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

#include <UpstreamDownstreamCollisionFilter.hh>

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

Collaboration 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)

virtual	~UpstreamDownstreamCollisionFilter ()

void	set_downstream_pose (core::pose::Pose const &downstream_pose)

void	set_num_geometric_constraints (Size n_geomcst)

void	set_chemical_bond_from_upstream_to_downstream (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 (Size geomcst_id, downstream::DownstreamBuilderCOP builder)

void	set_tolerated_overlap (Real setting)

virtual bool	passes_filter (match const &m) const
	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...

virtual bool	passes_filter (match_dspos1 const &m) const
	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)

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)

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

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< 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.

Definition at line 53 of file UpstreamDownstreamCollisionFilter.hh.

Member Typedef Documentation

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

Definition at line 56 of file UpstreamDownstreamCollisionFilter.hh.

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

Definition at line 55 of file UpstreamDownstreamCollisionFilter.hh.

Constructor & Destructor Documentation

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

Definition at line 48 of file UpstreamDownstreamCollisionFilter.cc.

protocols::match::output::UpstreamDownstreamCollisionFilter::~UpstreamDownstreamCollisionFilter ( )

virtual

Definition at line 58 of file UpstreamDownstreamCollisionFilter.cc.

Member Function Documentation

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

private

Definition at line 151 of file UpstreamDownstreamCollisionFilter.cc.

Referenced by passes_filter().

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

virtual

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.

Definition at line 113 of file UpstreamDownstreamCollisionFilter.cc.

References dsbuilders_.

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

virtual

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

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

Definition at line 125 of file UpstreamDownstreamCollisionFilter.cc.

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

Definition at line 200 of file UpstreamDownstreamCollisionFilter.cc.

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

Definition at line 109 of file UpstreamDownstreamCollisionFilter.hh.

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

Definition at line 184 of file UpstreamDownstreamCollisionFilter.cc.

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 ( 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.

Definition at line 94 of file UpstreamDownstreamCollisionFilter.cc.

References us_ds_chemical_bond_.

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

Definition at line 101 of file UpstreamDownstreamCollisionFilter.cc.

References dsbuilders_.

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose ( core::pose::Pose const & downstream_pose)

Definition at line 62 of file UpstreamDownstreamCollisionFilter.cc.

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

void protocols::match::output::UpstreamDownstreamCollisionFilter::set_num_geometric_constraints ( Size n_geomcst)

Definition at line 86 of file UpstreamDownstreamCollisionFilter.cc.

References dsbuilders_, and us_ds_chemical_bond_.

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

virtual

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

Definition at line 136 of file UpstreamDownstreamCollisionFilter.cc.

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

Definition at line 153 of file UpstreamDownstreamCollisionFilter.hh.

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

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

private

Definition at line 154 of file UpstreamDownstreamCollisionFilter.hh.

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

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

mutableprivate

NOT THREADSAFE!

Definition at line 152 of file UpstreamDownstreamCollisionFilter.hh.

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

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

private

Definition at line 147 of file UpstreamDownstreamCollisionFilter.hh.

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

Definition at line 145 of file UpstreamDownstreamCollisionFilter.hh.

Referenced by passes_hardsphere_filter(), and set_tolerated_overlap().

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

private

Definition at line 155 of file UpstreamDownstreamCollisionFilter.hh.

Referenced by passes_hardsphere_filter(), and set_downstream_pose().

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

private

Definition at line 149 of file UpstreamDownstreamCollisionFilter.hh.

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

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation