protocols::matdes::ClashCheckFilter Class Reference

#include <ClashCheckFilter.hh>

Inheritance diagram for protocols::matdes::ClashCheckFilter:

Public Types
typedef protocols::filters::Filter	Super
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP
typedef core::Real	Real
typedef core::pose::Pose	Pose
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap

Public Member Functions
	ClashCheckFilter ()
	ClashCheckFilter (core::pack::task::TaskFactoryOP task_factory, core::Real const c, std::string const &s, core::Size const n, core::Size const t, bool const v, bool const w)
	ClashCheckFilter (ClashCheckFilter const &rval)
	~ClashCheckFilter () override
protocols::filters::FilterOP	clone () const override
protocols::filters::FilterOP	fresh_instance () const override
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
void	clash_dist (core::Real const c)
void	sym_dof_names (std::string const &s)
void	nsub_bblock (core::Size const n)
void	threshold (core::Size const t)
void	verbose (bool const v)
void	write (bool const w)
core::pack::task::TaskFactoryOP	task_factory () const
core::Real	clash_dist () const
std::string	sym_dof_names () const
core::Size	nsub_bblock () const
core::Size	threshold () const
bool	verbose () const
bool	write () const
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	parse xml More...
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...
void	report (std::ostream &out, core::pose::Pose const &pose) const override
core::Size	compute (core::pose::Pose const &pose, bool const &v, bool const &w) const
	calc oligomeric AverageDegree More...
void	write_to_pdb (core::pose::Pose const &pose, std::string const &residue_name, core::Size const residue, std::string const &atom_name) const
void	write_pymol_string_to_pdb (std::string const &pymol_selection) const
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::pack::task::TaskFactoryOP	task_factory_
core::Real	clash_dist_
std::string	sym_dof_names_
core::Size	nsub_bblock_
core::Size	threshold_
bool	verbose_
bool	write_

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

Member Typedef Documentation

DataMap

typedef basic::datacache::DataMap protocols::matdes::ClashCheckFilter::DataMap

Filter

typedef protocols::filters::Filter protocols::matdes::ClashCheckFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::matdes::ClashCheckFilter::FilterOP

Pose

typedef core::pose::Pose protocols::matdes::ClashCheckFilter::Pose

Real

typedef core::Real protocols::matdes::ClashCheckFilter::Real

Super

typedef protocols::filters::Filter protocols::matdes::ClashCheckFilter::Super

TagCOP

typedef utility::tag::TagCOP protocols::matdes::ClashCheckFilter::TagCOP

Constructor & Destructor Documentation

ClashCheckFilter() [1/3]

protocols::matdes::ClashCheckFilter::ClashCheckFilter

(

)

ClashCheckFilter() [2/3]

protocols::matdes::ClashCheckFilter::ClashCheckFilter	(	core::pack::task::TaskFactoryOP	task_factory,
		core::Real const	c,
		std::string const &	s,
		core::Size const	n,
		core::Size const	t,
		bool const	v,
		bool const	w
	)

ClashCheckFilter() [3/3]

protocols::matdes::ClashCheckFilter::ClashCheckFilter ( ClashCheckFilter const &  rval )

default

~ClashCheckFilter()

protocols::matdes::ClashCheckFilter::~ClashCheckFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::matdes::ClashCheckFilter::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(), threshold_, protocols::matdes::TR(), verbose(), and write().

clash_dist() [1/2]

core::Real protocols::matdes::ClashCheckFilter::clash_dist

(

)

const

References clash_dist_.

Referenced by parse_my_tag().

clash_dist() [2/2]

void protocols::matdes::ClashCheckFilter::clash_dist

(

core::Real const

c

)

References clash_dist_.

class_name()

std::string protocols::matdes::ClashCheckFilter::class_name ( )

static

Referenced by protocols::matdes::ClashCheckFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

protocols::filters::FilterOP protocols::matdes::ClashCheckFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

compute()

core::Size protocols::matdes::ClashCheckFilter::compute	(	core::pose::Pose const &	pose,
		bool const &	v,
		bool const &	w
	)		const

calc oligomeric AverageDegree

References core::pose::Pose::aa(), core::conformation::Residue::atom_name(), clash_dist_, protocols::jd2::current_output_name(), core::kinematics::tree::distance_squared(), core::pose::symmetry::get_component_of_residue(), core::pose::symmetry::get_jump_name_to_subunits(), core::conformation::Residue::name3(), core::chemical::name_from_aa(), nsub_bblock_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), sym_dof_names_, core::pose::symmetry::symmetry_info(), task_factory(), protocols::matdes::TR(), write_pymol_string_to_pdb(), write_to_pdb(), and core::pose::Pose::xyz().

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

fresh_instance()

protocols::filters::FilterOP protocols::matdes::ClashCheckFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::matdes::ClashCheckFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_pymol_string_to_pdb(), and write_to_pdb().

nsub_bblock() [1/2]

core::Size protocols::matdes::ClashCheckFilter::nsub_bblock

(

)

const

References nsub_bblock_.

nsub_bblock() [2/2]

void protocols::matdes::ClashCheckFilter::nsub_bblock

(

core::Size const

n

)

References nsub_bblock_.

parse_my_tag()

void protocols::matdes::ClashCheckFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References clash_dist(), nsub_bblock_, core::pack::task::parse_task_operations(), sym_dof_names_, task_factory(), threshold_, verbose_, and write_.

provide_xml_schema()

void protocols::matdes::ClashCheckFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::matdes::ClashCheckFilterCreator::provide_xml_schema().

report()

void protocols::matdes::ClashCheckFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

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

report_sm()

core::Real protocols::matdes::ClashCheckFilter::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().

sym_dof_names() [1/2]

std::string protocols::matdes::ClashCheckFilter::sym_dof_names

(

)

const

References sym_dof_names_.

sym_dof_names() [2/2]

void protocols::matdes::ClashCheckFilter::sym_dof_names

(

std::string const &

s

)

References sym_dof_names_.

task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::matdes::ClashCheckFilter::task_factory

(

)

const

References task_factory_.

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

task_factory() [2/2]

void protocols::matdes::ClashCheckFilter::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

threshold() [1/2]

core::Size protocols::matdes::ClashCheckFilter::threshold

(

)

const

References threshold_.

threshold() [2/2]

void protocols::matdes::ClashCheckFilter::threshold

(

core::Size const

t

)

References protocols::hybridization::t, and threshold_.

verbose() [1/2]

bool protocols::matdes::ClashCheckFilter::verbose

(

)

const

References verbose_.

Referenced by apply().

verbose() [2/2]

void protocols::matdes::ClashCheckFilter::verbose

(

bool const

v

)

References verbose_.

write() [1/2]

bool protocols::matdes::ClashCheckFilter::write

(

)

const

References write_.

Referenced by apply().

write() [2/2]

void protocols::matdes::ClashCheckFilter::write

(

bool const

w

)

References write_.

write_pymol_string_to_pdb()

void protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb

(

std::string const &

pymol_selection

)

const

References protocols::jd2::add_string_to_current_job(), protocols::jd2::current_output_name(), protocols::filters::Filter::get_user_defined_name(), and name().

Referenced by compute().

write_to_pdb()

void protocols::matdes::ClashCheckFilter::write_to_pdb	(	core::pose::Pose const &	pose,
		std::string const &	residue_name,
		core::Size const	residue,
		std::string const &	atom_name
	)		const

References protocols::jd2::add_string_to_current_job(), protocols::filters::Filter::get_user_defined_name(), name(), and core::pose::Pose::pdb_info().

Referenced by compute().

Member Data Documentation

clash_dist_

core::Real protocols::matdes::ClashCheckFilter::clash_dist_

private

Referenced by clash_dist(), and compute().

nsub_bblock_

core::Size protocols::matdes::ClashCheckFilter::nsub_bblock_

private

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

sym_dof_names_

std::string protocols::matdes::ClashCheckFilter::sym_dof_names_

private

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

task_factory_

core::pack::task::TaskFactoryOP protocols::matdes::ClashCheckFilter::task_factory_

private

Referenced by task_factory().

threshold_

core::Size protocols::matdes::ClashCheckFilter::threshold_

private

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

verbose_

bool protocols::matdes::ClashCheckFilter::verbose_

private

Referenced by parse_my_tag(), and verbose().

write_

bool protocols::matdes::ClashCheckFilter::write_

private

Referenced by parse_my_tag(), and write().

---

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

• src/protocols/matdes/ClashCheckFilter.hh
• src/protocols/matdes/ClashCheckFilter.cc