Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
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

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 () 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::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

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::matdes::SymUnsatHbondFilter::TagCOP

Constructor & Destructor Documentation

◆ SymUnsatHbondFilter() [1/3]

protocols::matdes::SymUnsatHbondFilter::SymUnsatHbondFilter ( )

◆ SymUnsatHbondFilter() [2/3]

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 

◆ SymUnsatHbondFilter() [3/3]

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

◆ ~SymUnsatHbondFilter()

protocols::matdes::SymUnsatHbondFilter::~SymUnsatHbondFilter ( )

Member Function Documentation

◆ apply()

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

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), protocols::matdes::TR(), and upper_threshold().

◆ class_name()

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

◆ clone()

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

◆ compare_to_ref() [1/2]

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

References compare_to_ref_.

Referenced by compare_to_ref(), and parse_my_tag().

◆ compare_to_ref() [2/2]

void protocols::matdes::SymUnsatHbondFilter::compare_to_ref ( bool const  compare_to_ref)

◆ compute()

core::Real protocols::matdes::SymUnsatHbondFilter::compute ( core::pose::Pose const &  pose,
bool const &  verb,
bool const &  write 
) const

◆ fresh_instance()

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

◆ jump_num() [1/2]

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

References jump_num_.

Referenced by compute(), and parse_my_tag().

◆ jump_num() [2/2]

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

References jump_num_.

◆ mode() [1/2]

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

References mode_.

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

◆ mode() [2/2]

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

References mode(), and mode_.

◆ name()

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

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_pymol_string_to_pdb(), and write_to_pdb().

◆ parse_my_tag()

void protocols::matdes::SymUnsatHbondFilter::parse_my_tag ( TagCOP  ,

◆ provide_xml_schema()

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

◆ reference_pose() [1/2]

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose ( ) const

References reference_pose_.

Referenced by reference_pose().

◆ reference_pose() [2/2]

void protocols::matdes::SymUnsatHbondFilter::reference_pose ( core::pose::PoseOP const  reference_pose)

◆ report()

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

◆ report_sm()

core::Real protocols::matdes::SymUnsatHbondFilter::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::SymUnsatHbondFilter::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

◆ sym_dof_names() [2/2]

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

References sym_dof_names_.

◆ upper_threshold() [1/2]

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

References upper_threshold_.

Referenced by apply(), and parse_my_tag().

◆ upper_threshold() [2/2]

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

References upper_threshold_.

◆ verbose() [1/2]

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

References verbose_.

Referenced by parse_my_tag(), and report().

◆ verbose() [2/2]

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

References verbose_.

◆ write2pdb() [1/2]

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

References write2pdb_.

Referenced by parse_my_tag(), and report().

◆ write2pdb() [2/2]

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

References write2pdb_.

◆ write_pymol_string_to_pdb()

void protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb ( std::string const  pymol_selection) const

◆ write_to_pdb()

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

◆ compare_to_ref_

bool protocols::matdes::SymUnsatHbondFilter::compare_to_ref_

Referenced by compare_to_ref(), and compute().

◆ jump_num_

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

Referenced by jump_num().

◆ mode_

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

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

◆ reference_pose_

core::pose::PoseOP protocols::matdes::SymUnsatHbondFilter::reference_pose_

◆ sym_dof_names_

std::string protocols::matdes::SymUnsatHbondFilter::sym_dof_names_

Referenced by sym_dof_names().

◆ upper_threshold_

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

Referenced by upper_threshold().

◆ verbose_

bool protocols::matdes::SymUnsatHbondFilter::verbose_

Referenced by verbose().

◆ write2pdb_

bool protocols::matdes::SymUnsatHbondFilter::write2pdb_

Referenced by write2pdb().

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