–brief– More...

#include <FragmentScoreFilter.hh>

Inheritance diagram for protocols::frag_picker::FragmentScoreFilter:

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 () 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ FragmentScoreFilter()

protocols::frag_picker::FragmentScoreFilter::FragmentScoreFilter ( )

◆ ~FragmentScoreFilter()

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

overridedefault

Member Function Documentation

◆ apply()

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().

◆ class_name()

std::string protocols::frag_picker::FragmentScoreFilter::class_name ( )

static

Referenced by protocols::frag_picker::FragmentScoreFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::frag_picker::FragmentScoreFilter::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::frag_picker::FragmentScoreFilter::compute ( core::pose::Pose const pose ) const

◆ fresh_instance()

protocols::filters::FilterOP protocols::frag_picker::FragmentScoreFilter::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ get_result()

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().

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by compute().

◆ parse_my_tag()

void protocols::frag_picker::FragmentScoreFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References blast_pgp_, compute_, csblast_, direction_, end_res_, fragment_size_, frags_scoring_config_, n_candidates_, n_frags_, outputs_folder_, outputs_name_, core::pose::parse_resnum(), placeholder_seqs_, print_out_info_to_pdb_, psipred_, score_type_, sort_by_, sparks_x_, sparks_x_query_, start_res_, threshold_, and vall_path_.

◆ provide_xml_schema()

void protocols::frag_picker::FragmentScoreFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pose::attributes_for_parse_resnum(), core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::frag_picker::FragmentScoreFilterCreator::provide_xml_schema().

◆ report()

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().

◆ report_sm()

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().

◆ rescore_fragment_crmsd()

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().

◆ setup_fragment_picker()

void protocols::frag_picker::FragmentScoreFilter::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.

References blast_pgp_, protocols::frag_picker::convert_binary_checkpoint(), core::sequence::create_fasta_file(), csblast_, protocols::simple_filters::dssp(), fragment_size_, frags_scoring_config_, n_candidates_, n_frags_, outputs_folder_, outputs_name_, placeholder_seqs_, psipred_, core::sequence::read_fasta_file(), protocols::frag_picker::run_command(), sparks_x_, sparks_x_query_, protocols::frag_picker::TR(), and vall_path_.

Referenced by compute().

Member Data Documentation

◆ blast_pgp_

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

private

Location of BLAST PGP program.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ compute_

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().

◆ csblast_

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

private

Location of CSBLAST program.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ direction_

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().

◆ end_res_

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

private

Stop evaluating fragments after this residue.

Referenced by compute(), and parse_my_tag().

◆ fragment_size_

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().

◆ frags_scoring_config_

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

private

Path to scoring config file.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ n_candidates_

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

private

How many candidates per position?

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ n_frags_

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

private

How many fragments per position?

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ outputs_folder_

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

private

Folder to place sequence profile files.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ outputs_name_

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

private

Basename of sequence profile files.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ placeholder_seqs_

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().

◆ print_out_info_to_pdb_

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().

◆ psipred_

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

private

Path to run_psipred_single script.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ score_type_

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().

◆ sort_by_

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().

◆ sparks_x_

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

private

Location of SPARKS-X directory.

Referenced by parse_my_tag(), and setup_fragment_picker().

◆ sparks_x_query_

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().

◆ start_res_

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

private

Start evaluating fragments at this residue.

Referenced by compute(), and parse_my_tag().

◆ threshold_

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

private

Threshold number for passing or failing filter.

Referenced by apply(), and parse_my_tag().

◆ vall_path_

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:

src/protocols/frag_picker/FragmentScoreFilter.hh
src/protocols/frag_picker/FragmentScoreFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FragmentScoreFilter()

◆ ~FragmentScoreFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ fresh_instance()

◆ get_result()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ rescore_fragment_crmsd()

◆ setup_fragment_picker()

Member Data Documentation

◆ blast_pgp_

◆ compute_

◆ csblast_

◆ direction_

◆ end_res_

◆ fragment_size_

◆ frags_scoring_config_

◆ n_candidates_

◆ n_frags_

◆ outputs_folder_

◆ outputs_name_

◆ placeholder_seqs_

◆ print_out_info_to_pdb_

◆ psipred_

◆ score_type_

◆ sort_by_

◆ sparks_x_

◆ sparks_x_query_

◆ start_res_

◆ threshold_

◆ vall_path_