protocols::enzdes::EnzdesScorefileFilter Class Reference

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::EnzdesScorefileFilter:

Public Types
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP

Public Member Functions
	EnzdesScorefileFilter ()
	EnzdesScorefileFilter (EnzdesScorefileFilter const &other)
	~EnzdesScorefileFilter () override
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
FilterOP	clone () const override
FilterOP	fresh_instance () const override
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
void	set_cstio (toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io)
void	examine_pose (core::pose::Pose const &pose) const
utility::vector1< core::io::silent::SilentEnergy > const &	silent_Es () const
core::pose::PoseOP	rnl_pose ()
void	clear_rnl_pose ()
	clear rnl pose to save some memory More...
std::string	name () const override
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	~Filter () override
virtual void	report (std::ostream &, core::pose::Pose const &) const
virtual core::Real	report_sm (core::pose::Pose const &) const
	used to report filter internals through a score or silent file More...
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 Member Functions
void	initialize_value_evaluators_from_file (std::string const &filename)
void	compute_metrics_for_residue_subset (std::string sub_name, bool separate_out_constraints, core::pose::Pose const &calc_pose, utility::vector1< core::Size > const &res_subset) const
void	setup_pose_metric_calculators (core::pose::Pose const &pose, bool separate_out_constraints) const
	function to setup residue specific calculators for all the catalytic residues and the ligand More...

Private Attributes
bool	no_packstat_calc_
bool	native_comparison_
bool	repack_no_lig_
bool	keep_rnl_pose_
core::pose::PoseOP	rnl_pose_
core::scoring::ScoreFunctionOP	sfxn_
toolbox::match_enzdes_util::EnzConstraintIOCOP	enzcst_io_
std::map< core::Size, utility::vector1< std::pair< std::string, std::string > > >	residue_calculators_
utility::vector1< std::pair< std::string, std::string > >	native_compare_calculators_
DesignVsNativeComparisonOP	native_comp_
utility::vector1< core::io::silent::SilentEnergy >	silent_Es_
utility::vector1< std::string >	relevant_scoreterms_
utility::vector1< std::pair< core::Size, core::Size > >	spec_segments_
std::string	reqfile_name_

Static Private Attributes
static std::map< std::string, std::map< std::string, ValueEvaluator > >	evaluator_map_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

brief Class that calculates silent energies for an enzdes type scorefile these silent energies can then be written into a scorefile. class is derived from Filter because eventually it should be possible to have this class read in a requirement file and return false if any of the silent energies don't have the required value

Member Typedef Documentation

Filter

typedef protocols::filters::Filter protocols::enzdes::EnzdesScorefileFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::enzdes::EnzdesScorefileFilter::FilterOP

Constructor & Destructor Documentation

EnzdesScorefileFilter() [1/2]

protocols::enzdes::EnzdesScorefileFilter::EnzdesScorefileFilter

(

)

References native_comp_, native_compare_calculators_, native_comparison_, relevant_scoreterms_, residue_calculators_, silent_Es_, and spec_segments_.

EnzdesScorefileFilter() [2/2]

protocols::enzdes::EnzdesScorefileFilter::EnzdesScorefileFilter

(

EnzdesScorefileFilter const &

other

)

~EnzdesScorefileFilter()

protocols::enzdes::EnzdesScorefileFilter::~EnzdesScorefileFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::enzdes::EnzdesScorefileFilter::apply ( core::pose::Pose const &  pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References evaluator_map_, examine_pose(), reqfile_name_, silent_Es_, and protocols::enzdes::TR().

class_name()

std::string protocols::enzdes::EnzdesScorefileFilter::class_name ( )

static

Referenced by protocols::enzdes::EnzdesScorefileFilterCreator::keyname().

clear_rnl_pose()

void protocols::enzdes::EnzdesScorefileFilter::clear_rnl_pose

(

)

clear rnl pose to save some memory

References rnl_pose_.

clone()

FilterOP protocols::enzdes::EnzdesScorefileFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute_metrics_for_residue_subset()

void protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset ( std::string  sub_name, bool  separate_out_constraints, core::pose::Pose const &  calc_pose, utility::vector1< core::Size > const &  res_subset  ) const

private

References core::pose::Pose::energies(), protocols::mean_field::max(), core::pose::Pose::metric(), relevant_scoreterms_, residue_calculators_, core::scoring::Energies::residue_total_energies(), core::scoring::score_type_from_name(), silent_Es_, protocols::enzdes::enzutil::sum_constraint_scoreterms(), and core::scoring::Energies::weights().

Referenced by examine_pose().

examine_pose()

void protocols::enzdes::EnzdesScorefileFilter::examine_pose

(

core::pose::Pose const &

pose

)

const

References protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::enzutil::catalytic_res(), compute_metrics_for_residue_subset(), core::scoring::ScoreFunctionFactory::create_score_function(), core::sequence::end, core::pose::Pose::energies(), enzcst_io_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), keep_rnl_pose_, protocols::mean_field::max(), core::pose::Pose::metric(), native_comp_, native_compare_calculators_, native_comparison_, core::pose::Pose::observer_cache(), relevant_scoreterms_, repack_no_lig_, residue_calculators_, rnl_pose_, core::scoring::score_type_from_name(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_cstio(), setup_pose_metric_calculators(), sfxn_, protocols::enzdes::RepackLigandSiteWithoutLigandMover::silent_Es(), silent_Es_, spec_segments_, core::pose::datacache::SPECIAL_SEGMENTS_OBSERVER, protocols::enzdes::enzutil::sum_constraint_scoreterms(), core::id::to_string(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().

Referenced by apply().

fresh_instance()

FilterOP protocols::enzdes::EnzdesScorefileFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

initialize_value_evaluators_from_file()

void protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file ( std::string const &  filename )

private

References protocols::enzdes::ValueEvaluator::EQUALS, evaluator_map_, protocols::abinitio::filename(), protocols::enzdes::ValueEvaluator::LARGER, core::scoring::pair, protocols::enzdes::ValueEvaluator::SMALLER, protocols::sparta::split(), and protocols::enzdes::TR().

Referenced by parse_my_tag().

name()

std::string protocols::enzdes::EnzdesScorefileFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::enzdes::DiffAtomSasaFilter::class_name().

parse_my_tag()

void protocols::enzdes::EnzdesScorefileFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &    )

overridevirtual

not implemented yet

Reimplemented from protocols::filters::Filter.

References initialize_value_evaluators_from_file(), and reqfile_name_.

provide_xml_schema()

void protocols::enzdes::EnzdesScorefileFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::enzdes::DiffAtomSasaFilter::class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::enzdes::EnzdesScorefileFilterCreator::provide_xml_schema().

rnl_pose()

core::pose::PoseOP protocols::enzdes::EnzdesScorefileFilter::rnl_pose

(

)

References rnl_pose_.

set_cstio()

void protocols::enzdes::EnzdesScorefileFilter::set_cstio

(

toolbox::match_enzdes_util::EnzConstraintIOCOP

enzcst_io

)

References enzcst_io_.

setup_pose_metric_calculators()

void protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators ( core::pose::Pose const &  pose, bool  separate_out_constraints  ) const

private

function to setup residue specific calculators for all the catalytic residues and the ligand

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::enzdes::enzutil::catalytic_res(), core::pose::Pose::chain(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::metrics::CalculatorFactory::Instance(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_protein(), native_compare_calculators_, native_comparison_, no_packstat_calc_, core::scoring::pair, core::pose::metrics::CalculatorFactory::register_calculator(), residue_calculators_, core::pose::Pose::residue_type(), spec_segments_, and core::id::to_string().

Referenced by examine_pose().

silent_Es()

utility::vector1< core::io::silent::SilentEnergy > const& protocols::enzdes::EnzdesScorefileFilter::silent_Es ( ) const

inline

References silent_Es_.

Member Data Documentation

enzcst_io_

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::enzdes::EnzdesScorefileFilter::enzcst_io_

private

Referenced by examine_pose(), and set_cstio().

evaluator_map_

std::map< std::string, std::map< std::string, ValueEvaluator > > protocols::enzdes::EnzdesScorefileFilter::evaluator_map_

staticprivate

Referenced by apply(), and initialize_value_evaluators_from_file().

keep_rnl_pose_

bool protocols::enzdes::EnzdesScorefileFilter::keep_rnl_pose_

private

Referenced by examine_pose().

native_comp_

DesignVsNativeComparisonOP protocols::enzdes::EnzdesScorefileFilter::native_comp_

private

Referenced by EnzdesScorefileFilter(), and examine_pose().

native_compare_calculators_

utility::vector1< std::pair< std::string, std::string > > protocols::enzdes::EnzdesScorefileFilter::native_compare_calculators_

mutableprivate

Referenced by EnzdesScorefileFilter(), examine_pose(), and setup_pose_metric_calculators().

native_comparison_

bool protocols::enzdes::EnzdesScorefileFilter::native_comparison_

private

Referenced by EnzdesScorefileFilter(), examine_pose(), and setup_pose_metric_calculators().

no_packstat_calc_

bool protocols::enzdes::EnzdesScorefileFilter::no_packstat_calc_

private

Referenced by setup_pose_metric_calculators().

relevant_scoreterms_

utility::vector1< std::string > protocols::enzdes::EnzdesScorefileFilter::relevant_scoreterms_

private

Referenced by compute_metrics_for_residue_subset(), EnzdesScorefileFilter(), and examine_pose().

repack_no_lig_

bool protocols::enzdes::EnzdesScorefileFilter::repack_no_lig_

private

Referenced by examine_pose().

reqfile_name_

std::string protocols::enzdes::EnzdesScorefileFilter::reqfile_name_

private

Referenced by apply(), and parse_my_tag().

residue_calculators_

std::map< core::Size, utility::vector1< std::pair< std::string, std::string > > > protocols::enzdes::EnzdesScorefileFilter::residue_calculators_

mutableprivate

Referenced by compute_metrics_for_residue_subset(), EnzdesScorefileFilter(), examine_pose(), and setup_pose_metric_calculators().

rnl_pose_

core::pose::PoseOP protocols::enzdes::EnzdesScorefileFilter::rnl_pose_

mutableprivate

Referenced by clear_rnl_pose(), examine_pose(), and rnl_pose().

sfxn_

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesScorefileFilter::sfxn_

mutableprivate

Referenced by examine_pose().

silent_Es_

utility::vector1< core::io::silent::SilentEnergy > protocols::enzdes::EnzdesScorefileFilter::silent_Es_

mutableprivate

Referenced by apply(), compute_metrics_for_residue_subset(), EnzdesScorefileFilter(), examine_pose(), and silent_Es().

spec_segments_

utility::vector1< std::pair< core::Size, core::Size > > protocols::enzdes::EnzdesScorefileFilter::spec_segments_

mutableprivate

Referenced by EnzdesScorefileFilter(), examine_pose(), and setup_pose_metric_calculators().

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

• src/protocols/enzdes/EnzFilters.hh
• src/protocols/enzdes/EnzFilters.cc