protocols::match::output::UpstreamCollisionFilter Class Reference

This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol. More...

#include <UpstreamCollisionFilter.hh>

Inheritance diagram for protocols::match::output::UpstreamCollisionFilter:

Collaboration diagram for protocols::match::output::UpstreamCollisionFilter:

Public Types
typedef core::Real	Real
typedef MatchCollisionFilter	parent
Public Types inherited from protocols::match::output::MatchCollisionFilter
typedef core::Real	Real

Public Member Functions
	UpstreamCollisionFilter (std::string filter_name, UpstreamHitCacherOP coordinate_cacher)
virtual	~UpstreamCollisionFilter ()
virtual bool	passes_filter (match const &m) const
	Returns true if the given match does not contain too much residue-pair collision. More...
virtual bool	passes_filter (match_dspos1 const &m) const
	Returns true if the given match does not contain too much residue-pair collision. More...
bool	passes_hardsphere_filter (core::Size geomcst_a, core::Size geomcst_b, Hit const &upstream_hit_a, Hit const &upstream_hit_b) const
bool	passes_hardsphere_filter (core::conformation::Residue const &resA, core::conformation::Residue const &resB) const
Public Member Functions inherited from protocols::match::output::MatchCollisionFilter
	MatchCollisionFilter (std::string filter_name, UpstreamHitCacherOP coordinate_cacher)
virtual	~MatchCollisionFilter ()
void	set_filter_by_lj (bool setting)
void	set_lj_cutoff (Real setting)
void	set_lj_atr_weight (Real setting)
void	set_lj_rep_weight (Real setting)
void	set_lj_sol_weight (Real setting)
virtual void	set_tolerated_overlap (Real setting)
bool	filter_by_lj () const
Real	wfa_atr () const
Real	wfa_rep () const
Real	wfa_sol () const
Real	lj_cutoff () const
Real	tolerated_overlap () const
core::pose::PoseCOP	empty_pose () const
core::scoring::ScoreFunctionOP	empty_sfxn () const
core::scoring::methods::ShortRangeTwoBodyEnergyCOP	etable_energy () const
BumpGridCOP	bump_grid () const
Public Member Functions inherited from protocols::match::output::MatchFilter
	MatchFilter (std::string filter_name)
virtual	~MatchFilter ()
std::string	filter_name () const

Additional Inherited Members
Protected Attributes inherited from protocols::match::output::MatchCollisionFilter
UpstreamHitCacherOP	cacher_

Detailed Description

This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol.

Definition at line 125 of file UpstreamCollisionFilter.hh.

Member Typedef Documentation

typedef MatchCollisionFilter protocols::match::output::UpstreamCollisionFilter::parent

Definition at line 128 of file UpstreamCollisionFilter.hh.

typedef core::Real protocols::match::output::UpstreamCollisionFilter::Real

Definition at line 127 of file UpstreamCollisionFilter.hh.

Constructor & Destructor Documentation

protocols::match::output::UpstreamCollisionFilter::UpstreamCollisionFilter	(	std::string	filter_name,
		UpstreamHitCacherOP	coordinate_cacher
	)

Definition at line 146 of file UpstreamCollisionFilter.cc.

protocols::match::output::UpstreamCollisionFilter::~UpstreamCollisionFilter ( )

virtual

Definition at line 155 of file UpstreamCollisionFilter.cc.

Member Function Documentation

bool protocols::match::output::UpstreamCollisionFilter::passes_filter ( match const &  m) const

virtual

Returns true if the given match does not contain too much residue-pair collision.

Either sphere-overlap checks the atom pairs in the match residues, or evaluates the Etable energies. Returns false if any atom pair collides more than the cutoff threshold or if the residue pair energy exceeds the energy cutoff. Returns true otherwise.

Implements protocols::match::output::MatchCollisionFilter.

Definition at line 163 of file UpstreamCollisionFilter.cc.

bool protocols::match::output::UpstreamCollisionFilter::passes_filter ( match_dspos1 const &  m) const

virtual

Returns true if the given match does not contain too much residue-pair collision.

Implements protocols::match::output::MatchCollisionFilter.

Definition at line 171 of file UpstreamCollisionFilter.cc.

References protocols::match::output::MatchCollisionFilter::cacher_, protocols::match::output::MatchCollisionFilter::empty_pose(), protocols::match::output::MatchCollisionFilter::empty_sfxn(), protocols::match::output::MatchCollisionFilter::etable_energy(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, protocols::match::fake_hit(), protocols::match::output::MatchCollisionFilter::filter_by_lj(), protocols::match::output::MatchCollisionFilter::lj_cutoff(), passes_hardsphere_filter(), protocols::match::match_dspos1::upstream_hits, protocols::match::output::MatchCollisionFilter::wfa_atr(), protocols::match::output::MatchCollisionFilter::wfa_rep(), and protocols::match::output::MatchCollisionFilter::wfa_sol().

bool protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter	(	core::Size	geomcst_a,
		core::Size	geomcst_b,
		Hit const &	upstream_hit_a,
		Hit const &	upstream_hit_b
	)		const

Definition at line 204 of file UpstreamCollisionFilter.cc.

References protocols::match::output::MatchCollisionFilter::cacher_.

Referenced by passes_filter().

bool protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter ( core::conformation::Residue const &  resA, core::conformation::Residue const &  resB  ) const

inline

Definition at line 161 of file UpstreamCollisionFilter.hh.

References core::conformation::Residue::atom_type_index(), protocols::match::output::MatchCollisionFilter::bump_grid(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::nheavyatoms(), protocols::match::probe_radius_for_atom_type(), and core::conformation::Residue::xyz().

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

• src/protocols/match/output/UpstreamCollisionFilter.hh
• src/protocols/match/output/UpstreamCollisionFilter.cc