_query_phi_prediction_conf().

◆ query_positions_

utility::vector1<core::Size> protocols::frag_picker::FragmentPicker::query_positions_

private

◆ query_profile_

core::sequence::SequenceProfileOP protocols::frag_picker::FragmentPicker::query_profile_

private

Referenced by get_query_seq(), set_query_profile(), and size_of_query().

◆ query_psi_prediction_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_psi_prediction_

private

Referenced by get_query_psi_prediction().

◆ query_psi_prediction_conf_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_psi_prediction_conf_

private

Referenced by get_query_psi_prediction_conf().

◆ query_residue_depth_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_residue_depth_

private

Referenced by get_query_residue_depth().

◆ query_sa_prediction_

utility::vector1<core::Real> protocols::frag_picker::FragmentPicker::query_sa_prediction_

private

Referenced by get_query_sa_prediction().

◆ query_seq_as_string_

std::string protocols::frag_picker::FragmentPicker::query_seq_as_string_

private

Referenced by get_query_seq_string(), set_query_profile(), and size_of_query().

◆ query_ss_as_string_

std::map<std::string, std::string> protocols::frag_picker::FragmentPicker::query_ss_as_string_

private

Referenced by get_query_ss_string().

◆ query_ss_profile_

std::map<std::string, core::fragment::SecondaryStructureOP> protocols::frag_picker::FragmentPicker::query_ss_profile_

private

Referenced by count_query_ss(), and get_query_ss().

◆ scores_

utility::vector1<scores::FragmentScoreManagerOP> protocols::frag_picker::FragmentPicker::scores_

private

Referenced by add_scoring_method(), create_scores(), FragmentPicker(), get_score_manager(), and show_scoring_methods().

◆ selector_

FragmentSelectingRuleOP protocols::frag_picker::FragmentPicker::selector_

Referenced by set_selector().

◆ sidechain_contact_dist_cutoff_

SidechainContactDistCutoffOP protocols::frag_picker::FragmentPicker::sidechain_contact_dist_cutoff_

private

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

src/protocols/frag_picker/FragmentPicker.hh
src/protocols/frag_picker/FragmentPicker.cc

Public Member Functions

Public Attributes

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FragmentPicker() [1/2]

◆ FragmentPicker() [2/2]

◆ ~FragmentPicker()

Member Function Documentation

◆ add_chunk_filter()

◆ add_query_ss()

◆ add_scoring_method()

◆ bounded_protocol()

◆ count_query_ss()

◆ create_scores()

◆ fragment_contacts()

◆ get_candidates_collector()

◆ get_final_fragments() [1/2]

◆ get_final_fragments() [2/2]

◆ get_frag_sizes()

◆ get_n_candidates()

◆ get_n_frags()

◆ get_picked_positions()

◆ get_query_phi_prediction()

◆ get_query_phi_prediction_conf()

◆ get_query_psi_prediction()

◆ get_query_psi_prediction_conf()

◆ get_query_residue_depth()

◆ get_query_sa_prediction()

◆ get_query_seq()

◆ get_query_seq_string()

◆ get_query_ss()

◆ get_query_ss_string()

◆ get_score_manager()

◆ get_self_ptr() [1/2]

◆ get_self_ptr() [2/2]

◆ get_self_weak_ptr() [1/2]

◆ get_self_weak_ptr() [2/2]

◆ get_vall()

◆ getFragSet()

◆ is_valid_chunk() [1/2]

◆ is_valid_chunk() [2/2]

◆ keep_all_protocol()

◆ max_frag_len()

◆ nonlocal_pairs()

◆ nonlocal_pairs_at_position()

◆ output_fragments()

◆ output_pair_counts()

◆ parse_command_line()

◆ parse_quota_command_line()

◆ pick_candidates() [1/2]

◆ pick_candidates() [2/2]

◆ pick_chunk_candidates()

◆ quota_protocol()

◆ read_depth()

◆ read_psipred_ss2()

◆ read_spine_x()

◆ read_ss_file()

◆ read_ss_files()

◆ read_talos_ss()

◆ read_vall() [1/2]

◆ read_vall() [2/2]

◆ save_candidates()

◆ save_fragments()

◆ set_candidates_collector()

◆ set_frag_sizes()

◆ set_max_threads()

◆ set_n_candidates()

◆ set_n_frags()

◆ set_picked_positions() [1/2]

◆ set_picked_positions() [2/2]

◆ set_query_phi()

◆ set_query_phi_conf()

◆ set_query_profile()

◆ set_query_psi()

◆ set_query_psi_conf()

◆ set_query_sa()

◆ set_query_seq() [1/2]