protocols::match Namespace Reference

Namespaces
	downstream
	output
	upstream

Classes
class	Bool3DGrid
class	BumpGrid
class	Bool3DGridKinemageWriter
class	Hit
class	upstream_hit
class	downstream_hit
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...
class	Matcher
class	MatcherOutputStats
class	MatcherMover
class	MatcherMoverCreator
class	MatcherTask
class	MatchPositionModifier
	base class for objects that modify the match positions based on some criterion More...
class	SecondaryStructureMPM
	removes positions at which the pose does not have the desired secondary structure 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	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	AddAllPositionsMPM
	MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere. 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	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	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
class	MatchCounter
	Class for counting the number of matches given a particular discretization level. More...
struct	match_lite_equals
struct	match_lite_hasher
class	MatchOutputTracker
class	OccupiedSpaceHash
	This class keeps track of the active voxels "up until now" with 64 hashes. More...
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 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 basic::Tracer	TR ("protocols.match.Matcher")
static basic::Tracer	tr ("protocols.match.MatcherMover")
void	set_ligpose_rotamer (core::pose::Pose &ligpose)
static basic::Tracer	TR ("protocols.match.MatcherTask")
static 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

Bool3DGridCOP

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

Bool3DGridOP

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

BumpGridCOP

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

BumpGridOP

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

HitHasherCOP

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

HitHasherOP

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

HitPtrList

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

HitPtrListCOP

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

HitPtrListOP

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

match

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

match_lite

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

MatcherCOP

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

MatcherMoverCOP

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

MatcherMoverOP

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

MatcherOP

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

MatcherTaskCOP

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

MatcherTaskOP

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

MatchPositionModifierCOP

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

MatchPositionModifierOP

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

OccupiedSpaceHashCOP

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

OccupiedSpaceHashOP

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

Real6

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

Size3

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

Size4

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

Enumeration Type Documentation

ProbeRadius

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

advance_euler_angles()

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().

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().

Referenced by protocols::match::HitNeighborFinder::find_next_bin().

bump_grid_to_enclose_pose()

BumpGridOP protocols::match::bump_grid_to_enclose_pose

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_type_index(), 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::size(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

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

bump_grid_to_enclose_residue()

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().

bump_grid_to_enclose_residue_backbone()

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().

create_match_position_modifier()

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().

fake_hit() [1/2]

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().

fake_hit() [2/2]

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 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().

Referenced by protocols::match::output::SameChiBinComboGrouper::assign_group_for_match(), protocols::match::output::SameSequenceGrouper::assign_group_for_match(), protocols::match::Matcher::check_non_upstream_only_hit_incompatibility(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_etable_filter(), protocols::match::output::UpstreamCollisionFilter::passes_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::PDBWriter::record_match(), protocols::match::output::WriteKinemageOutputter::record_match(), protocols::match::Matcher::test_upstream_only_hit_incompatibility(), and protocols::match::output::CloudPDBWriter::write_match_groups().

fill_grid_with_backbone_heavyatom_spheres()

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().

fill_grid_with_residue_heavyatom_spheres()

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().

fill_grid_with_residue_spheres()

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().

full_hit()

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::PDBWriter::record_match(), protocols::match::output::WriteKinemageOutputter::record_match(), protocols::match::Matcher::test_upstream_only_hit_incompatibility(), and protocols::match::output::CloudPDBWriter::write_match_groups().

initialize_atomtype_2_probe_radius_map()

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

(

)

References C_ALA, C_CAR, core::chemical::AtomType::element(), core::chemical::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, TR(), and ZERO.

Referenced by probe_radius_for_atom_type().

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::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), and protocols::match::upstream::BuildSet::set_residue_type().

set_ligpose_rotamer()

void protocols::match::set_ligpose_rotamer

(

core::pose::Pose &

ligpose

)

References core::pack::rotamers::SingleResidueRotamerLibraryFactory::get(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::id::to_string().

Referenced by protocols::match::MatcherMover::process_pose().

TR() [1/3]

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

static

Referenced by protocols::match::Matcher::add_external_geometry_samples_for_constraint(), protocols::match::MatcherTask::append_upstream_resiue_as_defining_active_site(), protocols::match::MatcherTask::define_active_site_from_gridlig_file(), protocols::match::Matcher::estimate_n_matches_for_hit_subsets(), protocols::match::Matcher::finish_hit_generation_for_constraint(), protocols::match::MatcherTask::initialize_active_site_definition_from_command_line(), initialize_atomtype_2_probe_radius_map(), protocols::match::Matcher::initialize_bump_grids(), protocols::match::Matcher::initialize_from_file(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), protocols::match::MatcherTask::initialize_output_options_from_command_line(), protocols::match::Matcher::initialize_scaffold_build_points(), protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input(), protocols::match::Matcher::process_matches(), protocols::match::Matcher::process_matches_all_hit_combos_for_hit_subsets(), protocols::match::Matcher::process_matches_main_loop_enumerating_all_hit_combos(), protocols::match::Matcher::process_matches_where_one_geomcst_defines_downstream_location(), protocols::match::Matcher::refine_grid_and_subsample_for_hit_subsets(), protocols::match::MatcherTask::remove_downstream_object_from_upstream_pose(), protocols::match::MatcherTask::set_active_site_residue_list_to_preexisting_partial_match(), and protocols::match::Matcher::set_occupied_space_bounding_box().

TR() [2/3]

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

static

tr() [1/2]

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

static

Referenced by 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::MatcherMover::parse_my_tag(), protocols::match::MatcherMover::process_pose(), protocols::match::SecondaryStructureMPM::SecondaryStructureMPM(), protocols::match::MatcherMover::setup_seqpos_from_selectors(), and protocols::match::TaskOperationMPM::TaskOperationMPM().

TR() [3/3]

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

static

tr() [2/2]

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

static