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protocols::protein_interface_design::filters::AtomicContactCountFilter Class Reference

#include <AtomicContactCountFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::AtomicContactCountFilter:
Inheritance graph
[legend]

Public Member Functions

 AtomicContactCountFilter ()
 
 AtomicContactCountFilter (core::Real distance_cutoff)
 
 AtomicContactCountFilter (AtomicContactCountFilter const &copy)
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
 ~AtomicContactCountFilter () override
 
void initialize_all_atoms (core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)
 
void initialize_cross_jump (core::Size jump=0, std::string sym_dof_name="", core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool normalize_by_sasa=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)
 
void initialize_cross_chain (core::pack::task::TaskFactoryOP task_factoryA=nullptr, bool normalize_by_sasa=false, bool detect_chains_for_interface_by_task=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=nullptr, bool normalize_by_carbon_count=false, bool non_local=false, bool res_contact=false, bool count_SD_NE1=false)
 
void parse_my_tag (utility::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 &) 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...
 
core::Real compute (core::pose::Pose const &) 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 void report (std::ostream &, core::pose::Pose const &) const
 
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 Types

enum  Mode { ALL, CROSS_CHAIN_DETECTED, CROSS_CHAIN_ALL, CROSS_JUMP }
 

Private Attributes

core::pack::task::TaskFactoryOP task_factoryA_
 
core::pack::task::TaskFactoryOP task_factoryB_
 
core::Real distance_cutoff_
 
bool non_local_
 
bool res_contact_
 
bool count_SD_NE1_
 
Mode filter_mode_
 
bool normalize_by_sasa_
 
bool ss_only_
 
bool normalize_by_carbon_count_
 
bool individual_tasks_
 
core::Size jump_
 
std::string sym_dof_name_
 

Additional Inherited Members

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

Member Enumeration Documentation

Enumerator
ALL 
CROSS_CHAIN_DETECTED 
CROSS_CHAIN_ALL 
CROSS_JUMP 

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( )
protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( core::Real  distance_cutoff)
protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter ( AtomicContactCountFilter const &  copy)
default
protocols::protein_interface_design::filters::AtomicContactCountFilter::~AtomicContactCountFilter ( )
overridedefault

Member Function Documentation

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::apply ( core::pose::Pose const &  ) const
inlineoverridevirtual

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

Implements protocols::filters::Filter.

std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::AtomicContactCountFilter::clone ( ) const
overridevirtual
core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::compute ( core::pose::Pose const &  pose) const

References ALL, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::pose::Pose::chain(), core::conformation::Residue::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::simple_filters::InterfaceSasaFilter::compute(), core::pose::Pose::conformation(), count_SD_NE1_, core::pack::task::TaskFactory::create_packer_task(), CROSS_CHAIN_ALL, CROSS_CHAIN_DETECTED, CROSS_JUMP, core::conformation::Conformation::delete_residue_range_slow(), distance_cutoff_, protocols::simple_filters::dssp(), core::chemical::AtomType::element(), filter_mode_, core::conformation::Residue::first_sidechain_atom(), core::pose::Pose::fold_tree(), core::scoring::dssp::Dssp::get_dssp_reduced_IG_as_L_secstruct(), core::pose::symmetry::get_sym_aware_jump_num(), individual_tasks_, core::pose::symmetry::is_symmetric(), jump_, protocols::simple_filters::InterfaceSasaFilter::jumps(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::conformation::Residue::nheavyatoms(), non_local_, normalize_by_carbon_count_, normalize_by_sasa_, core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::symmetry::partition_by_symm_jumps(), res_contact_, core::pose::Pose::residue(), core::pose::Pose::size(), ss_only_, core::pose::symmetry::sym_dof_jump_num(), sym_dof_name_, protocols::simple_filters::InterfaceSasaFilter::sym_dof_names(), core::pose::symmetry::symmetry_info(), task_factoryA_, task_factoryB_, and core::conformation::Residue::xyz().

Referenced by report_sm().

protocols::filters::FilterOP protocols::protein_interface_design::filters::AtomicContactCountFilter::fresh_instance ( ) const
overridevirtual
void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_all_atoms ( core::pack::task::TaskFactoryOP  task_factoryA = nullptr,
bool  individual_tasks = false,
core::pack::task::TaskFactoryOP  task_factoryB = nullptr,
bool  normalize_by_carbon_count = false,
bool  non_local = false,
bool  res_contact = false,
bool  count_SD_NE1 = false 
)
void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_cross_chain ( core::pack::task::TaskFactoryOP  task_factoryA = nullptr,
bool  normalize_by_sasa = false,
bool  detect_chains_for_interface_by_task = false,
bool  individual_tasks = false,
core::pack::task::TaskFactoryOP  task_factoryB = nullptr,
bool  normalize_by_carbon_count = false,
bool  non_local = false,
bool  res_contact = false,
bool  count_SD_NE1 = false 
)
void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_cross_jump ( core::Size  jump = 0,
std::string  sym_dof_name = "",
core::pack::task::TaskFactoryOP  task_factoryA = nullptr,
bool  normalize_by_sasa = false,
bool  individual_tasks = false,
core::pack::task::TaskFactoryOP  task_factoryB = nullptr,
bool  normalize_by_carbon_count = false,
bool  non_local = false,
bool  res_contact = false,
bool  count_SD_NE1 = false 
)
std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::protein_interface_design::filters::AtomicContactCountFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::report_sm ( core::pose::Pose const &  pose) const
inlineoverridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::count_SD_NE1_
private
core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::distance_cutoff_
private

Referenced by compute(), and parse_my_tag().

Mode protocols::protein_interface_design::filters::AtomicContactCountFilter::filter_mode_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::individual_tasks_
private
core::Size protocols::protein_interface_design::filters::AtomicContactCountFilter::jump_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::non_local_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_carbon_count_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_sasa_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::res_contact_
private
bool protocols::protein_interface_design::filters::AtomicContactCountFilter::ss_only_
private
std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::sym_dof_name_
private
core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryA_
private
core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryB_
private

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