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

#include <AtomicContactCountFilter.hh>

Public Member Functions
	AtomicContactCountFilter ()
	AtomicContactCountFilter (core::Real distance_cutoff)
	AtomicContactCountFilter (AtomicContactCountFilter const &copy)
virtual protocols::filters::FilterOP	clone () const
virtual protocols::filters::FilterOP	fresh_instance () const
virtual	~AtomicContactCountFilter ()
virtual std::string	name () const
void	initialize_all_atoms (core::pack::task::TaskFactoryOP task_factoryA=NULL, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=NULL, bool normalize_by_carbon_count=false)
void	initialize_cross_jump (core::Size jump=0, std::string sym_dof_name="", core::pack::task::TaskFactoryOP task_factoryA=NULL, bool normalize_by_sasa=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=NULL, bool normalize_by_carbon_count=false)
void	initialize_cross_chain (core::pack::task::TaskFactoryOP task_factoryA=NULL, bool normalize_by_sasa=false, bool detect_chains_for_interface_by_task=false, bool individual_tasks=false, core::pack::task::TaskFactoryOP task_factoryB=NULL, bool normalize_by_carbon_count=false)
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
virtual bool	apply (core::pose::Pose const &) const
	Returns true if the given pose passes the filter, false otherwise. More...
virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &) const
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
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 void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)

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_
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

enum protocols::protein_interface_design::filters::AtomicContactCountFilter::Mode

private

Enumerator
ALL
CROSS_CHAIN_DETECTED
CROSS_CHAIN_ALL
CROSS_JUMP

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter

(

)

References filters, and initialize_all_atoms().

Referenced by clone(), and fresh_instance().

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter

(

core::Real

distance_cutoff

)

References initialize_all_atoms().

protocols::protein_interface_design::filters::AtomicContactCountFilter::AtomicContactCountFilter

(

AtomicContactCountFilter const &

copy

)

protocols::protein_interface_design::filters::AtomicContactCountFilter::~AtomicContactCountFilter ( )

virtual

Member Function Documentation

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

inlinevirtual

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

Implements protocols::filters::Filter.

protocols::filters::FilterOP protocols::protein_interface_design::filters::AtomicContactCountFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References AtomicContactCountFilter().

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::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::simple_filters::InterfaceSasaFilter::compute(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), CROSS_CHAIN_ALL, CROSS_CHAIN_DETECTED, CROSS_JUMP, core::conformation::Conformation::delete_residue_range_slow(), numeric::xyzVector< class >::distance(), 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::pose::Pose::n_residue(), core::conformation::Residue::nheavyatoms(), normalize_by_carbon_count_, normalize_by_sasa_, core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::pack::task::PackerTask::pack_residue(), core::kinematics::FoldTree::partition_by_jump(), core::pose::symmetry::partition_by_symm_jumps(), resi, core::pose::Pose::residue(), 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_, core::pose::Pose::total_residue(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by report_sm().

protocols::filters::FilterOP protocols::protein_interface_design::filters::AtomicContactCountFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References AtomicContactCountFilter().

void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_all_atoms	(	core::pack::task::TaskFactoryOP	task_factoryA = NULL,
		bool	individual_tasks = false,
		core::pack::task::TaskFactoryOP	task_factoryB = NULL,
		bool	normalize_by_carbon_count = false
	)

References ALL, filter_mode_, individual_tasks_, jump_, normalize_by_carbon_count_, normalize_by_sasa_, ss_only_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by AtomicContactCountFilter(), and parse_my_tag().

void protocols::protein_interface_design::filters::AtomicContactCountFilter::initialize_cross_chain	(	core::pack::task::TaskFactoryOP	task_factoryA = NULL,
		bool	normalize_by_sasa = false,
		bool	detect_chains_for_interface_by_task = false,
		bool	individual_tasks = false,
		core::pack::task::TaskFactoryOP	task_factoryB = NULL,
		bool	normalize_by_carbon_count = false
	)

References CROSS_CHAIN_ALL, CROSS_CHAIN_DETECTED, filter_mode_, individual_tasks_, jump_, normalize_by_carbon_count_, normalize_by_sasa_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by parse_my_tag().

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 = NULL,
		bool	normalize_by_sasa = false,
		bool	individual_tasks = false,
		core::pack::task::TaskFactoryOP	task_factoryB = NULL,
		bool	normalize_by_carbon_count = false
	)

References CROSS_JUMP, filter_mode_, individual_tasks_, jump_, normalize_by_carbon_count_, normalize_by_sasa_, sym_dof_name_, task_factoryA_, and task_factoryB_.

Referenced by parse_my_tag().

virtual std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::name ( ) const

inlinevirtual

Reimplemented from protocols::filters::Filter.

void protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented from protocols::filters::Filter.

References ALL, CROSS_CHAIN_DETECTED, distance_cutoff_, filter_mode_, basic::datacache::DataMap::get(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), jump_, normalize_by_sasa_, protocols::rosetta_scripts::parse_task_operations(), core::pack::task::TaskFactory::push_back(), ss_only_, utility::string_split(), and utility_exit_with_message.

virtual core::Real protocols::protein_interface_design::filters::AtomicContactCountFilter::report_sm ( core::pose::Pose const &  pose ) const

inlinevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Member Data Documentation

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

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::individual_tasks_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

core::Size protocols::protein_interface_design::filters::AtomicContactCountFilter::jump_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_carbon_count_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::normalize_by_sasa_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), initialize_cross_jump(), and parse_my_tag().

bool protocols::protein_interface_design::filters::AtomicContactCountFilter::ss_only_

private

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

std::string protocols::protein_interface_design::filters::AtomicContactCountFilter::sym_dof_name_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryA_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::filters::AtomicContactCountFilter::task_factoryB_

private

Referenced by compute(), initialize_all_atoms(), initialize_cross_chain(), and initialize_cross_jump().

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

• src/protocols/protein_interface_design/filters/AtomicContactCountFilter.hh
• src/protocols/protein_interface_design/filters/AtomicContactCountFilter.cc