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protocols::enzdes::ResidueConformerFilter Class Reference

filter that figures out which rotamer of a given rotamer lib is in the pose at apply time, and can be used to filter on it. supposed to be used for ligands, and for now only tested for them, but should also work with any other residue. can be used for example in specificity redesign, if one wants to divide up a bunch of designs according to the orientation in which they bind the ligand More...

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::ResidueConformerFilter:
Inheritance graph
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Public Types

typedef protocols::filters::Filter Filter
 
typedef
protocols::filters::FilterOP 
FilterOP
 

Public Member Functions

 ResidueConformerFilter ()
 
 ResidueConformerFilter (ResidueConformerFilter const &other)
 
 ~ResidueConformerFilter () 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 report (std::ostream &, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Size get_current_conformer (core::pose::Pose const &pose) const
 
std::string name () const override
 
- 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 Member Functions

void initialize_internal_data ()
 

Private Attributes

core::chemical::ResidueTypeCOP restype_
 
core::Size seqpos_
 
core::Size desired_conformer_
 
core::Real max_rms_
 
utility::vector1< core::Sizerelevant_atom_indices_
 
match::downstream::LigandConformerBuilderCOP lig_conformer_builder_
 

Additional Inherited Members

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

Detailed Description

filter that figures out which rotamer of a given rotamer lib is in the pose at apply time, and can be used to filter on it. supposed to be used for ligands, and for now only tested for them, but should also work with any other residue. can be used for example in specificity redesign, if one wants to divide up a bunch of designs according to the orientation in which they bind the ligand

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::enzdes::ResidueConformerFilter::ResidueConformerFilter ( )
protocols::enzdes::ResidueConformerFilter::ResidueConformerFilter ( ResidueConformerFilter const &  other)
default
protocols::enzdes::ResidueConformerFilter::~ResidueConformerFilter ( )
overridedefault

Member Function Documentation

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

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

Implements protocols::filters::Filter.

References desired_conformer_, get_current_conformer(), and protocols::enzdes::TR().

std::string protocols::enzdes::ResidueConformerFilter::class_name ( )
static
FilterOP protocols::enzdes::ResidueConformerFilter::clone ( ) const
inlineoverridevirtual
FilterOP protocols::enzdes::ResidueConformerFilter::fresh_instance ( ) const
inlineoverridevirtual
core::Size protocols::enzdes::ResidueConformerFilter::get_current_conformer ( core::pose::Pose const &  pose) const

this might actually need to be implemented differently for residue types that get their rotamers/conformers from the dunbrack library, as this is bb dependent. this filter however assumes that the conformer library for a given residue type is constant.

References lig_conformer_builder_, core::conformation::Residue::name3(), relevant_atom_indices_, core::pose::Pose::residue(), restype_, seqpos_, and core::pose::Pose::size().

Referenced by apply(), report(), and report_sm().

void protocols::enzdes::ResidueConformerFilter::initialize_internal_data ( )
private
std::string protocols::enzdes::ResidueConformerFilter::name ( ) const
overridevirtual
void protocols::enzdes::ResidueConformerFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References desired_conformer_, core::chemical::FA_STANDARD, initialize_internal_data(), max_rms_, relevant_atom_indices_, restype_, and seqpos_.

void protocols::enzdes::ResidueConformerFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::enzdes::ResidueConformerFilter::report ( std::ostream &  stream,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References get_current_conformer().

core::Real protocols::enzdes::ResidueConformerFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References get_current_conformer().

Member Data Documentation

core::Size protocols::enzdes::ResidueConformerFilter::desired_conformer_
private

Referenced by apply(), and parse_my_tag().

match::downstream::LigandConformerBuilderCOP protocols::enzdes::ResidueConformerFilter::lig_conformer_builder_
private
core::Real protocols::enzdes::ResidueConformerFilter::max_rms_
private
utility::vector1< core::Size > protocols::enzdes::ResidueConformerFilter::relevant_atom_indices_
private
core::chemical::ResidueTypeCOP protocols::enzdes::ResidueConformerFilter::restype_
private
core::Size protocols::enzdes::ResidueConformerFilter::seqpos_
private

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