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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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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< Sizefrag_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< Sizequery_positions_
 
VallProviderOP chunks_
 
utility::vector1
< VallChunkFilterOP
filters_
 
CandidatesSink candidates_sink_
 
utility::vector1< CandidatesSinkcandidates_sinks_
 
utility::vector1
< scores::FragmentScoreManagerOP
scores_
 
Size contacts_min_seq_sep_
 
std::set< ContactTypecontact_types_
 
Real contacts_dist_cutoff_squared_
 
utility::vector1< Realcontacts_dist_cutoffs_squared_
 
SidechainContactDistCutoffOP sidechain_contact_dist_cutoff_
 
Real nonlocal_min_contacts_per_res_
 
utility::vector1< Realquery_sa_prediction_
 
utility::vector1< Realquery_phi_prediction_
 
utility::vector1< Realquery_psi_prediction_
 
utility::vector1< Realquery_phi_prediction_conf_
 
utility::vector1< Realquery_psi_prediction_conf_
 
utility::vector1< Realquery_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
protocols::frag_picker::FragmentPicker::FragmentPicker ( std::string  fragment_score_manager_type)
inline
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 
)
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_)
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::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 
)
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

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.

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 ( )
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

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 ( )
void protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota ( )
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
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
utility::vector1<CandidatesSink> protocols::frag_picker::FragmentPicker::candidates_sinks_
private
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
QuotaDebug protocols::frag_picker::FragmentPicker::log_25_
static
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
utility::vector1<Real> protocols::frag_picker::FragmentPicker::query_phi_prediction_conf_
private
utility::vector1<Size> protocols::frag_picker::FragmentPicker::query_positions_
private
core::sequence::SequenceProfileOP protocols::frag_picker::FragmentPicker::query_profile_
private
utility::vector1<Real> protocols::frag_picker::FragmentPicker::query_psi_prediction_
private
utility::vector1<Real> protocols::frag_picker::FragmentPicker::query_psi_prediction_conf_
private
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
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
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: