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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:
Inheritance graph
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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)
 
 ~UpstreamCollisionFilter () override
 
bool passes_filter (match const &m) const override
 Returns true if the given match does not contain too much residue-pair collision. More...
 
bool passes_filter (match_dspos1 const &m) const override
 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)
 
 ~MatchCollisionFilter () override
 
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 const &filter_name)
 
 ~MatchFilter () override
 
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.

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

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

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.

bool protocols::match::output::UpstreamCollisionFilter::passes_filter ( match_dspos1 const &  m) const
overridevirtual
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
bool protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter ( core::conformation::Residue const &  resA,
core::conformation::Residue const &  resB 
) const
inline

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