This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds. More...

#include <OversaturatedHbondAcceptorFilter.hh>

Inheritance diagram for protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter:

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Public Member Functions
	OversaturatedHbondAcceptorFilter ()
	Default constructor. More...

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

	~OversaturatedHbondAcceptorFilter () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

protocols::filters::FilterOP	clone () const override
	Required in the context of the parser/scripting scheme. More...

protocols::filters::FilterOP	fresh_instance () const override
	Required in the context of the parser/scripting scheme. More...

virtual std::string	get_name () const

bool	apply (core::pose::Pose const &pose) const override
	Returns true if the structure passes the filter, false otherwise. More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	Required for reporting score values. More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	Allows printing a summary of this filter to a stream. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose) override
	Parse XML tag (to use this Mover in RosettaScripts). More...

void	set_max_allowed_oversaturated (core::Size const max_allowed)
	Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More...

core::Size	max_allowed_oversaturated () 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_donor_selector (core::select::residue_selector::ResidueSelectorCOP donor_selector_in)
	Set the residue selector for donor residues. More...

core::select::residue_selector::ResidueSelectorCOP	donor_selector () const
	Get the residue selector for donor residues. More...

void	set_acceptor_selector (core::select::residue_selector::ResidueSelectorCOP acceptor_selector_in)
	Set the residue selector for acceptor residues. More...

core::select::residue_selector::ResidueSelectorCOP	acceptor_selector () const
	Get the residue selector for acceptor residues. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction. More...

core::scoring::ScoreFunctionCOP	scorefxn () const
	Get the scorefunction. More...

std::string	name () const override

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string)

	Filter (Filter const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

Static Public Member Functions
static std::string	class_name ()

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

Private Member Functions
core::Size	max_allowed_hbonds (core::pose::Pose const &pose, core::Size const res_index, core::Size const atom_index) const
	Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive. More...

core::Size	compute (core::pose::Pose const &pose) const
	The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions. More...

Private Attributes
core::Size	max_allowed_oversaturated_
	What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor? More...

core::Real	hbond_energy_cutoff_
	The energy cutoff for considering something to be a hydrogen bond. More...

bool	consider_mainchain_only_
	Should we only consider mainchain hydrogen bond donors and acceptors? More...

core::select::residue_selector::ResidueSelectorCOP	donor_selector_
	Optional residue selector for the residues that could possibly be donating hydrogen bonds. More...

core::select::residue_selector::ResidueSelectorCOP	acceptor_selector_
	Optional residue selector for the residues that could possibly be accepting hydrogen bonds. More...

core::scoring::ScoreFunctionOP	scorefxn_
	The scorefunction to use for hydrogen bond scoring. More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds.

Constructor & Destructor Documentation

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter ( )

Default constructor.

Referenced by clone().

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter ( OversaturatedHbondAcceptorFilter const & src )

Copy constructor.

References acceptor_selector_, donor_selector_, and scorefxn_.

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::~OversaturatedHbondAcceptorFilter ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector ( ) const

Get the residue selector for acceptor residues.

References acceptor_selector_.

bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Returns true if the structure passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), and max_allowed_oversaturated().

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::class_name ( )

static

Referenced by get_name(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::keyname(), name(), and provide_xml_schema().

protocols::filters::FilterOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::clone ( ) const

overridevirtual

Required in the context of the parser/scripting scheme.

Make a copy of this object and return an owning pointer to the copy.

Implements protocols::filters::Filter.

References OversaturatedHbondAcceptorFilter().

Referenced by compute().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute ( core::pose::Pose const & pose ) const

private

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.

References acceptor_selector_, core::conformation::Residue::atom_name(), core::scoring::hbonds::calculate_intra_res_hbonds(), clone(), consider_mainchain_only(), consider_mainchain_only_, donor_selector_, core::scoring::get_score_function(), hbond_energy_cutoff(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), max_allowed_hbonds(), 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::size(), and protocols::cyclic_peptide::TR().

Referenced by apply(), report(), and report_sm().

bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector ( ) const

Get the residue selector for donor residues.

References donor_selector_.

protocols::filters::FilterOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::fresh_instance ( ) const

overridevirtual

Required in the context of the parser/scripting scheme.

Implements protocols::filters::Filter.

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::get_name ( ) const

virtual

References class_name().

core::Real const & protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds	(	core::pose::Pose const &	pose,
		core::Size const	res_index,
		core::Size const	atom_index
	)		const

private

Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive.

For now, this function returns 0 if this is not an acceptor, 2 if it is. This is crude, of course. Ultimately, it should figure out how many hbonds an atom can actually receive.

References core::chemical::ResidueType::atom(), core::chemical::Atom::is_acceptor(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by compute().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated ( ) const

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

References max_allowed_oversaturated_.

Referenced by apply(), parse_my_tag(), and report().

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

overridevirtual

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

Reimplemented from protocols::filters::Filter.

References consider_mainchain_only(), hbond_energy_cutoff(), max_allowed_oversaturated(), protocols::rosetta_scripts::parse_residue_selector(), protocols::rosetta_scripts::parse_score_function(), set_acceptor_selector(), set_consider_mainchain_only(), set_donor_selector(), set_hbond_energy_cutoff(), set_max_allowed_oversaturated(), and set_scorefxn().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), protocols::rosetta_scripts::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator::provide_xml_schema().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Allows printing a summary of this filter to a stream.

Reimplemented from protocols::filters::Filter.

References compute(), and max_allowed_oversaturated().

core::Real protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

Required for reporting score values.

Reimplemented from protocols::filters::Filter.

References compute().

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn ( ) const

Get the scorefunction.

References scorefxn_.

Referenced by compute().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_acceptor_selector ( core::select::residue_selector::ResidueSelectorCOP acceptor_selector_in )

Set the residue selector for acceptor residues.

Clones the input.

References acceptor_selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_donor_selector ( core::select::residue_selector::ResidueSelectorCOP donor_selector_in )

Set the residue selector for donor residues.

Clones the input.

References donor_selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_max_allowed_oversaturated ( core::Size const max_allowed )

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

References max_allowed_oversaturated_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction.

Clones the input.

References scorefxn_.

Referenced by parse_my_tag().

Member Data Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector_

private

Optional residue selector for the residues that could possibly be accepting hydrogen bonds.

Referenced by acceptor_selector(), compute(), OversaturatedHbondAcceptorFilter(), and set_acceptor_selector().

bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::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::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector_

private

Optional residue selector for the residues that could possibly be donating hydrogen bonds.

Referenced by compute(), donor_selector(), OversaturatedHbondAcceptorFilter(), and set_donor_selector().

core::Real protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::hbond_energy_cutoff_

private

The energy cutoff for considering something to be a hydrogen bond.

Defaults to -0.1.

Referenced by hbond_energy_cutoff(), and set_hbond_energy_cutoff().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated_

private

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

Defaults to 0.

Referenced by max_allowed_oversaturated(), and set_max_allowed_oversaturated().

core::scoring::ScoreFunctionOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn_

private

The scorefunction to use for hydrogen bond scoring.

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

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

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

src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.hh
src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation