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:

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 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, 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

"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 acceptors_, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_polar_hydrogen(), core::conformation::Residue::atom_type(), compute(), core::chemical::AtomType::is_acceptor(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

std::string protocols::hbnet::UnsatSelector::class_name ( )

static

Get the mover class name.

Referenced by get_name(), protocols::hbnet::UnsatSelectorCreator::keyname(), and provide_xml_schema().

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_, protocols::buns::energy, 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

Provide XSD information, allowing automatic evaluation of bad XML.

References core::scoring::attributes_for_parse_score_function(), class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by protocols::hbnet::UnsatSelectorCreator::provide_xml_schema().

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().

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

• src/protocols/hbnet/UnsatSelector.hh
• src/protocols/hbnet/UnsatSelector.cc