A metric to measure hydrogen bonds between a set of residues that are water-mediated. More...

#include <WaterMediatedHbondMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric:

Public Member Functions
	WaterMediatedHbondMetric ()
	Constructors ///. More...

	WaterMediatedHbondMetric (WaterMediatedHbondMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

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

std::map< core::Size, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_include_virt_waters (bool include_virt_waters)
	After packing, some waters become HOH_v if they don't match certain ref energy. The option -include_vrt false will have them all be HOH during packing. Set this option to true to incude them in our calculation if they are still virts. More...

void	set_residue_selector2 (core::select::residue_selector::ResidueSelectorCOP selector)
	Optionally set a second residue selector to get bridged hbonds between both selections. More...

void	set_depth (core::Size const depth)
	Set the depth we will go to find hbonds. Default is 1. IE resi - water -resj. More...

void	set_include_only_set_depth (bool include_only_depth)
	Set to include only the depth that is set instead of Up to the max depth. IE - if depth is set to 2, we only include hbond paths mediated by two waters. Default false. More...

void	set_include_self (bool include_self)
	Set to include hbonds as so: resi - water - resi Default false. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name of the metric. More...

void	find_hb_paths (core::scoring::hbonds::HBondSet const &local_hb_set, utility::vector1< core::Size > const &local_waters, std::map< std::string, core::Size > &paths, core::Size const current_res, core::Size const max_depth=1, std::string const &current_path="", core::Size const current_depth=0, core::scoring::hbonds::HBondCOP prev_hb=nullptr) const
	Recursive function to find all unique HBond paths involving water and ending with a residue that is not in our water list. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	called by parse_my_tag – should not be used directly More...

core::simple_metrics::SimpleMetricOP	clone () const override

Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
	PerResidueRealMetric ()

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

void	apply (pose::Pose &pose, std::string prefix="", std::string suffix="", bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix. More...

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for which we will calculate values over. More...

void	set_output_as_pdb_nums (bool output_as_pdb_nums)
	Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...

std::map< core::Size, core::Real >	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_cache=true) const
	Grab the data from the pose if it exists or calculate the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. More...

select::residue_selector::ResidueSelectorCOP	get_selector () const
	Get the set residue selector of this class. More...

virtual void	parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

Public Member Functions inherited from core::simple_metrics::SimpleMetric
	SimpleMetric (std::string const &simple_metric_type)

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

void	set_custom_type (std::string const &custom_type)

std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...

virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

std::string	simple_metric_type () const

std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...

virtual bool	simple_metric_provides_citation_info () const
	Does this simple metric 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	simple_metric_is_unpublished () const
	Does this simple metric 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	name_static ()
	Name of the class for creator. More...

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

Static Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
static void	add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
	Add options to the schema from this base class. More...

Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
bool	include_virt_waters_ = false

bool	include_self_ = false

bool	include_only_set_depth_ = false

core::Size	depth_ = 1

core::select::residue_selector::ResidueSelectorCOP	selector_two_ = nullptr

Detailed Description

A metric to measure hydrogen bonds between a set of residues that are water-mediated.

DEPTH: We only traverse a depth of 1 by default. Make sure to set the -ignore_waters flag to false in order to have Rosetta include the HOH residues.

SELECTION: If one residue selector is given, will calculate bridged waters between residues of the selection and all [OTHER] residues, otherwise it will calculate bridges between one selection and another.

If NO SELECTION is give, will report ALL bridged hbonds in a pose [by default without self-water-self hbonds].

HBOND: Since these are bridged hbonds, and h-bond networks can be rather complex, the numbers reported here are the unique h-bond paths from sele1 to sele2. If you give only a single residue selector, these are bridged hbonds from sele1 to OTHER residues in sele1. By default we do not include mediated hbonds back on itself, but this is an option.

TIPS: It is generally recommended to repack the waters using the OptH TaskOperation before input into this metric, especially if only Oxygens were present. Using the option -include_vrt false will keep all waters present in the resulting structure. Use the option -corrections::water::wat_rot_sampling 10 to decrease the angle of sampling from a default of 30 to 10. This will result in many more rotamers, but will improve networks.

Hydration shells can be calculated by passing selection1 as all waters in the pose, selection2 as the protein or chain, and then reporting only a single depth (with max_depth at 0 and 1 for the first and second shell waters."

It is also recommended to use the Beta scorefunction as this can improve hydrogen bond detection.

Constructor & Destructor Documentation

core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::WaterMediatedHbondMetric ( )

Constructors ///.

Default constructor

core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::WaterMediatedHbondMetric ( WaterMediatedHbondMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::~WaterMediatedHbondMetric ( )

override

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

Member Function Documentation

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Defined in RealMetric:

Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix.

Score is added through setExtraScorePose and is output into the score tables/file at pose output. Defined in PerResidueRealMetric Calculate the metric. This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

Implements core::simple_metrics::PerResidueRealMetric.

References depth_, find_hb_paths(), core::select::get_residues_from_subset(), core::simple_metrics::PerResidueRealMetric::get_selector(), include_only_set_depth_, include_self_, include_virt_waters_, core::chemical::ResidueType::is_water(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), selector_two_, core::pose::Pose::size(), and TR().

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::find_hb_paths	(	core::scoring::hbonds::HBondSet const &	local_hb_set,
		utility::vector1< core::Size > const &	local_waters,
		std::map< std::string, core::Size > &	paths,
		core::Size const	current_res,
		core::Size const	max_depth = `1`,
		std::string const &	current_path = `""`,
		core::Size const	current_depth = `0`,
		core::scoring::hbonds::HBondCOP	prev_hb = `nullptr`
	)		const

Recursive function to find all unique HBond paths involving water and ending with a residue that is not in our water list.

Populates paths as the reference. Path is a splittalbe string of the connections. ex: 191-221-333 where residue 221 is a water in our list.

References core::scoring::hbonds::find_hb_paths().

Referenced by calculate().

std::string core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

std::string core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

std::string core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::PerResidueRealMetric.

References depth_, include_only_set_depth_, include_self_, include_virt_waters_, core::simple_metrics::SimpleMetric::parse_base_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), core::select::residue_selector::parse_residue_selector(), set_depth(), set_include_only_set_depth(), set_include_self(), set_include_virt_waters(), and set_residue_selector2().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), name_static(), and core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetricCreator::provide_xml_schema().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_depth ( core::Size const depth )

Set the depth we will go to find hbonds. Default is 1. IE resi - water -resj.

References depth_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_only_set_depth ( bool include_only_depth )

Set to include only the depth that is set instead of Up to the max depth. IE - if depth is set to 2, we only include hbond paths mediated by two waters. Default false.

References include_only_set_depth_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_self ( bool include_self )

Set to include hbonds as so: resi - water - resi Default false.

Will only find these if selector1 and selector2 contain the same residue.

References include_self_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_include_virt_waters ( bool include_virt_waters )

After packing, some waters become HOH_v if they don't match certain ref energy. The option -include_vrt false will have them all be HOH during packing. Set this option to true to incude them in our calculation if they are still virts.

References include_virt_waters_.

Referenced by parse_my_tag().

void core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::set_residue_selector2 ( core::select::residue_selector::ResidueSelectorCOP selector )

Optionally set a second residue selector to get bridged hbonds between both selections.

References selector_two_.

Referenced by parse_my_tag().

Member Data Documentation

core::Size core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::depth_ = 1

private

Referenced by calculate(), parse_my_tag(), and set_depth().

bool core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::include_only_set_depth_ = false

private

Referenced by calculate(), parse_my_tag(), and set_include_only_set_depth().

bool core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::include_self_ = false

private

Referenced by calculate(), parse_my_tag(), and set_include_self().

bool core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::include_virt_waters_ = false

private

Referenced by calculate(), parse_my_tag(), and set_include_virt_waters().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::selector_two_ = nullptr

private

Referenced by calculate(), and set_residue_selector2().

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

src/core/simple_metrics/per_residue_metrics/WaterMediatedHbondMetric.hh
src/core/simple_metrics/per_residue_metrics/WaterMediatedHbondMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation