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:

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< bool >	us_ds_chemical_bond_
core::pose::PoseOP	downstream_pose_
	NOT THREADSAFE! More...
utility::vector1< core::Vector >	coords_
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

typedef MatchCollisionFilter protocols::match::output::UpstreamDownstreamCollisionFilter::parent

typedef core::Real protocols::match::output::UpstreamDownstreamCollisionFilter::Real

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

References protocols::match::output::MatchCollisionFilter::cacher_, coords_, downstream_atoms_, downstream_pose_, dsbuilders_, protocols::match::output::MatchCollisionFilter::empty_pose(), protocols::match::output::MatchCollisionFilter::empty_sfxn(), protocols::buns::energy, protocols::match::output::MatchCollisionFilter::etable_energy(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, protocols::match::fake_hit(), protocols::match::full_hit(), protocols::match::output::MatchCollisionFilter::lj_cutoff(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, protocols::match::match_dspos1::upstream_hits, us_ds_chemical_bond_, protocols::match::output::MatchCollisionFilter::wfa_atr(), protocols::match::output::MatchCollisionFilter::wfa_rep(), and protocols::match::output::MatchCollisionFilter::wfa_sol().

Referenced by passes_filter().

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

References coords_, downstream_atoms_, and dsbuilders_.

Referenced by passes_filter(), and passes_hardsphere_filter().

bool protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter ( core::Size  geomcst, Hit const &  upstream_hit, utility::vector1< core::Vector > const &  coords  ) const

inline

References core::conformation::Residue::atom_type_index(), protocols::match::output::MatchCollisionFilter::bump_grid(), protocols::match::output::MatchCollisionFilter::cacher_, core::kinematics::tree::distance_squared(), downstream_pose_, max_overlap_dis_, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), per_res_atom_ind_, and protocols::match::probe_radius_for_atom_type().

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

private

References coords_, downstream_atoms_, dsbuilders_, protocols::match::fake_hit(), protocols::match::full_hit(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, passes_hardsphere_filter(), protocols::match::match_dspos1::upstream_hits, and us_ds_chemical_bond_.

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

)

References coords_, downstream_atoms_, downstream_pose_, core::conformation::Residue::natoms(), per_res_atom_ind_, core::pose::Pose::residue(), and core::pose::Pose::size().

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_num_geometric_constraints

(

core::Size

n_geomcst

)

References dsbuilders_, and us_ds_chemical_bond_.

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_tolerated_overlap ( Real  setting )

overridevirtual

Reimplemented from protocols::match::output::MatchCollisionFilter.

References protocols::match::output::MatchCollisionFilter::bump_grid(), max_overlap_dis_, protocols::match::n_probe_radii, and protocols::match::output::MatchCollisionFilter::set_tolerated_overlap().

Member Data Documentation

utility::vector1< core::Vector > protocols::match::output::UpstreamDownstreamCollisionFilter::coords_

mutableprivate

Referenced by passes_etable_filter(), passes_hardsphere_filter(), and set_downstream_pose().

utility::vector1< core::id::AtomID > protocols::match::output::UpstreamDownstreamCollisionFilter::downstream_atoms_

private

Referenced by passes_etable_filter(), passes_hardsphere_filter(), and set_downstream_pose().

core::pose::PoseOP protocols::match::output::UpstreamDownstreamCollisionFilter::downstream_pose_

mutableprivate

NOT THREADSAFE!

Referenced by passes_etable_filter(), passes_hardsphere_filter(), and set_downstream_pose().

utility::vector1< downstream::DownstreamBuilderCOP > protocols::match::output::UpstreamDownstreamCollisionFilter::dsbuilders_

private

Referenced by passes_etable_filter(), passes_filter(), passes_hardsphere_filter(), set_downstream_builder(), and set_num_geometric_constraints().

Real protocols::match::output::UpstreamDownstreamCollisionFilter::max_overlap_dis_

private

Referenced by passes_hardsphere_filter(), and set_tolerated_overlap().

utility::vector1< utility::vector1< core::Size > > protocols::match::output::UpstreamDownstreamCollisionFilter::per_res_atom_ind_

private

Referenced by passes_hardsphere_filter(), and set_downstream_pose().

utility::vector1< bool > protocols::match::output::UpstreamDownstreamCollisionFilter::us_ds_chemical_bond_

private

Referenced by passes_etable_filter(), passes_hardsphere_filter(), set_chemical_bond_from_upstream_to_downstream(), and set_num_geometric_constraints().

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

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