A SimpleMetric that calculates the total number of atom-atom clashes from a residue in a residue selector to all other residues defined in a second residue selector using the LJ radius of each atom. More...

#include <PerResidueClashMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueClashMetric:

[legend]

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

	PerResidueClashMetric (select::residue_selector::ResidueSelectorCOP inner_selector, select::residue_selector::ResidueSelectorCOP outer_selector)
	Constructor with other residue selector set. The other selector is what we use to calculate clashes TO Default is to calculate clashes of each residue to ALL OTHER residues (including those in the primary selector) More...

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

	~PerResidueClashMetric () 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_secondary_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set the Residue Selector to use for TO other residues. More...

void	set_use_hydrogens (bool use_hydrogens)
	Should we calculate only heavy-heavy atom clashes Default True. More...

void	set_use_soft_clash (bool soft_clash_check)
	When we calculate atom-atom distances using LJ distances, Default True. More...

void	set_soft_dampening (core::Real dampening)
	Set the dampening of the LJ to use for soft-clash. Default=.33. More...

bool	is_clashing (core::pose::Pose const &pose, core::Size resA, core::Size atomA, core::Size resB, core::Size atomB) const
	Are these atoms clashing using soft or hard definition? More...

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

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

PerResidueRealMetric &	operator= (PerResidueRealMetric const &)

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

virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const=0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as `label` Must be implemented by derived classes. More...

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

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

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

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 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	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 Member Functions
core::Real	lj_radius_to_zero_e_radius (core::Real num) const
	Return the radius at which the energy is 0 (IE where energy goes from attraction to repulsion). More...

Private Attributes
bool	use_soft_clash_ = true

bool	use_hydrogens_ = false

core::Real	soft_clash_dampening_ = .33

core::select::residue_selector::ResidueSelectorCOP	selector2_ = nullptr

core::Real	lj_n_ = pow( 2, 1.0/6 )

Detailed Description

A SimpleMetric that calculates the total number of atom-atom clashes from a residue in a residue selector to all other residues defined in a second residue selector using the LJ radius of each atom.

Can use a soft radius, which reduces it by 33%.

Does NOT calculate INTRA-RESIDUE clashes! Default is to calculate clashes of each residue to ALL OTHER residues (including those in the primary selector) Set a secondary selector if you want other behavior

We use a SCORED pose to only calculate energies if fa_rep between a pair of residues under consideration is NOT 0 This is in order to speed up the calculation.

INTRA-residue clashes can be done through the PUBLIC is_clashing method to calculate atomic-clashes.

Constructor & Destructor Documentation

◆ PerResidueClashMetric() [1/3]

core::simple_metrics::per_residue_metrics::PerResidueClashMetric::PerResidueClashMetric ( )

Constructors ///.

Default constructor

Referenced by clone().

◆ PerResidueClashMetric() [2/3]

core::simple_metrics::per_residue_metrics::PerResidueClashMetric::PerResidueClashMetric	(	select::residue_selector::ResidueSelectorCOP	inner_selector,
		select::residue_selector::ResidueSelectorCOP	outer_selector
	)

Constructor with other residue selector set. The other selector is what we use to calculate clashes TO Default is to calculate clashes of each residue to ALL OTHER residues (including those in the primary selector)

References core::simple_metrics::PerResidueRealMetric::set_residue_selector(), and set_secondary_residue_selector().

◆ PerResidueClashMetric() [3/3]

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

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PerResidueClashMetric()

core::simple_metrics::per_residue_metrics::PerResidueClashMetric::~PerResidueClashMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueClashMetric::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 core::select::residue_selector::TrueResidueSelector::apply(), core::simple_metrics::PerResidueRealMetric::apply(), core::conformation::Residue::atom_type(), core::pose::Pose::conformation(), core::chemical::AtomType::element(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::Energies::energy_graph(), core::scoring::fa_rep, core::scoring::EnergyEdge::fill_energy_map(), core::scoring::EnergyGraph::find_energy_edge(), core::select::get_residues_from_subset(), core::simple_metrics::PerResidueRealMetric::get_selector(), core::conformation::Conformation::is_bonded(), is_clashing(), core::chemical::AtomType::is_virtual(), core::chemical::ResidueType::is_virtual_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), selector2_, soft_clash_dampening_, TR(), use_hydrogens_, and core::scoring::Energies::weights().

◆ clone()

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

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

References PerResidueClashMetric().

◆ is_clashing()

bool core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing	(	core::pose::Pose const &	pose,
		core::Size	resA,
		core::Size	atomA,
		core::Size	resB,
		core::Size	atomB
	)		const

Are these atoms clashing using soft or hard definition?

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_radius(), lj_radius_to_zero_e_radius(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), soft_clash_dampening_, TR(), use_soft_clash_, and core::conformation::Residue::xyz().

Referenced by calculate().

◆ lj_radius_to_zero_e_radius()

core::Real core::simple_metrics::per_residue_metrics::PerResidueClashMetric::lj_radius_to_zero_e_radius ( core::Real num ) const

private

Return the radius at which the energy is 0 (IE where energy goes from attraction to repulsion).

References lj_n_.

Referenced by is_clashing().

◆ metric()

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

◆ name()

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

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

◆ name_static()

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

static

Name of the class for creator.

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

◆ parse_my_tag()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::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 core::simple_metrics::SimpleMetric::parse_base_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), core::select::residue_selector::parse_residue_selector(), set_secondary_residue_selector(), set_soft_dampening(), set_use_hydrogens(), set_use_soft_clash(), soft_clash_dampening_, use_hydrogens_, and use_soft_clash_.

◆ provide_xml_schema()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::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::PerResidueClashMetricCreator::provide_xml_schema().

◆ set_secondary_residue_selector()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_secondary_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Set the Residue Selector to use for TO other residues.

References selector2_.

Referenced by parse_my_tag(), and PerResidueClashMetric().

◆ set_soft_dampening()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_soft_dampening ( core::Real dampening )

Set the dampening of the LJ to use for soft-clash. Default=.33.

References soft_clash_dampening_.

Referenced by parse_my_tag().

◆ set_use_hydrogens()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_use_hydrogens ( bool use_hydrogens )

Should we calculate only heavy-heavy atom clashes Default True.

References use_hydrogens_.

Referenced by parse_my_tag().

◆ set_use_soft_clash()

void core::simple_metrics::per_residue_metrics::PerResidueClashMetric::set_use_soft_clash ( bool soft_clash_check )

When we calculate atom-atom distances using LJ distances, Default True.

When we calculate atom-atom distances using LJ distances,.

clash if distance < (atomI_LJ + atomJ_LJ)*(1 - soft_clash)

References use_soft_clash_.

Referenced by parse_my_tag().

Member Data Documentation

◆ lj_n_

core::Real core::simple_metrics::per_residue_metrics::PerResidueClashMetric::lj_n_ = pow( 2, 1.0/6 )

private

Referenced by lj_radius_to_zero_e_radius().

◆ selector2_

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::per_residue_metrics::PerResidueClashMetric::selector2_ = nullptr

private

Referenced by calculate(), and set_secondary_residue_selector().

◆ soft_clash_dampening_

core::Real core::simple_metrics::per_residue_metrics::PerResidueClashMetric::soft_clash_dampening_ = .33

private

Referenced by calculate(), is_clashing(), parse_my_tag(), and set_soft_dampening().

◆ use_hydrogens_

bool core::simple_metrics::per_residue_metrics::PerResidueClashMetric::use_hydrogens_ = false

private

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

◆ use_soft_clash_

bool core::simple_metrics::per_residue_metrics::PerResidueClashMetric::use_soft_clash_ = true

private

Referenced by is_clashing(), parse_my_tag(), and set_use_soft_clash().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PerResidueClashMetric() [1/3]

◆ PerResidueClashMetric() [2/3]

◆ PerResidueClashMetric() [3/3]

◆ ~PerResidueClashMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ is_clashing()

◆ lj_radius_to_zero_e_radius()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_secondary_residue_selector()

◆ set_soft_dampening()

◆ set_use_hydrogens()

◆ set_use_soft_clash()

Member Data Documentation

◆ lj_n_

◆ selector2_

◆ soft_clash_dampening_

◆ use_hydrogens_

◆ use_soft_clash_