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

#include <FragmentPicker.hh>

Inheritance diagram for protocols::frag_picker::FragmentPicker:

Collaboration diagram for protocols::frag_picker::FragmentPicker:

Public Member Functions
	FragmentPicker ()

	FragmentPicker (std::string fragment_score_manager_type)

virtual	~FragmentPicker ()

void	parse_command_line ()

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

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

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

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

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_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< Real > &	get_query_sa_prediction ()
	Returns the solvent accessibility prediction. More...

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

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

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

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

utility::vector1< 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 > 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...

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

void	read_ss_file (std::string const &, std::string)
	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...

Size	size_of_query ()

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

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

void	pick_chunk_candidates (utility::vector1< VallChunkOP > const &chunks, Size const &index)
	picks fragment candidates. More...

void	pick_candidates ()

void	pick_candidates (Size i_pos, Size frag_len)

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

void	save_candidates ()

void	save_fragments ()

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

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

void	add_scoring_method (scores::FragmentScoringMethodOP scoring_term, Real weight, Size index=1)
	adds a new scoring method to the scoring scheme 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 (Size const frag_len, VallChunkOP chunk)

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

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

CandidatesCollectorOP	get_candidates_collector (Size frag_size, 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< Size >	frag_sizes_

Size	n_candidates_

Size	n_frags_

std::string	prefix_

FragmentSelectingRuleOP	selector_

Static Public Attributes
static QuotaDebug	log_25_

static QuotaDebug	log_200_

Private Attributes
Size	max_threads_

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< Size >	query_positions_

VallProviderOP	chunks_

utility::vector1 < VallChunkFilterOP >	filters_

CandidatesSink	candidates_sink_

utility::vector1< CandidatesSink >	candidates_sinks_

utility::vector1 < scores::FragmentScoreManagerOP >	scores_

Size	contacts_min_seq_sep_

std::set< ContactType >	contact_types_

Real	contacts_dist_cutoff_squared_

utility::vector1< Real >	contacts_dist_cutoffs_squared_

SidechainContactDistCutoffOP	sidechain_contact_dist_cutoff_

Real	nonlocal_min_contacts_per_res_

utility::vector1< Real >	query_sa_prediction_

utility::vector1< Real >	query_phi_prediction_

utility::vector1< Real >	query_psi_prediction_

utility::vector1< Real >	query_phi_prediction_conf_

utility::vector1< Real >	query_psi_prediction_conf_

utility::vector1< Real >	query_residue_depth_

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

Detailed Description

The core of the fragment picking machinery.

Detailed: 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

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_.

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_.

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

virtual

Member Function Documentation

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_.

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

Sets the query secondary structure.

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

inline

adds a new scoring method to the scoring scheme

References scores_.

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

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

Detailed: 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().

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

inline

Sets the query secondary structure.

References query_ss_profile_.

void protocols::frag_picker::FragmentPicker::fragment_contacts	(	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(), and protocols::forge::methods::replace().

CandidatesCollectorOP protocols::frag_picker::FragmentPicker::get_candidates_collector	(	Size	frag_size,
		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_.

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

inline

Returns the phi prediction.

References query_phi_prediction_.

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

inline

Returns the phi prediction confidence.

References query_phi_prediction_conf_.

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

inline

Returns the psi prediction.

References query_psi_prediction_.

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

inline

Returns the psi prediction confidence.

References query_psi_prediction_conf_.

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

inline

Returns residue depth values.

References query_residue_depth_.

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

inline

Returns the solvent accessibility prediction.

References query_sa_prediction_.

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

inline

References query_profile_.

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_.

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_.

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_.

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

inline

returns a pointer to a scoring manager

References scores_.

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

inline

Returns: a pointer to Vall provider

References chunks_.

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

References core::scoring::omega, protocols::swa::phi(), and protocols::swa::psi().

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

References protocols::frag_picker::tr().

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

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

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

Detailed: 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 protocols::frag_picker::tr().

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

inline

How long is the longest fragment?

References frag_sizes_.

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

References core::pose::add_score_line_string(), core::pack::dunbrack::c, protocols::frag_picker::CEN, protocols::frag_picker::contact_name(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::pose::is_ideal_pose(), core::fragment::make_pose_from_frags(), nonlocal_pairs_at_positions(), core::import_pose::pose_from_pdb(), core::sequence::read_aln(), core::scoring::ref, protocols::forge::methods::replace(), core::pose::Pose::residue(), core::pose::setPoseExtraScores(), core::io::serialization::size(), core::pose::Pose::total_residue(), protocols::frag_picker::tr(), and core::conformation::Residue::xyz().

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

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

Referenced by nonlocal_pairs().

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

References core::io::serialization::size(), and protocols::frag_picker::tr().

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().

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

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

References pick_chunk_candidates(), core::scoring::ref, core::io::serialization::size(), and protocols::frag_picker::tr().

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

References protocols::frag_picker::tr().

void protocols::frag_picker::FragmentPicker::pick_chunk_candidates	(	utility::vector1< VallChunkOP > const &	chunks,
		Size const &	index
	)

picks fragment candidates.

Detailed: 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().

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

References core::pack::dunbrack::c, protocols::simple_moves::insert, protocols::frag_picker::quota::QuotaSelector::select_fragments(), and protocols::frag_picker::tr().

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

Reads DEPTH residue depth values.

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.

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

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

References protocols::swa::phi(), and protocols::swa::psi().

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

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

References protocols::antibody2::l1, protocols::antibody2::l2, and protocols::antibody2::l3.

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

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

References protocols::frag_picker::tr().

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.

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

reads a vall file

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

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

References protocols::simple_moves::insert, and protocols::frag_picker::tr().

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

References protocols::simple_moves::insert, and protocols::frag_picker::tr().

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

inline

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

References candidates_sink_, and candidates_sinks_.

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

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

Referenced by set_query_profile(), and set_query_seq().

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

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

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().

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

inline

sets the query sequence

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

References query_profile_, query_seq_as_string_, and set_picked_positions().

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

inline

sets the query sequence

References query_profile_, query_seq_as_string_, and set_picked_positions().

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

References core::io::serialization::size(), and protocols::frag_picker::tr().

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

References protocols::frag_picker::tr().

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

inline

sets vall data

References chunks_.

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

inline

References scores_.

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

inline

References query_profile_, and query_seq_as_string_.

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

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

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

Member Data Documentation

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

private

CandidatesSink protocols::frag_picker::FragmentPicker::candidates_sink_

private

Referenced by get_candidates_collector(), and set_candidates_collector().

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

private

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

VallProviderOP protocols::frag_picker::FragmentPicker::chunks_

private

Referenced by get_vall(), and set_vall().

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

private

Real protocols::frag_picker::FragmentPicker::contacts_dist_cutoff_squared_

private

Referenced by FragmentPicker().

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

private

Size protocols::frag_picker::FragmentPicker::contacts_min_seq_sep_

private

Referenced by FragmentPicker().

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

private

Referenced by add_chunk_filter().

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

Referenced by max_frag_len().

QuotaDebug protocols::frag_picker::FragmentPicker::log_200_

static

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

QuotaDebug protocols::frag_picker::FragmentPicker::log_25_

static

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

Size protocols::frag_picker::FragmentPicker::max_frag_size_

private

Referenced by FragmentPicker().

Size protocols::frag_picker::FragmentPicker::max_threads_

private

Referenced by FragmentPicker().

Size protocols::frag_picker::FragmentPicker::n_candidates_

Size protocols::frag_picker::FragmentPicker::n_frags_

Real protocols::frag_picker::FragmentPicker::nonlocal_min_contacts_per_res_

private

Referenced by FragmentPicker().

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

Referenced by FragmentPicker().

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

private

Referenced by get_query_phi_prediction().

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

private

Referenced by get_query_phi_prediction_conf().

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

private

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

private

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

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

private

Referenced by get_query_psi_prediction().

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

private

Referenced by get_query_psi_prediction_conf().

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

private

Referenced by get_query_residue_depth().

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

private

Referenced by get_query_sa_prediction().

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

private

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

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

private

Referenced by get_query_ss_string().

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

private

Referenced by count_query_ss(), and get_query_ss().

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

private

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

FragmentSelectingRuleOP protocols::frag_picker::FragmentPicker::selector_

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 Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation