Namespaces
	downstream

	output

	upstream

Classes
class	AddAllPositionsMPM
	MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere. More...

class	BfactorMPM
	removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor More...

class	Bool3DGrid

class	Bool3DGridKinemageWriter

class	BumpGrid

class	downstream_hit

class	Hit

class	HitHasher
	This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width. More...

class	HitNeighborFinder

struct	match_dspos1
	Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position) More...

struct	match_lite_equals

struct	match_lite_hasher

class	MatchCounter
	Class for counting the number of matches given a particular discretization level. More...

class	Matcher

class	MatcherMover

class	MatcherMoverCreator

class	MatcherOutputStats

class	MatcherTask

class	MatchOutputTracker

class	MatchPositionModifier
	base class for objects that modify the match positions based on some criterion More...

class	NumNeighborsMPM
	removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward More...

class	OccupiedSpaceHash
	This class keeps track of the active voxels "up until now" with 64 hashes. More...

class	RemoveNorCTermMPM
	added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching More...

class	SecondaryStructureMPM
	removes positions at which the pose does not have the desired secondary structure More...

class	TaskOperationMPM
	mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position More...

class	upstream_hit

class	VoxelSetIterator
	Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers. More...

Typedefs
typedef utility::pointer::shared_ptr < Bool3DGrid >	Bool3DGridOP

typedef utility::pointer::shared_ptr < Bool3DGrid const >	Bool3DGridCOP

typedef utility::pointer::shared_ptr < BumpGrid >	BumpGridOP

typedef utility::pointer::shared_ptr < BumpGrid const >	BumpGridCOP

typedef numeric::geometry::hashing::Size3	Size3

typedef numeric::geometry::hashing::Size4	Size4

typedef numeric::geometry::hashing::Real6	Real6

typedef utility::vector1< Hit >	match

typedef numeric::kdtree::WrappedPrimitive < std::list< Hit const * > >	HitPtrList

typedef utility::pointer::shared_ptr < HitPtrList >	HitPtrListOP

typedef utility::pointer::shared_ptr < HitPtrList const >	HitPtrListCOP

typedef utility::pointer::shared_ptr < Matcher >	MatcherOP

typedef utility::pointer::shared_ptr < Matcher const >	MatcherCOP

typedef utility::pointer::shared_ptr < MatcherMover >	MatcherMoverOP

typedef utility::pointer::shared_ptr < MatcherMover const >	MatcherMoverCOP

typedef utility::pointer::shared_ptr < MatcherTask >	MatcherTaskOP

typedef utility::pointer::shared_ptr < MatcherTask const >	MatcherTaskCOP

typedef utility::pointer::shared_ptr < MatchPositionModifier >	MatchPositionModifierOP

typedef utility::pointer::shared_ptr < MatchPositionModifier const >	MatchPositionModifierCOP

typedef utility::pointer::shared_ptr < HitHasher >	HitHasherOP

typedef utility::pointer::shared_ptr < HitHasher const >	HitHasherCOP

typedef utility::vector1< Hit const * >	match_lite

typedef utility::pointer::shared_ptr < OccupiedSpaceHash >	OccupiedSpaceHashOP

typedef utility::pointer::shared_ptr < OccupiedSpaceHash const >	OccupiedSpaceHashCOP

Enumerations
enum	ProbeRadius { ZERO = 0, H_ARO, H_ALA, OXY, NIT, C_CAR, C_ALA, SULPH, n_probe_radii = SULPH }

Functions
static thread_local basic::Tracer	TR ("protocols.BumpGrid")

utility::vector1< ProbeRadius >	initialize_atomtype_2_probe_radius_map ()

ProbeRadius	probe_radius_for_atom_type (core::Size atomtype)

BumpGridOP	bump_grid_to_enclose_pose (core::pose::Pose const &pose)

BumpGridOP	bump_grid_to_enclose_residue_backbone (core::conformation::Residue const &residue, BumpGrid const &original_grid)
	Construct a BumpGrid that encloses the backbone atoms for a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together. More...

BumpGridOP	bump_grid_to_enclose_residue (core::conformation::Residue const &residue, BumpGrid const &original_grid)
	Construct a BumpGrid that encloses a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together. More...

void	fill_grid_with_residue_spheres (core::conformation::Residue const &residue, BumpGrid &grid)

void	fill_grid_with_residue_heavyatom_spheres (core::conformation::Residue const &residue, BumpGrid &grid)

void	fill_grid_with_backbone_heavyatom_spheres (core::conformation::Residue const &residue, BumpGrid &grid)

Hit	fake_hit (upstream_hit const &)
	Create a fake hit from an upstream_hit where hit.first()[4] and hit.second() are 0's. More...

Hit	fake_hit (downstream_hit const &)
	Create a fake hit from a downstream_hit where hit.first()[1-3] are 0's. More...

Hit	full_hit (match_dspos1 const &m)
	Create a hit with the full data from a given match_dspos1 representing the upstream conformation from the originating_geom_cst and its description of the downstream position. More...

static thread_local basic::Tracer	TR ("protocols.match.Matcher")

static thread_local basic::Tracer	tr ("protocols.match.MatcherMover")

static thread_local basic::Tracer	TR ("protocols.match.MatcherTask")

static thread_local basic::Tracer	tr ("protocols.match.MatchPositionModifiers")

MatchPositionModifierCOP	create_match_position_modifier (std::string const mpm_name, core::Size geom_cst, utility::vector1< std::string > const &input_tokens)
	"factory" function to create the match position modifiers More...

core::Size	advance_to_neighbor_bin (Real6 orig_point, Real6 steps, numeric::geometry::hashing::SixDCoordinateBinner const &binner, numeric::geometry::hashing::Bin6D &next_bin)
	Non-member function that handles the logic for finding a nearby bin in 6D when taking a step of a specified size from an existing bin. More...

numeric::geometry::hashing::Real3	advance_euler_angles (numeric::geometry::hashing::Real3 const &orig_angles, numeric::geometry::hashing::Real3 const &offsets)
	Increment the euler angles and then wrap them into their appropriate ranges. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< Bool3DGrid const > protocols::match::Bool3DGridCOP

typedef utility::pointer::shared_ptr< Bool3DGrid > protocols::match::Bool3DGridOP

typedef utility::pointer::shared_ptr< BumpGrid const > protocols::match::BumpGridCOP

typedef utility::pointer::shared_ptr< BumpGrid > protocols::match::BumpGridOP

typedef utility::pointer::shared_ptr< HitHasher const > protocols::match::HitHasherCOP

typedef utility::pointer::shared_ptr< HitHasher > protocols::match::HitHasherOP

typedef numeric::kdtree::WrappedPrimitive< std::list< Hit const * > > protocols::match::HitPtrList

typedef utility::pointer::shared_ptr< HitPtrList const > protocols::match::HitPtrListCOP

typedef utility::pointer::shared_ptr< HitPtrList > protocols::match::HitPtrListOP

typedef utility::vector1< Hit > protocols::match::match

typedef utility::vector1< Hit const * > protocols::match::match_lite

typedef utility::pointer::shared_ptr< Matcher const > protocols::match::MatcherCOP

typedef utility::pointer::shared_ptr< MatcherMover const > protocols::match::MatcherMoverCOP

typedef utility::pointer::shared_ptr< MatcherMover > protocols::match::MatcherMoverOP

typedef utility::pointer::shared_ptr< Matcher > protocols::match::MatcherOP

typedef utility::pointer::shared_ptr< MatcherTask const > protocols::match::MatcherTaskCOP

typedef utility::pointer::shared_ptr< MatcherTask > protocols::match::MatcherTaskOP

typedef utility::pointer::shared_ptr< MatchPositionModifier const > protocols::match::MatchPositionModifierCOP

typedef utility::pointer::shared_ptr< MatchPositionModifier > protocols::match::MatchPositionModifierOP

typedef utility::pointer::shared_ptr< OccupiedSpaceHash const > protocols::match::OccupiedSpaceHashCOP

typedef utility::pointer::shared_ptr< OccupiedSpaceHash > protocols::match::OccupiedSpaceHashOP

typedef numeric::geometry::hashing::Real6 protocols::match::Real6

typedef numeric::geometry::hashing::Size3 protocols::match::Size3

typedef numeric::geometry::hashing::Size4 protocols::match::Size4

Enumeration Type Documentation

enum protocols::match::ProbeRadius

The different radii types used in collision detection. These values are taken from Probe / Reduce from the Richardson lab. Code inside BumpGrid.cc assumes the radii listed here being in non-decreasing order, and that ZERO is the 0th element of this enumeration.

Enumerator
ZERO
H_ARO
H_ALA
OXY
NIT
C_CAR
C_ALA
SULPH
n_probe_radii

Function Documentation

numeric::geometry::hashing::Real3 protocols::match::advance_euler_angles	(	numeric::geometry::hashing::Real3 const &	orig_angles,
		numeric::geometry::hashing::Real3 const &	offsets
	)

Increment the euler angles and then wrap them into their appropriate ranges.

"Advance" the euler angles by a given offset (postive or negative), and wrap them back into their appropriate ranges ([0,360) for phi/psi, [0..180] for theta) as necessary. Requirements: orig_angles[ i ] + offsets[ i ] < 520 (360) && > -360 (-180) for phi/psi (theta).

Referenced by advance_to_neighbor_bin().

core::Size protocols::match::advance_to_neighbor_bin	(	Real6	orig_point,
		Real6	steps,
		numeric::geometry::hashing::SixDCoordinateBinner const &	binner,
		numeric::geometry::hashing::Bin6D &	next_bin
	)

Non-member function that handles the logic for finding a nearby bin in 6D when taking a step of a specified size from an existing bin.

References advance_euler_angles(), numeric::geometry::hashing::SixDCoordinateBinner::bin6(), numeric::geometry::hashing::SixDCoordinateBinner::bounding_box(), numeric::geometry::BoundingBox< class >::lower(), and numeric::geometry::BoundingBox< class >::upper().

Referenced by protocols::match::MatchCounter::count_n_matches(), and protocols::match::HitNeighborFinder::find_next_bin().

BumpGridOP protocols::match::bump_grid_to_enclose_pose ( core::pose::Pose const & pose )

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom(), core::chemical::Atom::atom_type_index(), numeric::xyzVector< class >::max(), core::conformation::Residue::natoms(), protocols::match::BumpGrid::probe_radius(), probe_radius_for_atom_type(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by protocols::match::Matcher::initialize_bump_grids(), and protocols::match::Matcher::set_bump_tolerance().

BumpGridOP protocols::match::bump_grid_to_enclose_residue	(	core::conformation::Residue const &	residue,
		BumpGrid const &	original_grid
	)

Construct a BumpGrid that encloses a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together.

References core::conformation::Residue::atom(), protocols::match::BumpGrid::create_new_bump_grid_for_bb(), core::conformation::Residue::natoms(), protocols::match::BumpGrid::probe_radius(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

BumpGridOP protocols::match::bump_grid_to_enclose_residue_backbone	(	core::conformation::Residue const &	residue,
		BumpGrid const &	original_grid
	)

Construct a BumpGrid that encloses the backbone atoms for a single residue. Use the original_grid as a starting point, copying over all pertinent data such that the two grids can later be merged together.

References core::conformation::Residue::atom(), protocols::match::BumpGrid::create_new_bump_grid_for_bb(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::natoms(), protocols::match::BumpGrid::probe_radius(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by protocols::match::Matcher::initialize_bump_grids().

MatchPositionModifierCOP protocols::match::create_match_position_modifier	(	std::string const	mpm_name,
		core::Size	geom_cst,
		utility::vector1< std::string > const &	input_tokens
	)

"factory" function to create the match position modifiers

Referenced by protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input().

Hit protocols::match::fake_hit ( upstream_hit const & uhit )

Create a fake hit from an upstream_hit where hit.first()[4] and hit.second() are 0's.

References utility::fixedsizearray1< T, S >::begin(), utility::fixedsizearray1< T, S >::end(), protocols::match::upstream_hit::external_geom_id(), protocols::match::Hit::first(), protocols::match::upstream_hit::scaffold_build_id(), protocols::match::Hit::second(), and protocols::match::upstream_hit::upstream_conf_id().

Hit protocols::match::fake_hit ( downstream_hit const & dhit )

Create a fake hit from a downstream_hit where hit.first()[1-3] are 0's.

References protocols::match::downstream_hit::downstream_conf_id(), protocols::match::Hit::first(), protocols::match::Hit::second(), and protocols::match::downstream_hit::second().

void protocols::match::fill_grid_with_backbone_heavyatom_spheres	(	core::conformation::Residue const &	residue,
		BumpGrid &	grid
	)

References core::conformation::Residue::atom(), core::conformation::Residue::last_backbone_atom(), protocols::match::BumpGrid::or_by_sphere(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by protocols::match::Matcher::initialize_bump_grids().

void protocols::match::fill_grid_with_residue_heavyatom_spheres	(	core::conformation::Residue const &	residue,
		BumpGrid &	grid
	)

References core::conformation::Residue::atom(), core::conformation::Residue::nheavyatoms(), protocols::match::BumpGrid::or_by_sphere(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

void protocols::match::fill_grid_with_residue_spheres	(	core::conformation::Residue const &	residue,
		BumpGrid &	grid
	)

References core::conformation::Residue::atom(), core::conformation::Residue::natoms(), protocols::match::BumpGrid::or_by_sphere(), probe_radius_for_atom_type(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Hit protocols::match::full_hit ( match_dspos1 const & m )

Create a hit with the full data from a given match_dspos1 representing the upstream conformation from the originating_geom_cst and its description of the downstream position.

References protocols::match::match_dspos1::downstream_conf_id, protocols::match::match_dspos1::dspos, protocols::match::Hit::first(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, protocols::match::Hit::second(), and protocols::match::match_dspos1::upstream_hits.

Referenced by protocols::match::output::SameSequenceAndDSPositionGrouper::assign_downstream_position_group_for_match(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_etable_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::WriteKinemageOutputter::record_match(), protocols::match::output::PDBWriter::record_match(), protocols::match::Matcher::test_upstream_only_hit_incompatibility(), and protocols::match::output::CloudPDBWriter::write_match_groups().

utility::vector1< ProbeRadius > protocols::match::initialize_atomtype_2_probe_radius_map ( )

References C_ALA, C_CAR, core::chemical::AtomType::element(), FA_STANDARD, H_ALA, H_ARO, core::chemical::AtomType::lj_radius(), n_probe_radii, core::chemical::AtomType::name(), NIT, OXY, protocols::match::BumpGrid::probe_radius(), SULPH, and ZERO.

Referenced by probe_radius_for_atom_type().

ProbeRadius protocols::match::probe_radius_for_atom_type ( core::Size atomtype )

References initialize_atomtype_2_probe_radius_map().

Referenced by protocols::match::downstream::DownstreamAlgorithm::are_colliding(), bump_grid_to_enclose_pose(), bump_grid_to_enclose_residue(), bump_grid_to_enclose_residue_backbone(), fill_grid_with_backbone_heavyatom_spheres(), fill_grid_with_residue_heavyatom_spheres(), fill_grid_with_residue_spheres(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::LigandConformerBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), and protocols::match::upstream::BuildSet::set_residue_type().

static thread_local basic::Tracer protocols::match::TR ( "protocols.BumpGrid" )

static

static thread_local basic::Tracer protocols::match::tr ( "protocols.match.MatcherMover" )

static

Referenced by protocols::match::MatcherMover::apply(), protocols::match::BfactorMPM::BfactorMPM(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::match::BfactorMPM::modified_match_positions(), protocols::match::NumNeighborsMPM::NumNeighborsMPM(), protocols::match::SecondaryStructureMPM::SecondaryStructureMPM(), and protocols::match::TaskOperationMPM::TaskOperationMPM().

static thread_local basic::Tracer protocols::match::tr ( "protocols.match.MatchPositionModifiers" )

static

static thread_local basic::Tracer protocols::match::TR ( "protocols.match.MatcherTask" )

static

static thread_local basic::Tracer protocols::match::TR ( "protocols.match.Matcher" )

static

Namespaces

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation