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protocols::match::output::UpstreamDownstreamCollisionFilter Class Reference

This class is used to detect collisions between upstream residues and downstream poses. More...

#include <UpstreamDownstreamCollisionFilter.hh>

Inheritance diagram for protocols::match::output::UpstreamDownstreamCollisionFilter:
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

 UpstreamDownstreamCollisionFilter (std::string filter_name, UpstreamHitCacherOP coordinate_cacher)
 
 ~UpstreamDownstreamCollisionFilter () override
 
void set_downstream_pose (core::pose::Pose const &downstream_pose)
 
void set_num_geometric_constraints (core::Size n_geomcst)
 
void set_chemical_bond_from_upstream_to_downstream (core::Size geomcst_id)
 Do not perform any collision detection between an upstream residue and the downstream pose if there is a chemical bond between them. More...
 
void set_downstream_builder (core::Size geomcst_id, downstream::DownstreamBuilderCOP builder)
 
void set_tolerated_overlap (Real setting) override
 
bool passes_filter (match const &m) const override
 Returns true if there is at least one placement of the downstream partner which does not exceed the collision tolerance with any of the upstream residues. More...
 
bool passes_filter (match_dspos1 const &m) const override
 Returns true if the specified downstream position does not collide more than tolerated with any of the upstream residues. More...
 
bool passes_hardsphere_filter (core::Size geomcst_up, core::Size geomcst_down, Hit const &upstream_hit, Hit const &downstream_hit) const
 
bool passes_hardsphere_filter (core::Size geomcst, Hit const &upstream_hit, utility::vector1< core::Vector > const &coords) 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)
 
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
 

Private Member Functions

bool passes_etable_filter (match_dspos1 const &m) const
 
bool passes_hardsphere_filter (match_dspos1 const &m) const
 

Private Attributes

Real max_overlap_dis_
 
utility::vector1
< downstream::DownstreamBuilderCOP
dsbuilders_
 
utility::vector1< boolus_ds_chemical_bond_
 
core::pose::PoseOP downstream_pose_
 NOT THREADSAFE! More...
 
utility::vector1< core::Vectorcoords_
 
utility::vector1
< core::id::AtomID
downstream_atoms_
 
utility::vector1
< utility::vector1< core::Size > > 
per_res_atom_ind_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::match::output::MatchCollisionFilter
UpstreamHitCacherOP cacher_
 

Detailed Description

This class is used to detect collisions between upstream residues and downstream poses.

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_etable_filter ( match_dspos1 const &  m) const
private
bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_filter ( match const &  m) const
overridevirtual

Returns true if there is at least one placement of the downstream partner which does not exceed the collision tolerance with any of the upstream residues.

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

References dsbuilders_.

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

Returns true if the specified downstream position does not collide more than tolerated with any of the upstream residues.

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

References protocols::match::output::MatchCollisionFilter::filter_by_lj(), passes_etable_filter(), and passes_hardsphere_filter().

bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter ( core::Size  geomcst_up,
core::Size  geomcst_down,
Hit const &  upstream_hit,
Hit const &  downstream_hit 
) const
bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter ( core::Size  geomcst,
Hit const &  upstream_hit,
utility::vector1< core::Vector > const &  coords 
) const
inline
bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter ( match_dspos1 const &  m) const
private
void protocols::match::output::UpstreamDownstreamCollisionFilter::set_chemical_bond_from_upstream_to_downstream ( core::Size  geomcst_id)

Do not perform any collision detection between an upstream residue and the downstream pose if there is a chemical bond between them.

References us_ds_chemical_bond_.

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_builder ( core::Size  geomcst_id,
downstream::DownstreamBuilderCOP  builder 
)

References dsbuilders_.

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose ( core::pose::Pose const &  downstream_pose)
void protocols::match::output::UpstreamDownstreamCollisionFilter::set_num_geometric_constraints ( core::Size  n_geomcst)
void protocols::match::output::UpstreamDownstreamCollisionFilter::set_tolerated_overlap ( Real  setting)
overridevirtual

Member Data Documentation

utility::vector1< core::Vector > protocols::match::output::UpstreamDownstreamCollisionFilter::coords_
mutableprivate
utility::vector1< core::id::AtomID > protocols::match::output::UpstreamDownstreamCollisionFilter::downstream_atoms_
private
core::pose::PoseOP protocols::match::output::UpstreamDownstreamCollisionFilter::downstream_pose_
mutableprivate
utility::vector1< downstream::DownstreamBuilderCOP > protocols::match::output::UpstreamDownstreamCollisionFilter::dsbuilders_
private
Real protocols::match::output::UpstreamDownstreamCollisionFilter::max_overlap_dis_
private
utility::vector1< utility::vector1< core::Size > > protocols::match::output::UpstreamDownstreamCollisionFilter::per_res_atom_ind_
private
utility::vector1< bool > protocols::match::output::UpstreamDownstreamCollisionFilter::us_ds_chemical_bond_
private

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