Rosetta 3.4
Public Member Functions | Public Attributes | Static Public Attributes
protocols::frag_picker::FragmentPicker Class Reference

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

#include <FragmentPicker.hh>

Inheritance diagram for protocols::frag_picker::FragmentPicker:
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List of all members.

Public Member Functions

 FragmentPicker ()
 FragmentPicker (std::string fragment_score_manager_type)
 ~FragmentPicker ()
void parse_command_line ()
void keep_all_protocol ()
 Picks fragments and saves them into proper files - independently for each query position.
void bounded_protocol ()
 Picks fragments and saves them into proper files - uses bounded queue.
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
void read_vall (std::string const &fn)
 reads a vall file
void read_vall (utility::vector1< std::string > const &fns)
void set_vall (VallProviderOP vall_chunks)
 sets vall data
VallProviderOP get_vall ()
void set_query_seq (core::sequence::SequenceProfileOP query_sequence)
 sets the query sequence
void set_query_seq (std::string &query_sequence)
 sets the query sequence
std::string & get_query_seq_string ()
 Returns the sequence we are picking fragments for (as a string)
core::sequence::SequenceProfileOP get_query_seq ()
utility::vector1< Real > & get_query_sa_prediction ()
 Returns the solvent accessibility prediction.
utility::vector1< Real > & get_query_phi_prediction ()
 Returns the phi prediction.
utility::vector1< Real > & get_query_psi_prediction ()
 Returns the psi prediction.
utility::vector1< Real > & get_query_phi_prediction_conf ()
 Returns the phi prediction confidence.
utility::vector1< Real > & get_query_psi_prediction_conf ()
 Returns the psi prediction confidence.
utility::vector1< Real > & get_query_residue_depth ()
 Returns residue depth values.
void set_query_profile (core::sequence::SequenceProfileOP profile)
 Sets the sequence object we are picking fragments for.
core::fragment::SecondaryStructureOP get_query_ss (std::string prediction_name)
 Returns the query secondary structure as a SecondaryStructure object.
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.
std::string & get_query_ss_string (std::string prediction_name)
 Returns the query secondary structure as a string.
void add_query_ss (std::string, std::string)
 Sets the query secondary structure.
Size count_query_ss ()
 Sets the query secondary structure.
void read_ss_file (std::string const &, std::string)
 Identifies if the ss file is psipred or talos, calls appropriate reader.
void read_spine_x (std::string const &file_name)
 Reads spine-x phi, psi, and solvent accessibility predictions.
void read_depth (std::string const &file_name)
 Reads DEPTH residue depth values.
Size size_of_query ()
void set_picked_positions (Size, Size)
 Asks the picker to pick fragments from a given range in a query sequence.
void set_picked_positions (utility::vector1< Size >)
 Asks the picker to pick fragments for given positions in a query sequence.
void pick_chunk_candidates (utility::vector1< VallChunkOP > const &chunks, Size const &index)
 picks fragment candidates.
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)
void save_candidates ()
void save_fragments ()
Size max_frag_len ()
 How long is the longest fragment?
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
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.
void read_talos_ss (std::string const &, std::string)
 Reads query secondary structure prediction from a Talos+ file.
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
CandidatesCollectorOP get_candidates_collector (Size frag_size, Size index=1)
 returns a pointer to the candidates collector currently used
void add_chunk_filter (VallChunkFilterOP filter)
 adds a chunk filter that will be used to screen chunks before they are cut into fragments

Public Attributes

utility::vector1< Sizefrag_sizes_
Size n_candidates_
Size n_frags_
std::string prefix_
FragmentSelectingRuleOP selector_

Static Public Attributes

static QuotaDebug log_25_
static QuotaDebug log_200_

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 prefix_.

protocols::frag_picker::FragmentPicker::FragmentPicker ( std::string  fragment_score_manager_type) [inline]

References prefix_.

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

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

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

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.
Size protocols::frag_picker::FragmentPicker::count_query_ss ( ) [inline]

Sets the query secondary structure.

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

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

Returns the phi prediction.

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

Returns the phi prediction confidence.

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

Returns the psi prediction.

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

Returns the psi prediction confidence.

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

Returns residue depth values.

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

Returns the solvent accessibility prediction.

core::sequence::SequenceProfileOP protocols::frag_picker::FragmentPicker::get_query_seq ( ) [inline]
std::string& protocols::frag_picker::FragmentPicker::get_query_seq_string ( ) [inline]

Returns the sequence we are picking fragments for (as a 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.

std::string& protocols::frag_picker::FragmentPicker::get_query_ss_string ( std::string  prediction_name) [inline]

Returns the query secondary structure as a string.

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

returns a pointer to a scoring manager

VallProviderOP protocols::frag_picker::FragmentPicker::get_vall ( ) [inline]
Returns:
a pointer to Vall provider
utility::vector1< ConstantLengthFragSetOP > protocols::frag_picker::FragmentPicker::getFragSet ( int  residueInPose_)
bool protocols::frag_picker::FragmentPicker::is_valid_chunk ( VallChunkOP  chunk)
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::trPicker().

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 
)
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 
)
void protocols::frag_picker::FragmentPicker::output_fragments ( Size const  fragment_size,
utility::vector1< Candidates > const &  final_fragments 
)
void protocols::frag_picker::FragmentPicker::parse_command_line ( )
void protocols::frag_picker::FragmentPicker::parse_quota_command_line ( )
void protocols::frag_picker::FragmentPicker::pick_candidates ( )
void protocols::frag_picker::FragmentPicker::pick_candidates ( Size  i_pos,
Size  frag_len 
)
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

References make_table_of_pilot_apps::f.

Referenced by pick_candidates().

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

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::trPicker().

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

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_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_query_profile ( core::sequence::SequenceProfileOP  profile) [inline]

Sets the sequence object we are picking fragments for.

References 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 set_picked_positions().

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

sets the query sequence

References set_picked_positions().

void protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style ( )
void protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota ( )
void protocols::frag_picker::FragmentPicker::set_vall ( VallProviderOP  vall_chunks) [inline]

sets vall data

void protocols::frag_picker::FragmentPicker::show_scoring_methods ( std::ostream &  out,
Size  index = 1 
) [inline]
Size protocols::frag_picker::FragmentPicker::size_of_query ( ) [inline]
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

Referenced by max_frag_len().

Referenced by FragmentPicker().


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