Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::matdes::ClashCheckFilter Class Reference

#include <ClashCheckFilter.hh>

Inheritance diagram for protocols::matdes::ClashCheckFilter:
Inheritance graph

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

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ 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)

◆ ~ClashCheckFilter()

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

Member Function Documentation

◆ apply()

bool protocols::matdes::ClashCheckFilter::apply ( core::pose::Pose const &  pose) const

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 ( )

◆ clone()

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

◆ compute()

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

◆ fresh_instance()

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

◆ name()

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

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 

◆ provide_xml_schema()

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

◆ report()

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

◆ report_sm()

core::Real protocols::matdes::ClashCheckFilter::report_sm ( core::pose::Pose const &  ) const

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)

◆ 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

◆ 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

Member Data Documentation

◆ clash_dist_

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

Referenced by clash_dist(), and compute().

◆ nsub_bblock_

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

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

◆ sym_dof_names_

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

◆ task_factory_

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

Referenced by task_factory().

◆ threshold_

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

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

◆ verbose_

bool protocols::matdes::ClashCheckFilter::verbose_

Referenced by parse_my_tag(), and verbose().

◆ write_

bool protocols::matdes::ClashCheckFilter::write_

Referenced by parse_my_tag(), and write().

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