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core::select::residue_selector::SSElementSelector Class Reference

The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle. More...

#include <SSElementSelector.hh>

Inheritance diagram for core::select::residue_selector::SSElementSelector:
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Classes

struct  SSElement
 

Public Member Functions

 SSElementSelector ()
 
 SSElementSelector (SSElementSelector const &src)
 Copy constructor. More...
 
ResidueSelectorOP clone () const override
 Clone operator. More...
 
 ~SSElementSelector () override
 Destructor. More...
 
utility::vector1< SSElementparse_ss (core::pose::Pose const &pose) const
 parses the secondary structure elements More...
 
SSElementSelector::SSElement get_SSElement (utility::vector1< SSElementSelector::SSElement > ss_elements, int goal_position, char type, std::string description) const
 
utility::vector1< Sizeconvert_string_to_residues (utility::vector1< SSElementSelector::SSElement > ss_elements, std::string description) const
 
ResidueSubset combine_residue_selections (utility::vector1< Size > start_selection_residues, utility::vector1< Size > end_selection_residues, core::pose::Pose const &pose) const
 
ResidueSubset apply (core::pose::Pose const &pose) const override
 apply. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 tag parsing More...
 
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 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 Attributes

std::string start_
 
std::string end_
 
std::string chain_
 
core::Size reassign_short_terminal_loop_
 

Detailed Description

The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle.

you can also select with n_term or c_term. Examples: selection="3,H,S" to_selection="4,H,E" Would select from the start of Helix 3 to the end of helix 4. selection="-1,H,S" to_selection="4,L,E" Would select from the start of the last helix and go to the end of the fourth loop. (order is not important) selection="n_term" to_selection="3,L,M" Would select from the n_term to the middle of the third loop

Constructor & Destructor Documentation

core::select::residue_selector::SSElementSelector::SSElementSelector ( )
default
core::select::residue_selector::SSElementSelector::SSElementSelector ( SSElementSelector const &  src)
default

Copy constructor.

core::select::residue_selector::SSElementSelector::~SSElementSelector ( )
overridedefault

Destructor.

Member Function Documentation

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

Clone operator.

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

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

ResidueSubset core::select::residue_selector::SSElementSelector::combine_residue_selections ( utility::vector1< Size start_selection_residues,
utility::vector1< Size end_selection_residues,
core::pose::Pose const &  pose 
) const

References core::pose::Pose::size().

Referenced by apply().

utility::vector1< Size > core::select::residue_selector::SSElementSelector::convert_string_to_residues ( utility::vector1< SSElementSelector::SSElement ss_elements,
std::string  description 
) const
std::string core::select::residue_selector::SSElementSelector::get_name ( ) const
overridevirtual
SSElementSelector::SSElement core::select::residue_selector::SSElementSelector::get_SSElement ( utility::vector1< SSElementSelector::SSElement ss_elements,
int  goal_position,
char  type,
std::string  description 
) const
void core::select::residue_selector::SSElementSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
utility::vector1< SSElementSelector::SSElement > core::select::residue_selector::SSElementSelector::parse_ss ( core::pose::Pose const &  pose) const
void core::select::residue_selector::SSElementSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

std::string core::select::residue_selector::SSElementSelector::chain_
private

Referenced by parse_my_tag(), and parse_ss().

std::string core::select::residue_selector::SSElementSelector::end_
private

Referenced by apply(), and parse_my_tag().

core::Size core::select::residue_selector::SSElementSelector::reassign_short_terminal_loop_
private

Referenced by parse_my_tag(), and parse_ss().

std::string core::select::residue_selector::SSElementSelector::start_
private

Referenced by apply(), and parse_my_tag().


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