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protocols::hbnet::UnsatSelector Class Reference

A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences). More...

#include <UnsatSelector.hh>

Inheritance diagram for protocols::hbnet::UnsatSelector:
Inheritance graph
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Public Member Functions

 UnsatSelector ()
 Constructor. More...
 
 ~UnsatSelector () override
 Destructor. More...
 
core::select::residue_selector::ResidueSelectorOP clone () const override
 Clone function. More...
 
core::select::residue_selector::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_mode (bool const input_setting)
 Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More...
 
bool mode () const
 Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More...
 
void set_hbond_energy_cutoff (core::Real const &input_value)
 Set the threshold for considering something to be a hydrogen bond. More...
 
core::Real const & hbond_energy_cutoff () const
 Get the threshold for considering something to be a hydrogen bond. More...
 
void set_consider_mainchain_only (bool const input_setting)
 Set whether we only consider mainchain hydrogen bond donors and acceptors. More...
 
bool consider_mainchain_only () const
 Get whether we only consider mainchain hydrogen bond donors and acceptors. More...
 
void set_legacy (bool const input_setting)
 Set whether legacy option should be used. More...
 
bool legacy () const
 Get the legacy preference. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction. More...
 
core::scoring::ScoreFunctionCOP scorefxn () const
 Get the scorefunction. 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, allowing automatic evaluation of bad XML. More...
 

Private Member Functions

utility::vector1
< utility::vector1< core::Size > > 
compute (core::pose::Pose const &pose) const
 This function checks if a hbond is in a vector—written by Scott Boyken. More...
 

Private Attributes

core::Real hbond_energy_cutoff_
 What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor? More...
 
bool consider_mainchain_only_
 Should we only consider mainchain hydrogen bond donors and acceptors? More...
 
bool acceptors_
 
core::scoring::ScoreFunctionOP scorefxn_
 The scorefunction to use for hydrogen bond scoring. More...
 
bool legacy_
 should I use legacy option or hbnet style hbond detection More...
 

Detailed Description

A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences).

Constructor & Destructor Documentation

protocols::hbnet::UnsatSelector::UnsatSelector ( )

Constructor.

protocols::hbnet::UnsatSelector::~UnsatSelector ( )
overridedefault

Destructor.

Member Function Documentation

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

Clone function.

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

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

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

Referenced by compute().

utility::vector1< utility::vector1< core::Size > > protocols::hbnet::UnsatSelector::compute ( core::pose::Pose const &  pose) const
private

This function checks if a hbond is in a vector—written by Scott Boyken.

The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions.

The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions.

Returns the number of atoms receiving more than the allowed number of hydrogen bonds.

Returns the number of atoms receiving more than the allowed number of hydrogen bonds.

References acceptors_, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_type(), core::scoring::hbonds::calculate_intra_res_hbonds(), clone(), consider_mainchain_only(), consider_mainchain_only_, core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::get_score_function(), core::scoring::hbonds::hb_energy(), hbond_energy_cutoff(), protocols::hbnet::hbond_exists_in_vector(), core::scoring::hbonds::HBondSet::hbond_options(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_polar_hydrogen(), legacy_, core::conformation::Residue::natoms(), core::conformation::Residue::nbrs(), core::pose::Pose::residue(), scorefxn(), scorefxn_, core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::pose::Pose::total_residue(), and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

Referenced by apply().

bool protocols::hbnet::UnsatSelector::consider_mainchain_only ( ) const

Get whether we only consider mainchain hydrogen bond donors and acceptors.

References consider_mainchain_only_.

Referenced by compute(), and parse_my_tag().

std::string protocols::hbnet::UnsatSelector::get_name ( ) const
overridevirtual

Get the mover class name.

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

References class_name().

core::Real const & protocols::hbnet::UnsatSelector::hbond_energy_cutoff ( ) const

Get the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by compute(), and parse_my_tag().

bool protocols::hbnet::UnsatSelector::legacy ( ) const

Get the legacy preference.

Get the legacy mode default=false.

References legacy_.

Referenced by parse_my_tag().

bool protocols::hbnet::UnsatSelector::mode ( ) const

Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.

Get whether we are checking acceptors or selectors.

References acceptors_.

Referenced by parse_my_tag().

void protocols::hbnet::UnsatSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual

XML parse.

Parse XML tag (to use this Mover in RosettaScripts).

Parse RosettaScripts tags and set up this mover.

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

References consider_mainchain_only(), hbond_energy_cutoff(), legacy(), mode(), core::scoring::parse_score_function(), set_consider_mainchain_only(), set_hbond_energy_cutoff(), set_legacy(), set_mode(), and set_scorefxn().

void protocols::hbnet::UnsatSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::scoring::ScoreFunctionCOP protocols::hbnet::UnsatSelector::scorefxn ( ) const

Get the scorefunction.

References scorefxn_.

Referenced by compute().

void protocols::hbnet::UnsatSelector::set_consider_mainchain_only ( bool const  input_setting)

Set whether we only consider mainchain hydrogen bond donors and acceptors.

References consider_mainchain_only_.

Referenced by parse_my_tag().

void protocols::hbnet::UnsatSelector::set_hbond_energy_cutoff ( core::Real const &  input_value)

Set the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by parse_my_tag().

void protocols::hbnet::UnsatSelector::set_legacy ( bool const  input_setting)

Set whether legacy option should be used.

Set whether we are checking acceptors or selectors.

References legacy_.

Referenced by parse_my_tag().

void protocols::hbnet::UnsatSelector::set_mode ( bool const  input_setting)

Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.

Set whether we are checking acceptors or selectors.

References acceptors_.

Referenced by parse_my_tag().

void protocols::hbnet::UnsatSelector::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction.

Clones the input.

References scorefxn_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::hbnet::UnsatSelector::acceptors_
private

Referenced by apply(), compute(), mode(), and set_mode().

bool protocols::hbnet::UnsatSelector::consider_mainchain_only_
private

Should we only consider mainchain hydrogen bond donors and acceptors?

Defaults to true.

Referenced by compute(), consider_mainchain_only(), and set_consider_mainchain_only().

core::Real protocols::hbnet::UnsatSelector::hbond_energy_cutoff_
private

What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor?

Defaults to 0. The energy cutoff for considering something to be a hydrogen

Defaults to -0.1.

Referenced by hbond_energy_cutoff(), and set_hbond_energy_cutoff().

bool protocols::hbnet::UnsatSelector::legacy_
private

should I use legacy option or hbnet style hbond detection

if nothing selected, default is false

Referenced by compute(), legacy(), and set_legacy().

core::scoring::ScoreFunctionOP protocols::hbnet::UnsatSelector::scorefxn_
private

The scorefunction to use for hydrogen bond scoring.

If no scorefunction is provided, then the default scorefunction is used.

Referenced by compute(), scorefxn(), and set_scorefxn().


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