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protocols::enzdes::EnzdesScorefileFilter Class Reference

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::EnzdesScorefileFilter:
Inheritance graph
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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 (Filter 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 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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 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

Constructor & Destructor Documentation

protocols::enzdes::EnzdesScorefileFilter::EnzdesScorefileFilter ( )
protocols::enzdes::EnzdesScorefileFilter::EnzdesScorefileFilter ( EnzdesScorefileFilter const &  other)
protocols::enzdes::EnzdesScorefileFilter::~EnzdesScorefileFilter ( )
overridedefault

Member Function Documentation

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().

std::string protocols::enzdes::EnzdesScorefileFilter::class_name ( )
static
void protocols::enzdes::EnzdesScorefileFilter::clear_rnl_pose ( )

clear rnl pose to save some memory

References rnl_pose_.

FilterOP protocols::enzdes::EnzdesScorefileFilter::clone ( ) const
inlineoverridevirtual
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
void protocols::enzdes::EnzdesScorefileFilter::examine_pose ( core::pose::Pose const &  pose) const
FilterOP protocols::enzdes::EnzdesScorefileFilter::fresh_instance ( ) const
inlineoverridevirtual
void protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file ( std::string const &  filename)
private
std::string protocols::enzdes::EnzdesScorefileFilter::name ( ) const
overridevirtual
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_.

void protocols::enzdes::EnzdesScorefileFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::pose::PoseOP protocols::enzdes::EnzdesScorefileFilter::rnl_pose ( )

References rnl_pose_.

void protocols::enzdes::EnzdesScorefileFilter::set_cstio ( toolbox::match_enzdes_util::EnzConstraintIOCOP  enzcst_io)

References enzcst_io_.

void protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators ( core::pose::Pose const &  pose,
bool  separate_out_constraints 
) const
private
utility::vector1< core::io::silent::SilentEnergy > const& protocols::enzdes::EnzdesScorefileFilter::silent_Es ( ) const
inline

References silent_Es_.

Member Data Documentation

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

Referenced by examine_pose(), and set_cstio().

std::map< std::string, std::map< std::string, ValueEvaluator > > protocols::enzdes::EnzdesScorefileFilter::evaluator_map_
staticprivate
bool protocols::enzdes::EnzdesScorefileFilter::keep_rnl_pose_
private

Referenced by examine_pose().

DesignVsNativeComparisonOP protocols::enzdes::EnzdesScorefileFilter::native_comp_
private
utility::vector1< std::pair< std::string, std::string > > protocols::enzdes::EnzdesScorefileFilter::native_compare_calculators_
mutableprivate
bool protocols::enzdes::EnzdesScorefileFilter::native_comparison_
private
bool protocols::enzdes::EnzdesScorefileFilter::no_packstat_calc_
private
utility::vector1< std::string > protocols::enzdes::EnzdesScorefileFilter::relevant_scoreterms_
private
bool protocols::enzdes::EnzdesScorefileFilter::repack_no_lig_
private

Referenced by examine_pose().

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

Referenced by apply(), and parse_my_tag().

std::map< core::Size, utility::vector1< std::pair< std::string, std::string > > > protocols::enzdes::EnzdesScorefileFilter::residue_calculators_
mutableprivate
core::pose::PoseOP protocols::enzdes::EnzdesScorefileFilter::rnl_pose_
mutableprivate
core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesScorefileFilter::sfxn_
private

Referenced by examine_pose().

utility::vector1< core::io::silent::SilentEnergy > protocols::enzdes::EnzdesScorefileFilter::silent_Es_
mutableprivate
utility::vector1< std::pair< core::Size, core::Size > > protocols::enzdes::EnzdesScorefileFilter::spec_segments_
mutableprivate

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