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:

[legend]

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...

utility::vector1< core::Size >	selection_positions (core::pose::Pose const &pose) const
	Calls apply and returns the Rosetta numbering corresponding to the selected residues. More...

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 ()
	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

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP protocols::cyclic_peptide::RamaMutationSelector::ResidueSelectorOP

◆ ResidueSubset

typedef core::select::residue_selector::ResidueSubset protocols::cyclic_peptide::RamaMutationSelector::ResidueSubset

Constructor & Destructor Documentation

◆ RamaMutationSelector() [1/2]

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

Constructor.

◆ RamaMutationSelector() [2/2]

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

default

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

◆ ~RamaMutationSelector()

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

overridedefault

Destructor.

Member Function Documentation

◆ apply()

RamaMutationSelector::ResidueSubset protocols::cyclic_peptide::RamaMutationSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

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

References core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResidueTypeBase::custom_variant_types(), core::scoring::ScoringManager::get_RamaPrePro(), core::chemical::ResidueTypeFinder::get_representative_type(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer(), is_terminus(), core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::name(), core::scoring::rama, rama_prepro_multiplier(), core::pose::Pose::residue(), core::chemical::ResidueTypeFinder::residue_base_name(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_ptr(), core::pose::Pose::residue_type_set_for_pose(), score_threshold(), target_type(), core::pose::Pose::total_residue(), protocols::cyclic_peptide::TR(), core::chemical::ResidueType::upper_connect_id(), core::chemical::ResidueTypeBase::variant_type_enums(), and core::chemical::ResidueTypeFinder::variants().

◆ class_name()

std::string protocols::cyclic_peptide::RamaMutationSelector::class_name ( )

static

Get the mover class name.

Referenced by get_name(), protocols::cyclic_peptide::RamaMutationSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

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.

◆ get_name()

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

overridevirtual

Get the mover class name.

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

References class_name().

◆ is_terminus()

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().

◆ parse_my_tag()

void protocols::cyclic_peptide::RamaMutationSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

XML parse.

Parse RosettaScripts tags and set up this mover.

Reimplemented from core::select::residue_selector::ResidueSelector.

References rama_prepro_multiplier(), score_threshold(), set_rama_prepro_multiplier(), set_score_threshold(), set_target_type(), and target_type().

◆ provide_xml_schema()

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().

◆ rama_prepro_multiplier()

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().

◆ score_threshold()

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().

◆ set_rama_prepro_multiplier()

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().

◆ set_score_threshold()

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().

◆ set_target_type()

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().

◆ target_type()

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

◆ rama_prepro_multiplier_

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().

◆ score_threshold_

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().

◆ target_type_

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:

src/protocols/cyclic_peptide/RamaMutationSelector.hh
src/protocols/cyclic_peptide/RamaMutationSelector.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ResidueSelectorOP

◆ ResidueSubset

Constructor & Destructor Documentation

◆ RamaMutationSelector() [1/2]

◆ RamaMutationSelector() [2/2]

◆ ~RamaMutationSelector()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_name()

◆ is_terminus()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ rama_prepro_multiplier()

◆ score_threshold()

◆ set_rama_prepro_multiplier()

◆ set_score_threshold()

◆ set_target_type()

◆ target_type()

Member Data Documentation

◆ rama_prepro_multiplier_

◆ score_threshold_

◆ target_type_