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protocols::matdes::SymUnsatHbondFilter Class Reference

filters based on an upper bound # of buried unsatisfied polar residues More...

#include <SymUnsatHbondFilter.hh>

Inheritance diagram for protocols::matdes::SymUnsatHbondFilter:
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

 SymUnsatHbondFilter ()
 
 SymUnsatHbondFilter (core::Size const upper_cutoff, core::Size const jump, std::string const sym_dofs, bool verb, bool write, std::string const mode, bool compare_to_ref, core::pose::PoseOP const reference_pose)
 
 SymUnsatHbondFilter (SymUnsatHbondFilter const &rval)
 
 ~SymUnsatHbondFilter () override=default
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
void upper_threshold (core::Size const upper_cutoff)
 
void jump_num (core::Size const jump)
 
void sym_dof_names (std::string const sym_dofs)
 
void verbose (bool const verb)
 
void write2pdb (bool const write)
 
void mode (std::string const mode)
 
void reference_pose (core::pose::PoseOP const reference_pose)
 
void compare_to_ref (bool const compare_to_ref)
 
core::Size upper_threshold () const
 
core::Size jump_num () const
 
std::string sym_dof_names () const
 
bool verbose () const
 
bool write2pdb () const
 
std::string mode () const
 
core::pose::PoseOP reference_pose () const
 
bool compare_to_ref () const
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. 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::Real compute (core::pose::Pose const &pose, bool const &verb, bool const &write) const
 
void write_to_pdb (core::pose::Pose const &pose, std::string const mode, 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::Size upper_threshold_
 
core::Size jump_num_
 
std::string sym_dof_names_
 
bool verbose_
 
bool write2pdb_
 
std::string mode_
 
bool compare_to_ref_
 
core::pose::PoseOP reference_pose_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

filters based on an upper bound # of buried unsatisfied polar residues

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( )
protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( core::Size const  upper_cutoff,
core::Size const  jump,
std::string const  sym_dofs,
bool  verb,
bool  write,
std::string const  mode,
bool  compare_to_ref,
core::pose::PoseOP const  reference_pose 
)
protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( SymUnsatHbondFilter const &  rval)
default
protocols::matdes::SymUnsatHbondFilter::~SymUnsatHbondFilter ( )
overridedefault

Member Function Documentation

bool protocols::matdes::SymUnsatHbondFilter::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(), protocols::matdes::TR(), and upper_threshold().

std::string protocols::matdes::SymUnsatHbondFilter::class_name ( )
static
protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::clone ( ) const
overridevirtual
void protocols::matdes::SymUnsatHbondFilter::compare_to_ref ( bool const  compare_to_ref)
bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref ( ) const

References compare_to_ref_.

Referenced by compare_to_ref(), and parse_my_tag().

core::Real protocols::matdes::SymUnsatHbondFilter::compute ( core::pose::Pose const &  pose,
bool const &  verb,
bool const &  write 
) const
protocols::filters::FilterOP protocols::matdes::SymUnsatHbondFilter::fresh_instance ( ) const
overridevirtual
void protocols::matdes::SymUnsatHbondFilter::jump_num ( core::Size const  jump)

References jump_num_.

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num ( ) const

References jump_num_.

Referenced by compute(), and parse_my_tag().

void protocols::matdes::SymUnsatHbondFilter::mode ( std::string const  mode)

References mode(), and mode_.

std::string protocols::matdes::SymUnsatHbondFilter::mode ( ) const

References mode_.

Referenced by mode(), and parse_my_tag().

std::string protocols::matdes::SymUnsatHbondFilter::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::SymUnsatHbondFilter::parse_my_tag ( TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::matdes::SymUnsatHbondFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::matdes::SymUnsatHbondFilter::reference_pose ( core::pose::PoseOP const  reference_pose)
core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose ( ) const

References reference_pose_.

Referenced by reference_pose().

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

Reimplemented from protocols::filters::Filter.

References compute(), verbose(), and write2pdb().

core::Real protocols::matdes::SymUnsatHbondFilter::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::SymUnsatHbondFilter::sym_dof_names ( std::string const  sym_dofs)

References sym_dof_names_.

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

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

void protocols::matdes::SymUnsatHbondFilter::upper_threshold ( core::Size const  upper_cutoff)

References upper_threshold_.

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold ( ) const

References upper_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::matdes::SymUnsatHbondFilter::verbose ( bool const  verb)

References verbose_.

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

References verbose_.

Referenced by parse_my_tag(), and report().

void protocols::matdes::SymUnsatHbondFilter::write2pdb ( bool const  write)

References write2pdb_.

bool protocols::matdes::SymUnsatHbondFilter::write2pdb ( ) const

References write2pdb_.

Referenced by parse_my_tag(), and report().

void protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb ( std::string const  pymol_selection) const
void protocols::matdes::SymUnsatHbondFilter::write_to_pdb ( core::pose::Pose const &  pose,
std::string const  mode,
std::string const  residue_name,
core::Size const  residue,
std::string const  atom_name 
) const

Member Data Documentation

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref_
private

Referenced by compare_to_ref(), and compute().

core::Size protocols::matdes::SymUnsatHbondFilter::jump_num_
private

Referenced by jump_num().

std::string protocols::matdes::SymUnsatHbondFilter::mode_
private

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

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose_
private
std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names_
private

Referenced by sym_dof_names().

core::Size protocols::matdes::SymUnsatHbondFilter::upper_threshold_
private

Referenced by upper_threshold().

bool protocols::matdes::SymUnsatHbondFilter::verbose_
private

Referenced by verbose().

bool protocols::matdes::SymUnsatHbondFilter::write2pdb_
private

Referenced by write2pdb().


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