The InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset. More...

#include <InterGroupInterfaceByVectorSelector.hh>

Inheritance diagram for core::select::residue_selector::InterGroupInterfaceByVectorSelector:

[legend]

Public Member Functions
	InterGroupInterfaceByVectorSelector ()

	InterGroupInterfaceByVectorSelector (InterGroupInterfaceByVectorSelector const &src)
	Copy constructor. More...

	InterGroupInterfaceByVectorSelector (ResidueSelectorCOP group1, ResidueSelectorCOP group2)

ResidueSelectorOP	clone () const override
	Clone operator. More...

	~InterGroupInterfaceByVectorSelector () override

ResidueSubset	apply (core::pose::Pose const &pose) const override
	Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	Initialize this object from a Tag. More...

ResidueSelectorCOP	group1_selector () const

void	group1_selector (ResidueSelectorCOP setting)

std::set< Size > const &	group1_set () const

void	group1_set (std::set< Size > const &setting)
	This has the side-effect of resetting the group1_selector_ pointer to 0 since the ResidueSelector and explicit std::set schemes are mutually exclusive. More...

std::string const &	group1_resstring () const

void	group1_resstring (std::string const &setting)

ResidueSelectorCOP	group2_selector () const

void	group2_selector (ResidueSelectorCOP setting)

std::set< Size > const &	group2_set () const

void	group2_set (std::set< Size > const &setting)
	This has the side-effect of resetting the group2_selector_ pointer to 0 since the ResidueSelector and explicit std::set schemes are mutually exclusive. More...

std::string const &	group2_resstring () const

void	group2_resstring (std::string const &setting)

Real	cb_dist_cut () const

Real	nearby_atom_cut () const

Real	vector_angle_cut () const

Real	vector_dist_cut () const

void	cb_dist_cut (Real setting)

void	nearby_atom_cut (Real setting)

void	vector_angle_cut (Real setting)

void	vector_dist_cut (Real setting)

std::string	get_name () const override

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 ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	set_from_residue_selector (core::pose::Pose const &pose, ResidueSelector const &selector, std::set< Size > &subset) const

void	set_from_residue_list_string (core::pose::Pose const &pose, std::string const &res_list_string, std::set< Size > &subset) const

Private Attributes
ResidueSelectorCOP	group1_selector_

std::set< core::Size >	group1_set_

std::string	group1_resstring_

ResidueSelectorCOP	group2_selector_

std::set< core::Size >	group2_set_

std::string	group2_resstring_

Real	cb_dist_cut_

Real	nearby_atom_cut_

Real	vector_angle_cut_

Real	vector_dist_cut_

Detailed Description

The InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset.

Constructor & Destructor Documentation

◆ InterGroupInterfaceByVectorSelector() [1/3]

core::select::residue_selector::InterGroupInterfaceByVectorSelector::InterGroupInterfaceByVectorSelector ( )

◆ InterGroupInterfaceByVectorSelector() [2/3]

core::select::residue_selector::InterGroupInterfaceByVectorSelector::InterGroupInterfaceByVectorSelector ( InterGroupInterfaceByVectorSelector const & src )

Copy constructor.

◆ InterGroupInterfaceByVectorSelector() [3/3]

core::select::residue_selector::InterGroupInterfaceByVectorSelector::InterGroupInterfaceByVectorSelector	(	ResidueSelectorCOP	group1,
		ResidueSelectorCOP	group2
	)

References group1_selector(), and group2_selector().

◆ ~InterGroupInterfaceByVectorSelector()

core::select::residue_selector::InterGroupInterfaceByVectorSelector::~InterGroupInterfaceByVectorSelector ( )

overridedefault

Member Function Documentation

◆ apply()

ResidueSubset core::select::residue_selector::InterGroupInterfaceByVectorSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

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

References core::select::util::calc_interacting_vector(), cb_dist_cut_, group1_resstring_, group1_selector_, group1_set_, group2_resstring_, group2_selector_, group2_set_, nearby_atom_cut_, set_from_residue_list_string(), set_from_residue_selector(), vector_angle_cut_, and vector_dist_cut_.

◆ cb_dist_cut() [1/2]

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut ( ) const

References cb_dist_cut_.

Referenced by parse_my_tag().

◆ cb_dist_cut() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut ( Real setting )

References cb_dist_cut_.

◆ class_name()

std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::class_name ( )

static

Referenced by get_name(), core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

ResidueSelectorOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::clone ( ) const

overridevirtual

Clone operator.

Copy this object and return an owning pointer to the new object.

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

◆ get_name()

std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::get_name ( ) const

overridevirtual

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

References class_name().

◆ group1_resstring() [1/2]

std::string const & core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring ( ) const

References group1_resstring_.

Referenced by parse_my_tag().

◆ group1_resstring() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring ( std::string const & setting )

References group1_resstring_, group1_selector_, and group1_set_.

◆ group1_selector() [1/2]

ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector ( ) const

References group1_selector_.

Referenced by InterGroupInterfaceByVectorSelector(), and parse_my_tag().

◆ group1_selector() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector ( ResidueSelectorCOP setting )

this has the side-effect of clearing out the group1_set_, since the ResidueSelector and std:set schemes are meant to be mutually exclusive.

References group1_resstring_, group1_selector_, and group1_set_.

◆ group1_set() [1/2]

std::set< Size > const & core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set ( ) const

References group1_set_.

◆ group1_set() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set ( std::set< Size > const & setting )

This has the side-effect of resetting the group1_selector_ pointer to 0 since the ResidueSelector and explicit std::set schemes are mutually exclusive.

References group1_resstring_, group1_selector_, and group1_set_.

◆ group2_resstring() [1/2]

std::string const & core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring ( ) const

References group2_resstring_.

Referenced by parse_my_tag().

◆ group2_resstring() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring ( std::string const & setting )

References group2_resstring_, group2_selector_, and group2_set_.

◆ group2_selector() [1/2]

ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector ( ) const

References group2_selector_.

Referenced by InterGroupInterfaceByVectorSelector(), and parse_my_tag().

◆ group2_selector() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector ( ResidueSelectorCOP setting )

this has the side-effect of clearing out the group2_set_, since the ResidueSelector and std:set schemes are meant to be mutually exclusive.

References group2_resstring_, group2_selector_, and group2_set_.

◆ group2_set() [1/2]

std::set< Size > const & core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set ( ) const

References group2_set_.

◆ group2_set() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set ( std::set< Size > const & setting )

This has the side-effect of resetting the group2_selector_ pointer to 0 since the ResidueSelector and explicit std::set schemes are mutually exclusive.

References group2_resstring_, group2_selector_, and group2_set_.

◆ nearby_atom_cut() [1/2]

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut ( ) const

References nearby_atom_cut_.

Referenced by parse_my_tag().

◆ nearby_atom_cut() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut ( Real setting )

References nearby_atom_cut_.

◆ parse_my_tag()

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Initialize this object from a Tag.

Exceptions

utility::excn::EXCN_Msg_Exception if neither a grp1_selector nor a grp1_residues option is provided, or if neither a grp2_selector nor a grp2_residues option is provided.

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

References cb_dist_cut(), protocols::pack_daemon::error_message, core::select::residue_selector::get_residue_selector(), group1_resstring(), group1_selector(), group2_resstring(), group2_selector(), nearby_atom_cut(), vector_angle_cut(), and vector_dist_cut().

◆ provide_xml_schema()

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors().

Referenced by core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::provide_xml_schema().

◆ set_from_residue_list_string()

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_list_string	(	core::pose::Pose const &	pose,
		std::string const &	res_list_string,
		std::set< Size > &	subset
	)		const

private

References core::pose::get_resnum_list().

Referenced by apply().

◆ set_from_residue_selector()

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_selector	(	core::pose::Pose const &	pose,
		ResidueSelector const &	selector,
		std::set< Size > &	subset
	)		const

private

References core::select::residue_selector::ResidueSelector::apply(), and core::pose::Pose::size().

Referenced by apply().

◆ vector_angle_cut() [1/2]

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut ( ) const

References vector_angle_cut_.

Referenced by parse_my_tag().

◆ vector_angle_cut() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut ( Real setting )

References vector_angle_cut_.

◆ vector_dist_cut() [1/2]

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut ( ) const

References vector_dist_cut_.

Referenced by parse_my_tag().

◆ vector_dist_cut() [2/2]

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut ( Real setting )

References vector_dist_cut_.

Member Data Documentation

◆ cb_dist_cut_

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut_

private

Referenced by apply(), and cb_dist_cut().

◆ group1_resstring_

std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring_

private

Referenced by apply(), group1_resstring(), group1_selector(), and group1_set().

◆ group1_selector_

ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector_

private

Referenced by apply(), group1_resstring(), group1_selector(), and group1_set().

◆ group1_set_

std::set< core::Size > core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set_

private

Referenced by apply(), group1_resstring(), group1_selector(), and group1_set().

◆ group2_resstring_

std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring_

private

Referenced by apply(), group2_resstring(), group2_selector(), and group2_set().

◆ group2_selector_

ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector_

private

Referenced by apply(), group2_resstring(), group2_selector(), and group2_set().

◆ group2_set_

std::set< core::Size > core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set_

private

Referenced by apply(), group2_resstring(), group2_selector(), and group2_set().

◆ nearby_atom_cut_

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut_

private

Referenced by apply(), and nearby_atom_cut().

◆ vector_angle_cut_

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut_

private

Referenced by apply(), and vector_angle_cut().

◆ vector_dist_cut_

Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut_

private

Referenced by apply(), and vector_dist_cut().

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

src/core/select/residue_selector/InterGroupInterfaceByVectorSelector.hh
src/core/select/residue_selector/InterGroupInterfaceByVectorSelector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ InterGroupInterfaceByVectorSelector() [1/3]

◆ InterGroupInterfaceByVectorSelector() [2/3]

◆ InterGroupInterfaceByVectorSelector() [3/3]

◆ ~InterGroupInterfaceByVectorSelector()

Member Function Documentation

◆ apply()

◆ cb_dist_cut() [1/2]

◆ cb_dist_cut() [2/2]

◆ class_name()

◆ clone()

◆ get_name()

◆ group1_resstring() [1/2]

◆ group1_resstring() [2/2]

◆ group1_selector() [1/2]

◆ group1_selector() [2/2]

◆ group1_set() [1/2]

◆ group1_set() [2/2]

◆ group2_resstring() [1/2]

◆ group2_resstring() [2/2]

◆ group2_selector() [1/2]

◆ group2_selector() [2/2]

◆ group2_set() [1/2]

◆ group2_set() [2/2]

◆ nearby_atom_cut() [1/2]

◆ nearby_atom_cut() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_from_residue_list_string()

◆ set_from_residue_selector()

◆ vector_angle_cut() [1/2]

◆ vector_angle_cut() [2/2]

◆ vector_dist_cut() [1/2]

◆ vector_dist_cut() [2/2]

Member Data Documentation

◆ cb_dist_cut_

◆ group1_resstring_

◆ group1_selector_

◆ group1_set_

◆ group2_resstring_

◆ group2_selector_

◆ group2_set_

◆ nearby_atom_cut_

◆ vector_angle_cut_

◆ vector_dist_cut_