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protocols::cyclic_peptide::RamaMutationSelector Class Reference

Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type. More...

#include <RamaMutationSelector.hh>

Inheritance diagram for protocols::cyclic_peptide::RamaMutationSelector:
Inheritance graph
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Public Types

typedef
core::select::residue_selector::ResidueSelectorOP 
ResidueSelectorOP
 
typedef
core::select::residue_selector::ResidueSubset 
ResidueSubset
 

Public Member Functions

 RamaMutationSelector ()
 Constructor. More...
 
 RamaMutationSelector (RamaMutationSelector const &src)
 Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs) More...
 
 ~RamaMutationSelector () override
 Destructor. More...
 
ResidueSelectorOP clone () const override
 Clone operator. More...
 
ResidueSubset apply (core::pose::Pose const &pose) const override
 "Apply" function. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 XML parse. More...
 
std::string get_name () const override
 Get the mover class name. More...
 
void set_target_type (std::string const &type_in)
 Set the residue type (full name) to which we are considering mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position. More...
 
void set_score_threshold (core::Real const &threshold_in)
 Set the score threshold. More...
 
void set_rama_prepro_multiplier (core::Real const &multiplier_in)
 Set the weight multiplier of the rama_prepro term. More...
 
std::string const & target_type () const
 Get the residue type (full name) to which we are considering mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position. More...
 
core::Real const & score_threshold () const
 Get the score threshold. More...
 
core::Real const & rama_prepro_multiplier () const
 Get the weight multiplier of the rama_prepro term. More...
 
- Public Member Functions inherited from core::select::residue_selector::ResidueSelector
 ResidueSelector ()
 Constructor. More...
 
 ~ResidueSelector () override
 Destructor. More...
 
virtual bool residue_selector_provides_citation_info () const
 Does this residue selector 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 residue_selector_is_unpublished () const
 Does this residue selector 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 ()
 Get the mover class name. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Provide XSD information, enabling mechanical validation of input XML. More...
 

Private Member Functions

bool is_terminus (core::conformation::Residue const &rsd) const
 Is a position in a pose a terminal position? More...
 

Private Attributes

std::string target_type_
 The residue type (full name) to which we are considering mutations. If left blank, selection is based on rama_prepro scoring of the residue type at each position. More...
 
core::Real score_threshold_
 The rama_prepro score threshold above which residues are not selected. More...
 
core::Real rama_prepro_multiplier_
 The weight in the scorefunction of the rama_prepro term. More...
 

Detailed Description

Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::cyclic_peptide::RamaMutationSelector::RamaMutationSelector ( )

Constructor.

protocols::cyclic_peptide::RamaMutationSelector::RamaMutationSelector ( RamaMutationSelector const &  src)
default

Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs)

protocols::cyclic_peptide::RamaMutationSelector::~RamaMutationSelector ( )
overridedefault

Destructor.

Member Function Documentation

RamaMutationSelector::ResidueSubset protocols::cyclic_peptide::RamaMutationSelector::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::cyclic_peptide::RamaMutationSelector::class_name ( )
static
core::select::residue_selector::ResidueSelectorOP protocols::cyclic_peptide::RamaMutationSelector::clone ( ) const
overridevirtual

Clone operator.

Clone function.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

Copy this object and return owning pointer to the copy (created on the heap).

Implements core::select::residue_selector::ResidueSelector.

std::string protocols::cyclic_peptide::RamaMutationSelector::get_name ( ) const
overridevirtual

Get the mover class name.

Implements core::select::residue_selector::ResidueSelector.

References class_name().

bool protocols::cyclic_peptide::RamaMutationSelector::is_terminus ( core::conformation::Residue const &  rsd) const
private

Is a position in a pose a terminal position?

Returns true if (a) it has a terminal type, (b) its lower_connect is missing, (c) its lower_connect is unconnected, (d) its upper_connect is missing, or (e) its upper_connect is unconnected.

References core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), and core::conformation::Residue::is_terminus().

Referenced by apply().

void protocols::cyclic_peptide::RamaMutationSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::cyclic_peptide::RamaMutationSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Provide XSD information, enabling mechanical validation of input XML.

References class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by protocols::cyclic_peptide::RamaMutationSelectorCreator::provide_xml_schema().

core::Real const& protocols::cyclic_peptide::RamaMutationSelector::rama_prepro_multiplier ( ) const
inline

Get the weight multiplier of the rama_prepro term.

Defaults to 0.45 to match beta_nov15.

References rama_prepro_multiplier_.

Referenced by apply(), and parse_my_tag().

core::Real const& protocols::cyclic_peptide::RamaMutationSelector::score_threshold ( ) const
inline

Get the score threshold.

Positions which, when mutated to the target type, have a rama_prepro score above this threshold are not selected.

References score_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::cyclic_peptide::RamaMutationSelector::set_rama_prepro_multiplier ( core::Real const &  multiplier_in)

Set the weight multiplier of the rama_prepro term.

Defaults to 0.45 to match beta_nov15.

References rama_prepro_multiplier_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

void protocols::cyclic_peptide::RamaMutationSelector::set_score_threshold ( core::Real const &  threshold_in)

Set the score threshold.

Positions which, when mutated to the target type, have a rama_prepro score above this threshold are not selected.

References score_threshold_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

void protocols::cyclic_peptide::RamaMutationSelector::set_target_type ( std::string const &  type_in)

Set the residue type (full name) to which we are considering mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position.

References target_type_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

std::string const& protocols::cyclic_peptide::RamaMutationSelector::target_type ( ) const
inline

Get the residue type (full name) to which we are considering mutations. If set to an empty string, selection is based on rama_prepro scoring of the residue type at each position.

References target_type_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

core::Real protocols::cyclic_peptide::RamaMutationSelector::rama_prepro_multiplier_
private

The weight in the scorefunction of the rama_prepro term.

Defaults to 0.45 to match beta_nov15.

Referenced by rama_prepro_multiplier(), and set_rama_prepro_multiplier().

core::Real protocols::cyclic_peptide::RamaMutationSelector::score_threshold_
private

The rama_prepro score threshold above which residues are not selected.

Referenced by score_threshold(), and set_score_threshold().

std::string protocols::cyclic_peptide::RamaMutationSelector::target_type_
private

The residue type (full name) to which we are considering mutations. If left blank, selection is based on rama_prepro scoring of the residue type at each position.

Referenced by set_target_type(), and target_type().


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