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core::select::residue_selector::InterGroupInterfaceByVectorSelector Class Reference

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:
Inheritance graph
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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...
 
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 ()
 
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::Sizegroup1_set_
 
std::string group1_resstring_
 
ResidueSelectorCOP group2_selector_
 
std::set< core::Sizegroup2_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

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

Copy constructor.

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

Member Function Documentation

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_.

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

References cb_dist_cut_.

Referenced by parse_my_tag().

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

References cb_dist_cut_.

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

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

References group1_resstring_.

Referenced by parse_my_tag().

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring ( std::string const &  setting)
ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector ( ) const
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_.

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

References group1_set_.

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_.

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

References group2_resstring_.

Referenced by parse_my_tag().

void core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring ( std::string const &  setting)
ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector ( ) const
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_.

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

References group2_set_.

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_.

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

References nearby_atom_cut_.

Referenced by parse_my_tag().

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

References nearby_atom_cut_.

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_Exceptionif 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().

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

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

References vector_angle_cut_.

Referenced by parse_my_tag().

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

References vector_angle_cut_.

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

References vector_dist_cut_.

Referenced by parse_my_tag().

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

References vector_dist_cut_.

Member Data Documentation

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

Referenced by apply(), and cb_dist_cut().

std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring_
private
ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector_
private
std::set< core::Size > core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set_
private
std::string core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring_
private
ResidueSelectorCOP core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector_
private
std::set< core::Size > core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set_
private
Real core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut_
private

Referenced by apply(), and nearby_atom_cut().

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

Referenced by apply(), and vector_angle_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: