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protocols::frag_picker::FragmentScoreFilter Class Reference

–brief– More...

#include <FragmentScoreFilter.hh>

Inheritance diagram for protocols::frag_picker::FragmentScoreFilter:
Inheritance graph
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Public Member Functions

 FragmentScoreFilter ()
 
 ~FragmentScoreFilter () override
 
bool apply (core::pose::Pose const &pose) const override
 returns true if the structure passes the filter, false otherwise More...
 
void rescore_fragment_crmsd (core::pose::PoseOP const pose, utility::vector1< frag_picker::Candidate > candidates, frag_picker::scores::FragmentCrmsd *fc) const
 Function is required to get FragmentCrmsd scores from the RosettaScripts pose; if FragmentCrmsd is calculated using the ScoreMap, it tries to get a pose from the command line. Similar functions will likely need to be implemented for pose-dependent fragment scores. TO DO: Make this function take weight and priority based on weights file, then have it call a constructor with the RosettaScripts pose for ANY fragment scoretype. This will rescore everything with the new pose no matter what scoretype is used. More...
 
void setup_fragment_picker (core::pose::PoseOP const pose, frag_picker::FragmentPickerOP picker) const
 Setup the FragmentPicker. Replicates much of the functionality from the FragmentPicker's parse_my_tag() function. More...
 
core::Real compute (core::pose::Pose const pose) const
 Compute filter value. More...
 
core::Real get_result (utility::vector1< core::Real >) const
 Given a list of scores, find the one the user is interested in. More...
 
core::Real report_sm (core::pose::Pose const &pose) const override
 required for reporting score values More...
 
void report (std::ostream &os, core::pose::Pose const &pose) const override
 allows printing data to a stream More...
 
std::string name () const override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Filter in Rosetta Scripts) More...
 
protocols::filters::FilterOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::filters::FilterOP clone () const override
 required in the context of the parser/scripting scheme More...
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

core::Real threshold_
 Threshold number for passing or failing filter. More...
 
std::string direction_
 Choose whether numbers that are higher or numbers that are lower than the filter pass. More...
 
std::string score_type_ = "FragmentCrmsd"
 Choose which score type to filter based on. More...
 
core::pose::ResidueIndexDescriptionCOP start_res_
 Start evaluating fragments at this residue. More...
 
core::pose::ResidueIndexDescriptionCOP end_res_
 Stop evaluating fragments after this residue. More...
 
core::Size fragment_size_ = 9
 Size of fragments to evaluate. More...
 
std::string compute_ = "maximum"
 Should the final score be the minimum, maximum, or average of the positions queried? More...
 
std::string sort_by_ = "FragmentCrmsd"
 How to choose the best fragment at each position (by default, it takes the lowest FragmentCrmsd at each position and returns the average FragmentCrmsd of all positions; however, suggested use is to set sort_by_ to 'average', which calculates the average of the score_type for each fragment. You may specify a different score type (including TotalScore) here and it will choose the fragment with the lowest of that score type at each position.) More...
 
std::string outputs_folder_
 Folder to place sequence profile files. More...
 
std::string outputs_name_ = "pose"
 Basename of sequence profile files. More...
 
std::string csblast_
 Location of CSBLAST program. More...
 
std::string blast_pgp_
 Location of BLAST PGP program. More...
 
std::string placeholder_seqs_
 Location of sequence database for BLAST PGP. More...
 
std::string sparks_x_
 Location of SPARKS-X directory. More...
 
std::string sparks_x_query_
 Location of SPARKS-X query script. More...
 
std::string psipred_
 Path to run_psipred_single script. More...
 
std::string vall_path_
 Path to vall database. More...
 
std::string frags_scoring_config_
 Path to scoring config file. More...
 
core::Size n_frags_
 How many fragments per position? More...
 
core::Size n_candidates_
 How many candidates per position? More...
 
bool print_out_info_to_pdb_
 Prints scores for all residues to the pdb. More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

–brief–

Constructor & Destructor Documentation

protocols::frag_picker::FragmentScoreFilter::FragmentScoreFilter ( )
protocols::frag_picker::FragmentScoreFilter::~FragmentScoreFilter ( )
overridedefault

Member Function Documentation

bool protocols::frag_picker::FragmentScoreFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References compute(), direction_, threshold_, and protocols::frag_picker::TR().

std::string protocols::frag_picker::FragmentScoreFilter::class_name ( )
static
protocols::filters::FilterOP protocols::frag_picker::FragmentScoreFilter::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

core::Real protocols::frag_picker::FragmentScoreFilter::compute ( core::pose::Pose const  pose) const
protocols::filters::FilterOP protocols::frag_picker::FragmentScoreFilter::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

core::Real protocols::frag_picker::FragmentScoreFilter::get_result ( utility::vector1< core::Real scores) const

Given a list of scores, find the one the user is interested in.

References compute_.

Referenced by compute().

std::string protocols::frag_picker::FragmentScoreFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by compute().

void protocols::frag_picker::FragmentScoreFilter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::frag_picker::FragmentScoreFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::frag_picker::FragmentScoreFilter::report ( std::ostream &  os,
core::pose::Pose const &  pose 
) const
overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::frag_picker::FragmentScoreFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd ( core::pose::PoseOP const  pose,
utility::vector1< frag_picker::Candidate candidates,
frag_picker::scores::FragmentCrmsd fc 
) const

Function is required to get FragmentCrmsd scores from the RosettaScripts pose; if FragmentCrmsd is calculated using the ScoreMap, it tries to get a pose from the command line. Similar functions will likely need to be implemented for pose-dependent fragment scores. TO DO: Make this function take weight and priority based on weights file, then have it call a constructor with the RosettaScripts pose for ANY fragment scoretype. This will rescore everything with the new pose no matter what scoretype is used.

References protocols::frag_picker::scores::FragmentCrmsd::score(), protocols::frag_picker::scores::FragmentCrmsd::set_pose(), and protocols::frag_picker::TR().

Referenced by compute().

void protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker ( core::pose::PoseOP const  pose,
frag_picker::FragmentPickerOP  picker 
) const

Member Data Documentation

std::string protocols::frag_picker::FragmentScoreFilter::blast_pgp_
private

Location of BLAST PGP program.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::compute_ = "maximum"
private

Should the final score be the minimum, maximum, or average of the positions queried?

Referenced by get_result(), and parse_my_tag().

std::string protocols::frag_picker::FragmentScoreFilter::csblast_
private

Location of CSBLAST program.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::direction_
private

Choose whether numbers that are higher or numbers that are lower than the filter pass.

Referenced by apply(), and parse_my_tag().

core::pose::ResidueIndexDescriptionCOP protocols::frag_picker::FragmentScoreFilter::end_res_
private

Stop evaluating fragments after this residue.

Referenced by compute(), and parse_my_tag().

core::Size protocols::frag_picker::FragmentScoreFilter::fragment_size_ = 9
private

Size of fragments to evaluate.

Referenced by compute(), parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::frags_scoring_config_
private

Path to scoring config file.

Referenced by parse_my_tag(), and setup_fragment_picker().

core::Size protocols::frag_picker::FragmentScoreFilter::n_candidates_
private

How many candidates per position?

Referenced by parse_my_tag(), and setup_fragment_picker().

core::Size protocols::frag_picker::FragmentScoreFilter::n_frags_
private

How many fragments per position?

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::outputs_folder_
private

Folder to place sequence profile files.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::outputs_name_ = "pose"
private

Basename of sequence profile files.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::placeholder_seqs_
private

Location of sequence database for BLAST PGP.

Referenced by parse_my_tag(), and setup_fragment_picker().

bool protocols::frag_picker::FragmentScoreFilter::print_out_info_to_pdb_
private

Prints scores for all residues to the pdb.

Referenced by compute(), and parse_my_tag().

std::string protocols::frag_picker::FragmentScoreFilter::psipred_
private

Path to run_psipred_single script.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::score_type_ = "FragmentCrmsd"
private

Choose which score type to filter based on.

Referenced by compute(), and parse_my_tag().

std::string protocols::frag_picker::FragmentScoreFilter::sort_by_ = "FragmentCrmsd"
private

How to choose the best fragment at each position (by default, it takes the lowest FragmentCrmsd at each position and returns the average FragmentCrmsd of all positions; however, suggested use is to set sort_by_ to 'average', which calculates the average of the score_type for each fragment. You may specify a different score type (including TotalScore) here and it will choose the fragment with the lowest of that score type at each position.)

Referenced by compute(), and parse_my_tag().

std::string protocols::frag_picker::FragmentScoreFilter::sparks_x_
private

Location of SPARKS-X directory.

Referenced by parse_my_tag(), and setup_fragment_picker().

std::string protocols::frag_picker::FragmentScoreFilter::sparks_x_query_
private

Location of SPARKS-X query script.

Referenced by parse_my_tag(), and setup_fragment_picker().

core::pose::ResidueIndexDescriptionCOP protocols::frag_picker::FragmentScoreFilter::start_res_
private

Start evaluating fragments at this residue.

Referenced by compute(), and parse_my_tag().

core::Real protocols::frag_picker::FragmentScoreFilter::threshold_
private

Threshold number for passing or failing filter.

Referenced by apply(), and parse_my_tag().

std::string protocols::frag_picker::FragmentScoreFilter::vall_path_
private

Path to vall database.

Referenced by parse_my_tag(), and setup_fragment_picker().


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