protocols::enzdes::LigInterfaceEnergyFilter Class Reference

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::LigInterfaceEnergyFilter:

Public Types
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP

Public Member Functions
	LigInterfaceEnergyFilter ()
	LigInterfaceEnergyFilter (core::scoring::ScoreFunctionOP scorefxn, core::Real const threshold, bool const include_cstE=false, core::Size const rb_jump=1, core::Real const interface_distance_cutoff=8.0)
	LigInterfaceEnergyFilter (LigInterfaceEnergyFilter const &init)
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
FilterOP	clone () const override
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::Real	compute (core::pose::Pose const &pose) const
core::Real	constraint_energy (core::pose::Pose const &pose, int which_res) const
	~LigInterfaceEnergyFilter () 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...
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
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	threshold_
bool	include_cstE_
core::Size	rb_jump_
core::Real	interface_distance_cutoff_

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

Member Typedef Documentation

Filter

typedef protocols::filters::Filter protocols::enzdes::LigInterfaceEnergyFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::enzdes::LigInterfaceEnergyFilter::FilterOP

Constructor & Destructor Documentation

LigInterfaceEnergyFilter() [1/3]

protocols::enzdes::LigInterfaceEnergyFilter::LigInterfaceEnergyFilter ( )

inline

LigInterfaceEnergyFilter() [2/3]

protocols::enzdes::LigInterfaceEnergyFilter::LigInterfaceEnergyFilter	(	core::scoring::ScoreFunctionOP	scorefxn,
		core::Real const	threshold,
		bool const	include_cstE = false,
		core::Size const	rb_jump = 1,
		core::Real const	interface_distance_cutoff = 8.0
	)

References protocols::enzdes::enzutil::enable_constraint_scoreterms(), and scorefxn_.

LigInterfaceEnergyFilter() [3/3]

protocols::enzdes::LigInterfaceEnergyFilter::LigInterfaceEnergyFilter

(

LigInterfaceEnergyFilter const &

init

)

References core::init::init(), and scorefxn_.

~LigInterfaceEnergyFilter()

protocols::enzdes::LigInterfaceEnergyFilter::~LigInterfaceEnergyFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::enzdes::LigInterfaceEnergyFilter::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::Pose::conformation(), core::conformation::Conformation::num_chains(), threshold_, and protocols::enzdes::TR().

class_name()

std::string protocols::enzdes::LigInterfaceEnergyFilter::class_name ( )

static

Referenced by protocols::enzdes::LigInterfaceEnergyFilterCreator::keyname().

clone()

FilterOP protocols::enzdes::LigInterfaceEnergyFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::enzdes::LigInterfaceEnergyFilter::compute

(

core::pose::Pose const &

pose

)

const

References constraint_energy(), protocols::enzdes::enzutil::enable_constraint_scoreterms(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), include_cstE_, core::pose::Pose::metric(), scorefxn_, protocols::enzdes::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), and report_sm().

constraint_energy()

core::Real protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy	(	core::pose::Pose const &	pose,
		int	which_res
	)		const

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().

Referenced by compute(), protocols::enzdes::EnzScoreFilter::compute(), and report().

fresh_instance()

FilterOP protocols::enzdes::LigInterfaceEnergyFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::enzdes::LigInterfaceEnergyFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::enzdes::DiffAtomSasaFilter::class_name().

parse_my_tag()

void protocols::enzdes::LigInterfaceEnergyFilter::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 include_cstE_, interface_distance_cutoff_, core::scoring::parse_score_function(), rb_jump_, scorefxn_, and threshold_.

provide_xml_schema()

void protocols::enzdes::LigInterfaceEnergyFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::scoring::attributes_for_parse_score_function(), protocols::enzdes::DiffAtomSasaFilter::class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::enzdes::LigInterfaceEnergyFilterCreator::provide_xml_schema().

report()

void protocols::enzdes::LigInterfaceEnergyFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::comparative_modeling::features::A, protocols::scoring::Interface::calculate(), constraint_energy(), protocols::scoring::Interface::distance(), core::pose::Pose::energies(), core::chemical::element::F, core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::pose::Pose::fold_tree(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::chemical::element::I, include_cstE_, interface_distance_cutoff_, protocols::scoring::Interface::is_interface(), core::conformation::Residue::name3(), core::pose::Pose::num_jump(), core::conformation::membrane::out, core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::pdb_info(), rb_jump_, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::pose::Pose::size(), protocols::analysis::total, core::scoring::total_score, and core::pose::Pose::update_residue_neighbors().

report_sm()

core::Real protocols::enzdes::LigInterfaceEnergyFilter::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(), and protocols::buns::energy.

Member Data Documentation

include_cstE_

bool protocols::enzdes::LigInterfaceEnergyFilter::include_cstE_

private

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

interface_distance_cutoff_

core::Real protocols::enzdes::LigInterfaceEnergyFilter::interface_distance_cutoff_

private

Referenced by parse_my_tag(), and report().

rb_jump_

core::Size protocols::enzdes::LigInterfaceEnergyFilter::rb_jump_

private

Referenced by parse_my_tag(), and report().

scorefxn_

core::scoring::ScoreFunctionOP protocols::enzdes::LigInterfaceEnergyFilter::scorefxn_

private

Referenced by compute(), LigInterfaceEnergyFilter(), and parse_my_tag().

threshold_

core::Real protocols::enzdes::LigInterfaceEnergyFilter::threshold_

private

Referenced by apply(), and parse_my_tag().

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

• src/protocols/enzdes/EnzFilters.hh
• src/protocols/enzdes/EnzFilters.cc