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protocols::matdes::ClashCheckFilter Class Reference

#include <ClashCheckFilter.hh>

Inheritance diagram for protocols::matdes::ClashCheckFilter:
Inheritance graph
[legend]

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 (Filter 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 bool filter_provides_citation_info () const
 Does this filter 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 filter_is_unpublished () const
 Does this filter 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 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

typedef basic::datacache::DataMap protocols::matdes::ClashCheckFilter::DataMap
typedef utility::tag::TagCOP protocols::matdes::ClashCheckFilter::TagCOP

Constructor & Destructor Documentation

protocols::matdes::ClashCheckFilter::ClashCheckFilter ( )
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 
)
protocols::matdes::ClashCheckFilter::ClashCheckFilter ( ClashCheckFilter const &  rval)
default
protocols::matdes::ClashCheckFilter::~ClashCheckFilter ( )
overridedefault

Member Function Documentation

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().

void protocols::matdes::ClashCheckFilter::clash_dist ( core::Real const  c)
core::Real protocols::matdes::ClashCheckFilter::clash_dist ( ) const

References clash_dist_.

Referenced by parse_my_tag().

std::string protocols::matdes::ClashCheckFilter::class_name ( )
static
protocols::filters::FilterOP protocols::matdes::ClashCheckFilter::clone ( ) const
overridevirtual
core::Size protocols::matdes::ClashCheckFilter::compute ( core::pose::Pose const &  pose,
bool const &  v,
bool const &  w 
) const
protocols::filters::FilterOP protocols::matdes::ClashCheckFilter::fresh_instance ( ) const
overridevirtual
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().

void protocols::matdes::ClashCheckFilter::nsub_bblock ( core::Size const  n)

References nsub_bblock_.

core::Size protocols::matdes::ClashCheckFilter::nsub_bblock ( ) const

References nsub_bblock_.

void protocols::matdes::ClashCheckFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::matdes::ClashCheckFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::matdes::ClashCheckFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

void protocols::matdes::ClashCheckFilter::sym_dof_names ( std::string const &  s)

References sym_dof_names_.

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

References sym_dof_names_.

void protocols::matdes::ClashCheckFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::pack::task::TaskFactoryOP protocols::matdes::ClashCheckFilter::task_factory ( ) const

References task_factory_.

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

void protocols::matdes::ClashCheckFilter::threshold ( core::Size const  t)
core::Size protocols::matdes::ClashCheckFilter::threshold ( ) const

References threshold_.

void protocols::matdes::ClashCheckFilter::verbose ( bool const  v)

References verbose_.

bool protocols::matdes::ClashCheckFilter::verbose ( ) const

References verbose_.

Referenced by apply().

void protocols::matdes::ClashCheckFilter::write ( bool const  w)

References write_.

bool protocols::matdes::ClashCheckFilter::write ( ) const

References write_.

Referenced by apply().

void protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb ( std::string const &  pymol_selection) const
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

Member Data Documentation

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

Referenced by clash_dist(), and compute().

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

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

std::string protocols::matdes::ClashCheckFilter::sym_dof_names_
private
core::pack::task::TaskFactoryOP protocols::matdes::ClashCheckFilter::task_factory_
private

Referenced by task_factory().

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

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

bool protocols::matdes::ClashCheckFilter::verbose_
private

Referenced by parse_my_tag(), and verbose().

bool protocols::matdes::ClashCheckFilter::write_
private

Referenced by parse_my_tag(), and write().


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