returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class More...

#include <HbondsToResidueFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::HbondsToResidueFilter:

[legend]

Public Types
typedef core::Real	Real

typedef core::Size	Size

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

	HbondsToResidueFilter (core::Size const resnum, core::Size const partners, Real const &energy_cutoff=-0.5, bool const backbone=false, bool const sidechain=true, bool const bb_bb=true, bool const from_other_chains=true, bool const from_same_chain=true)
	Constructor. More...

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

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

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

void	report (std::ostream &out, core::pose::Pose const &pose) const override

core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...

core::Size	compute (core::pose::Pose const &pose, core::Size const resnum_rosetta) const
	Actually compute the number of hydrogen bonds to the target residue. More...

	~HbondsToResidueFilter () override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

void	set_partners (core::Size const val)
	Set the minimum number of H-bond partners that this residue must have for the filter to pass. More...

core::Size	partners () const
	Get the minimum number of H-bond partners that this residue must have for the filter to pass. More...

void	set_energy_cutoff (core::Real const val)
	Set the threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...

core::Real	energy_cutoff () const
	Get the threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...

void	set_backbone (bool const val)
	Set whether to include backbone hydrogen bonds. More...

void	set_sidechain (bool const val)
	Set whether to include backbone hydrogen bonds. More...

void	set_bb_bb (bool const val)
	Set whether to include backbone-backbone hydrogen bonds. More...

bool	backbone () const
	Get whether to include backbone hydrogen bonds. More...

bool	sidechain () const
	Get whether to include backbone hydrogen bonds. More...

bool	bb_bb () const
	Get whether to include backbone-backbone hydrogen bonds. More...

void	set_resnum (std::string const &input)
	Set the residue number (as a string to be parsed at apply time). More...

void	set_resnum (core::Size const val)
	Set the residue number (as an integer – Rosetta numbering). More...

std::string	resnum () const
	Get the residue number (a string to be parsed at apply time). More...

void	set_from_other_chains (bool const val)
	Set whether hydrogen bonds from other chains should be counted. More...

bool	from_other_chains () const
	Get whether hydrogen bonds from other chains should be counted. More...

void	set_from_same_chain (bool const val)
	Set whether hydrogen bonds from the same chain should be counted. More...

bool	from_same_chain () const
	Get whether hydrogen bonds from the same chain should be counted. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction to use for hbond calculation. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the ResidueSelector to use. More...

std::string	name () const override

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

	Filter (std::string 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)

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 ()

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

Private Attributes
std::string	resnum_
	The current residue, stored as a string to be parsed at apply time. More...

core::Size	partners_
	The minimum number of H-bond partners that this residue must have for the filter to pass. More...

Real	energy_cutoff_
	The threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...

bool	backbone_
	Include backbone hydrogen bonds? More...

bool	sidechain_
	Include sidechain hydrogen bonds? More...

bool	bb_bb_
	Include backbone-backbone hydrogen bonds? More...

bool	from_other_chains_
	If true, hydrogen bonds from other chains will be counted. True by default. More...

bool	from_same_chain_
	If true, hydrogen bonds from the same chain will be counted. True by default. More...

core::scoring::ScoreFunctionOP	sfxn_
	Owning pointer to the scorefunction to use. More...

core::select::residue_selector::ResidueSelectorCOP	selector_
	Owning pointer to a ResidueSelector, optionally used to select the residues to count. More...

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

Detailed Description

returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class

Member Typedef Documentation

◆ Real

typedef core::Real protocols::protein_interface_design::filters::HbondsToResidueFilter::Real

◆ Size

typedef core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::Size

Constructor & Destructor Documentation

◆ HbondsToResidueFilter() [1/3]

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter ( )

Default constructor.

◆ HbondsToResidueFilter() [2/3]

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter	(	core::Size const	resnum,
		core::Size const	partners,
		Real const &	energy_cutoff = `-0.5`,
		bool const	backbone = `false`,
		bool const	sidechain = `true`,
		bool const	bb_bb = `true`,
		bool const	from_other_chains = `true`,
		bool const	from_same_chain = `true`
	)

Constructor.

References energy_cutoff_, resnum(), and resnum_.

◆ HbondsToResidueFilter() [3/3]

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter ( HbondsToResidueFilter const & src )

Copy constructor.

References sfxn_.

◆ ~HbondsToResidueFilter()

protocols::protein_interface_design::filters::HbondsToResidueFilter::~HbondsToResidueFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), core::pose::parse_resnum(), partners_, resnum_, and protocols::protein_interface_design::filters::TR().

◆ backbone()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::backbone ( ) const

inline

Get whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References backbone_.

◆ bb_bb()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::bb_bb ( ) const

inline

Get whether to include backbone-backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References bb_bb_.

◆ class_name()

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::class_name ( )

static

Referenced by protocols::protein_interface_design::filters::HbondsToResidueFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::protein_interface_design::filters::HbondsToResidueFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::compute	(	core::pose::Pose const &	pose,
		core::Size const	resnum_rosetta
	)		const

Actually compute the number of hydrogen bonds to the target residue.

References backbone_, bb_bb_, core::pose::Pose::chain(), energy_cutoff_, from_other_chains(), from_same_chain(), core::scoring::get_score_function(), protocols::protein_interface_design::hbonded(), selector_, sfxn_, sidechain_, core::pose::Pose::size(), and protocols::protein_interface_design::filters::TR().

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

◆ energy_cutoff()

core::Real protocols::protein_interface_design::filters::HbondsToResidueFilter::energy_cutoff ( ) const

inline

Get the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

References energy_cutoff_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::protein_interface_design::filters::HbondsToResidueFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ from_other_chains()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_other_chains ( ) const

inline

Get whether hydrogen bonds from other chains should be counted.

References from_other_chains_.

Referenced by compute(), and parse_my_tag().

◆ from_same_chain()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_same_chain ( ) const

inline

Get whether hydrogen bonds from the same chain should be counted.

References from_same_chain_.

Referenced by compute(), and parse_my_tag().

◆ name()

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag	(	utility::tag::TagCOP	,
		basic::datacache::DataMap &
	)

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References from_other_chains(), from_same_chain(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), partners(), resnum(), set_backbone(), set_bb_bb(), set_energy_cutoff(), set_from_other_chains(), set_from_same_chain(), set_partners(), set_resnum(), set_scorefxn(), set_selector(), set_sidechain(), and protocols::protein_interface_design::filters::TR().

◆ partners()

core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::partners ( ) const

inline

Get the minimum number of H-bond partners that this residue must have for the filter to pass.

References partners_.

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::protein_interface_design::filters::HbondsToResidueFilterCreator::provide_xml_schema().

◆ report()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::membrane::out, core::pose::parse_resnum(), and resnum().

◆ report_sm()

core::Real protocols::protein_interface_design::filters::HbondsToResidueFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), core::pose::parse_resnum(), and resnum().

◆ resnum()

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::resnum ( ) const

inline

Get the residue number (a string to be parsed at apply time).

References resnum_.

Referenced by HbondsToResidueFilter(), parse_my_tag(), report(), and report_sm().

◆ set_backbone()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_backbone ( bool const val )

inline

Set whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References backbone_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_bb_bb()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_bb_bb ( bool const val )

inline

Set whether to include backbone-backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References bb_bb_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_energy_cutoff()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_energy_cutoff ( core::Real const val )

inline

Set the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

References energy_cutoff_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_from_other_chains()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_other_chains ( bool const val )

inline

Set whether hydrogen bonds from other chains should be counted.

References from_other_chains_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_from_same_chain()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_same_chain ( bool const val )

inline

Set whether hydrogen bonds from the same chain should be counted.

References from_same_chain_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_partners()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_partners ( core::Size const val )

inline

Set the minimum number of H-bond partners that this residue must have for the filter to pass.

References partners_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_resnum() [1/2]

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum ( core::Size const val )

Set the residue number (as an integer – Rosetta numbering).

References set_resnum(), and protocols::hybridization::val.

◆ set_resnum() [2/2]

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum ( std::string const & input )

inline

Set the residue number (as a string to be parsed at apply time).

References resnum_.

Referenced by parse_my_tag(), and set_resnum().

◆ set_scorefxn()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction to use for hbond calculation.

References sfxn_.

Referenced by parse_my_tag().

◆ set_selector()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set the ResidueSelector to use.

Only hydrogen bonds between this residue and the residues selected by the ResidueSelector will be counted, if a ResidueSelector is provided.

References selector_.

Referenced by parse_my_tag().

◆ set_sidechain()

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_sidechain ( bool const val )

inline

Set whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References sidechain_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ sidechain()

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::sidechain ( ) const

inline

Get whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References sidechain_.

Member Data Documentation

◆ backbone_

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::backbone_

private

Include backbone hydrogen bonds?

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

Referenced by backbone(), compute(), and set_backbone().

◆ bb_bb_

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::bb_bb_

private

Include backbone-backbone hydrogen bonds?

I'm pretty sure that this is not implemented properly. (VKM – 6 July 2015).

Referenced by bb_bb(), compute(), and set_bb_bb().

◆ energy_cutoff_

Real protocols::protein_interface_design::filters::HbondsToResidueFilter::energy_cutoff_

private

The threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

Referenced by compute(), energy_cutoff(), HbondsToResidueFilter(), and set_energy_cutoff().

◆ from_other_chains_

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_other_chains_

private

If true, hydrogen bonds from other chains will be counted. True by default.

Referenced by from_other_chains(), and set_from_other_chains().

◆ from_same_chain_

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_same_chain_

private

If true, hydrogen bonds from the same chain will be counted. True by default.

Referenced by from_same_chain(), and set_from_same_chain().

◆ partners_

core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::partners_

private

The minimum number of H-bond partners that this residue must have for the filter to pass.

Referenced by apply(), partners(), and set_partners().

◆ resnum_

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::resnum_

private

The current residue, stored as a string to be parsed at apply time.

This could be a PDB number (e.g. 32A), a Rosetta number (e.g. 32), or a reference pose number (e.g. refpose(snapshot1,34).

Referenced by apply(), HbondsToResidueFilter(), resnum(), and set_resnum().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::protein_interface_design::filters::HbondsToResidueFilter::selector_

private

Owning pointer to a ResidueSelector, optionally used to select the residues to count.

Only hydrogen bonds between this residue and the residues selected by the ResidueSelector will be counted, if a ResidueSelector is provided.

Referenced by compute(), and set_selector().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::HbondsToResidueFilter::sfxn_

private

Owning pointer to the scorefunction to use.

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

◆ sidechain_

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::sidechain_

private

Include sidechain hydrogen bonds?

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

Referenced by compute(), set_sidechain(), and sidechain().

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

src/protocols/protein_interface_design/filters/HbondsToResidueFilter.hh
src/protocols/protein_interface_design/filters/HbondsToResidueFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Real

◆ Size

Constructor & Destructor Documentation

◆ HbondsToResidueFilter() [1/3]

◆ HbondsToResidueFilter() [2/3]

◆ HbondsToResidueFilter() [3/3]

◆ ~HbondsToResidueFilter()

Member Function Documentation

◆ apply()

◆ backbone()

◆ bb_bb()

◆ class_name()

◆ clone()

◆ compute()

◆ energy_cutoff()

◆ fresh_instance()

◆ from_other_chains()

◆ from_same_chain()

◆ name()

◆ parse_my_tag()

◆ partners()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ resnum()

◆ set_backbone()

◆ set_bb_bb()

◆ set_energy_cutoff()

◆ set_from_other_chains()

◆ set_from_same_chain()

◆ set_partners()

◆ set_resnum() [1/2]

◆ set_resnum() [2/2]

◆ set_scorefxn()

◆ set_selector()

◆ set_sidechain()

◆ sidechain()

Member Data Documentation

◆ backbone_

◆ bb_bb_

◆ energy_cutoff_

◆ from_other_chains_

◆ from_same_chain_

◆ partners_

◆ resnum_

◆ selector_

◆ sfxn_

◆ sidechain_