#include <Matcher.hh>

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef core::Vector	Vector

typedef numeric::geometry::BoundingBox < Vector >	BoundingBox

typedef std::list< Hit >	HitList

typedef std::list< Hit >::iterator	HitListIterator

typedef std::list< Hit > ::const_iterator	HitListConstIterator

Public Member Functions
	Matcher ()
	Construction and Destruction. More...

virtual	~Matcher ()

void	set_upstream_pose (core::pose::Pose const &pose)
	Setup. More...

void	set_downstream_pose (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > orientation_atoms)

void	set_original_scaffold_build_points (utility::vector1< Size > const &resids)

void	set_original_scaffold_build_points_for_constraint (Size cst_id, utility::vector1< Size > const &resids)

void	set_n_geometric_constraints (Size n_constraints)

Size	n_geometric_constraints () const

void	add_upstream_restype_for_constraint (Size cst_id, core::chemical::ResidueTypeCOP restype)

void	desymmeterize_upstream_restype_for_constraint (Size cst_id)

void	set_sample_startegy_for_constraint (Size cst_id, core::chemical::ResidueTypeCOP restype, Size chi, upstream::SampleStrategyData const &strat)

void	set_fa_dun_cutoff_for_constraint (Size cst_id, core::chemical::ResidueTypeCOP restype, core::Real fa_dun_cutoff)

void	add_external_geometry_samples_for_constraint (Size cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, toolbox::match_enzdes_util::ExternalGeomSampler const &exgeom, Size const exgeom_id, bool enumerate_ligand_rotamers=false, bool catalytic_bond=false, bool build_round1_hits_twice=false)

void	add_secondary_upstream_match_geometry_for_constraint (Size geom_cst_id, Size target_geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype, utility::vector1< Size > const &candidate_atids, utility::vector1< Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose)

void	add_secondary_downstream_match_geometry_for_constraint (Size geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP downstream_restype, utility::vector1< Size > const &candidate_atids, utility::vector1< Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose, bool catalytic_bond)

void	set_occupied_space_bounding_box (BoundingBox const &bb)

void	set_hash_euclidean_bin_width (Real width)

void	set_hash_euler_bin_width (Real width)

void	set_hash_euclidean_bin_widths (Vector widths)

void	set_hash_euler_bin_widths (Vector widths)

void	set_bump_tolerance (Real permitted_overlap)

void	initialize_from_task (MatcherTask const &task)
	The primary way to initialize a Matcher is through a MatcherTask. More...

void	initialize_from_file (toolbox::match_enzdes_util::EnzConstraintIO const &enz_data, MatcherTask const &task)
	Intialize the geometric constraints from the EnzConstraionIO object. More...

bool	find_hits ()
	Main worker function. More...

void	process_matches (output::MatchProcessor &processor) const
	After find_hits completes, use this function to have the Matcher enerate the hit-combinations (matches) and send those matches to the specified match-processor. The match processor may do what it pleases with the matches. More...

core::pose::PoseCOP	upstream_pose () const
	Data accessors. More...

core::pose::PoseCOP	downstream_pose () const

upstream::ScaffoldBuildPointCOP	build_point (Size index) const

upstream::UpstreamBuilderCOP	upstream_builder (Size cst_id) const

utility::vector1< Size > const &	get_pose_build_resids () const

downstream::DownstreamBuilderCOP	downstream_builder (Size cst_id) const
	Return const access to a representative downstream builder for a particular geometric constraint. All downstream builders for a single geometric constraint are required to behave the same when reconstructing the coordinates of the downstream partner from a hit; therefore, a single representative is sufficient to recover hit coordinates for any hit from a particular geometric constraint. More...

std::list < downstream::DownstreamAlgorithmCOP >	downstream_algorithms (Size cst_id) const

downstream::DownstreamAlgorithmCOP	representative_downstream_algorithm (Size cst_id) const

HitList const &	hits (Size cst_id) const

OccupiedSpaceHashCOP	occ_space_hash () const

utility::vector1 < upstream::ScaffoldBuildPointCOP > const &	per_constraint_build_points (Size cst_id) const

upstream::ScaffoldBuildPointOP	build_point (Size index)
	Non-const access. More...

upstream::UpstreamBuilderOP	upstream_builder (Size cst_id)

bool	has_upstream_only_geomcsts () const

downstream::DownstreamBuilderOP	downstream_builder (Size)
	Return non-const access to a representative downstream builder for a particular geometric constraint. More...

std::list < downstream::DownstreamBuilderOP > const &	downstream_builders (Size cst_id) const
	Return non-const access to all of the downstream builders for a particular geometric constraint. More...

std::list < downstream::DownstreamAlgorithmOP > const &	nonconst_downstream_algorithms (Size cst_id)
	Non-const access to the set of downstream algorithms for a particular geometric constraint – note that the list containing these algorithms is itself const. More...

OccupiedSpaceHashOP	occ_space_hash ()

HitListIterator	hit_list_begin (Size geom_cst_id)
	Return a non-constant iterator to a HitList for a particular geometric constraint. DANGER DANGER DANGER. This access is intended to allow a DownstreamAlgorithm to delete its own non-viable hits and also to allow a DownstreamAlgorithm to delete another algorithm's non-viable hits; Actual deletion requires invoking the method Matcher::erase_hit(). This non-const access is not intended for any other class. More...

HitListIterator	hit_list_end (Size geom_cst_id)
	Return a non-constant iterator to the end position for a HitList for a particular geometric constraint. See comments for hit_list_begin() More...

void	erase_hit (downstream::DownstreamAlgorithm const &dsalg, Size geom_cst_id_for_hit, HitListIterator const &iter)
	To be invoked by a downstream algorithm. Downstream algorithms may prune their old, inviable hits, through this method – they should pass themselves in as an argument – and they may also prune this hits for other rounds. If the should prune other-round hits, then they will trigger an update to the hit_lists_with_primary_modificiations_ list, leading to an additional pass over the geometric constraints in a primary/peripheral pattern. More...

Private Member Functions
bool	generate_hits ()

void	prepare_for_hit_generation_for_constraint (Size cst_id)

void	generate_hits_for_constraint (Size cst_id)

void	regenerate_round1_hits ()

bool	finish_hit_generation_for_constraint (Size cst_id)

bool	initialize_scaffold_build_points ()

void	initialize_bump_grids ()

void	initialize_active_site_grid ()

void	initialize_occupied_space_hash ()

void	initialize_downstream_algorithms ()

downstream::DownstreamBuilderOP	create_ds_builder (Size const cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, bool enumerate_ligand_rotamers, bool catalytic_bond)

void	select_hit_representatives (utility::vector1< utility::vector1< Hit const * > > const &hit_vectors, utility::vector1< Size > &n_hits_per_geomcst, utility::vector1< utility::vector1< Size > > &reps) const
	Selects a subset of all possible hit combinations (e.g. by clustering hits) for a particular bin. Useful if there are too many matches found. More...

bool	check_non_upstream_only_hit_incompatibility (match_dspos1 const &m1, utility::LexicographicalIterator &lex, output::MatchProcessor const &processor) const
	Returns false if all non-upstream-only hits are compatible. Returns true if any non-upstream-only hits are incompatible, and increments the lexicographical iterator at the most-significant dimension possible. More...

bool	check_downstream_hit_incompatibility (match const &m, utility::LexicographicalIterator &lex) const
	very similar to above function, the difference being that in checks whether all the downstream builders agree that their hits are compatible with each other flo sep'13 there was a problem with this in that for secondary downstream matching the mather doesn't have downstream builders i.e., compatibility can't be checked. bugfix is to also as the downstream algorithm for its dsbuilder another potential fix could be to set the dsbuilders in the matcher itself when the algorithms are created, but i'm not sure if this would interfere with other things? More...

bool	test_upstream_only_hit_incompatibility (match const &m, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const

bool	test_upstream_only_hit_incompatibility (match_dspos1 const &m1, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const

bool	increment_upstream_only_hit_combination (utility::vector1< HitPtrListCOP > const &upstream_only_hits, Size starting_point, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced) const

void	process_matches_main_loop_enumerating_all_hit_combos (output::MatchProcessor &processor) const

utility::vector1< std::list < Hit const * > >	refine_grid_and_subsample_for_hit_subsets (Vector &good_euclidean_bin_widths, Vector &good_euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const

utility::vector1< std::list < Hit const * > >	subsample_hits (Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const

Size	predict_n_matches_for_hit_subsets (Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits, Size accuracy_threshold) const

MatcherOutputStats	process_matches_all_hit_combos_for_hit_subsets (output::MatchProcessor &processor, HitHasher &hit_hasher, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const

void	process_matches_where_one_geomcst_defines_downstream_location (output::MatchProcessor &processor) const

void	note_primary_change_to_geom_csts_hitlist (Size geom_cst_id)
	Note that a change has occurred for a particular hit list. More...

	Matcher (Matcher const &)
	uncopyable – unimplemented More...

Matcher const &	operator= (Matcher const &rhs)

Private Attributes
core::pose::PoseOP	upstream_pose_

core::pose::PoseOP	downstream_pose_

utility::vector1 < core::id::AtomID >	downstream_orientation_atoms_

bool	same_build_resids_for_all_csts_

utility::vector1< Size >	pose_build_resids_

utility::vector1 < utility::vector1< Size > >	per_cst_build_resids_

utility::vector1 < upstream::ScaffoldBuildPointOP >	all_build_points_

utility::vector1 < utility::vector1 < upstream::ScaffoldBuildPointCOP > >	per_constraint_build_points_

Size	n_geometric_constraints_

utility::vector1< HitList >	hits_

utility::vector1 < upstream::UpstreamBuilderOP >	upstream_builders_

utility::vector1< std::map < std::string, Size > >	build_set_id_for_restype_

utility::vector1 < downstream::DownstreamAlgorithmOP >	representative_downstream_algorithm_

utility::vector1< std::list < downstream::DownstreamAlgorithmOP > >	downstream_algorithms_

utility::vector1< bool >	geomcst_is_upstream_only_

std::list< Size >	geom_csts_with_primary_hitlist_modificiations_

utility::vector1< bool >	geom_cst_has_primary_modification_

utility::vector1< std::list < downstream::DownstreamBuilderOP > >	downstream_builders_

std::list < downstream::DownstreamBuilderOP >	all_downstream_builders_

std::list < downstream::DownstreamAlgorithmOP >	all_downstream_algorithms_

BumpGridOP	bb_grid_

utility::vector1< BumpGridOP >	original_scaffold_residue_bump_grids_

BoundingBox	occ_space_bounding_box_

Vector	euclidean_bin_widths_

Vector	euler_bin_widths_

OccupiedSpaceHashOP	occ_space_hash_

downstream::ActiveSiteGridOP	active_site_grid_

bool	read_gridlig_file_

std::string	gridlig_fname_

std::list< std::pair< Size, Real > >	upstream_resids_and_radii_defining_active_site_

std::list< core::id::AtomID >	downstream_atoms_required_inside_active_site_

utility::vector1 < core::id::AtomID >	relevant_downstream_atoms_

bool	use_input_sc_

bool	dynamic_grid_refinement_

bool	output_matches_as_singular_downstream_positioning_

bool	check_potential_dsbuilder_incompatibility_

utility::vector1< bool >	output_match_dspos1_for_geomcst_

bool	build_round1_hits_twice_

Detailed Description

Overview: The matcher algorithm was originally concieved of within the domain of enzyme design. The transition state for the desired reqction is contacted by several amino acids each with a particular geometry. The goal of the matcher is to find a set of backbone positions on a given protein-backbone scaffold where those amino acids could be grafted such that they would contact the ligand in the desired geometry.

Consider a case where the transition state is contacted by an asparagine, an aspartate and a histadine. The user designing an enzyme for this transition state knows the geometry that describes the orientation of the transition state with respect to each of these side chains; what they do not know is into what protein and at what positions they should introduce these amino acids. The user will give the matcher a description of the geometry between the amind acids and the transition state. This geometry is in the form of 6 parameters: 3 diherals, 2 angles, and 1 distance (more on these later). Given the coordinates of a particular side chain and the geometry describing the transition state relative to the side chain, the coordinates of the transition state may be computed. In a sense, the transition state may be grown off of the end of a side chain in the desired geoemtry.

(Usually, the user will specify many different possible values for each of the 6 parameters, and the matcher will then consider all combinations of those values. E.g. the ideal distance might be 2.0 A, but the user might ask the matcher to consider the values 1.95 and 2.05 A additionally. Each assignment of values to these 6 parameters fully specifies the coordinates of the transition state.)

The matcher examines each geometric constraint one at a time. It builds rotamers for one or more amino acids capable of satisfying a desired geometry (e.g. both ASP and GLU if an acid group is needed) at each of several active-site positions, and for each rotamer, it grows the transition state. The matcher does a quick collision check between the atoms of the transition state and the backbone of the protein, rejecting transition-state conformations that collide. If the conformation is collision-free, then the matcher measures the coordinates of the transition state as a point in a 6-dimensional space. (It is no coincidence that there are 6 geometric parameters and that there are 6 dimensions in the space describing the transition state's coordinates). With this 6-dimensional coordinate, the matcher can recover the coordinates for the transition state – the 6-D coordinate and the full euclidean coordinates of the transition state are interconvertable. The matcher can also bin the coordinate. If two coordinates in 6-D are close, they will be assigned to the same bin. This is the fundamental insight of the matching algorithm: the matcher will grow the transition state from different catalytic residues, and when the 6-d coordinates from different catalytic residues are assigned to the same bin, then the matcher has found a set of conformations of the transition state that are compatible with more than one catalytic geometry.

Each collision-free placement of the transition state is called a "hit". If there are N geometric-constrains that the matcher is asked to satisfy, then a set of N hits, one per constraint, that fall into the same bin are called a "match".

In the general case, the Matcher builds hits for each of several geometric constraints. The protein scaffold in the enzyme-design example generalizes to any macro-molecular polymer scaffold. The protein rotamers in the enzyme-design example generalizes to a set of conformations for the "upstream" partner. The transition state gene in the enzyme-design example generalizes to a "downstream" partner, which itself may have multiple conformations. "Upstream" and "Downstream" refer to the order in which the coordinates of the two partners are computed. The upstream coordinates are built first, the downstream coordinates second. Changes to the coordinates of the upstream partner propagate to the coordinates of the downstream partner. In the enzyme-design example, the transition state is considered to be rigid; in the general case the transition state may have multiple conformations. The downstream partner could also be an entire protein – and may have it's own set of rotameric states. E.G. one might want to match a hydrogen-bond donor on the scaffold to a serine side-chain on the target (downstream) protein. The downstream partner should then be able to examine many serine rotamers for each conformation of the upstream rotamer.

A hit is represented in two parts: a discrete part and a continuous part. The discrete portion consists of four integers: 1. the build-point index on the scaffold, 2. the rotamer index on the upstream partner,

the external-geometry index, and 4. the rotamer index on the downstream partner. The continuous portion consists of 6 double-precision values representing the coordinate of the downstream partner in 6D. The first three values are the x,y and z coordinates of a particular atom in the downstream partner. The second three values are the phi, psi, and theta values describing the coordinate frame at this atom. These three "Euler angle" parameters describe three rotations: Z(psi) * X(theta) * Z(phi) * I. They are described in greater detail in src/numeric/HomogeneousTransform.hh. "Phi" and "psi" here have nothing to do with the protein-backbone angles. When a hit is binned, there are two sets of parameters that describe how wide the bins in each dimension should be: the Euclidean bin widths are for the xyz coordinates, and the Euler bin widths are for the Euler angles. The Euclidean bin widths are in Angstroms and the Euler bin widths are in degrees.

A Matcher object should be initialized from a MatcherTask object through the intialize_from_task() method. A MatcherTask will contain an EnzConstraintIO object, and the function Matcher::initialize_from_file() will be invoked as the Matcher is intialied from a MatcherTask. The documentation for Matcher::inialize_from_file() describes the format of extra data that may be included in the enzyme-design constraint file. This data should live within a ALGORITHM_INFO:: match ... ALGORITHM::END block inside a CST::BEGIN ... CST::END block in the constraint file.

find_hits() is the main worker function. After the matcher finishes find_hits(), the matches can be read by a MatchProcessor in a call to process_matches.

Member Typedef Documentation

typedef numeric::geometry::BoundingBox< Vector > protocols::match::Matcher::BoundingBox

typedef std::list< Hit > protocols::match::Matcher::HitList

typedef std::list< Hit >::const_iterator protocols::match::Matcher::HitListConstIterator

typedef std::list< Hit >::iterator protocols::match::Matcher::HitListIterator

typedef core::Real protocols::match::Matcher::Real

typedef core::Size protocols::match::Matcher::Size

typedef core::Vector protocols::match::Matcher::Vector

Constructor & Destructor Documentation

protocols::match::Matcher::Matcher ( )

Construction and Destruction.

References relevant_downstream_atoms_.

protocols::match::Matcher::~Matcher ( )

virtual

protocols::match::Matcher::Matcher ( Matcher const & )

private

uncopyable – unimplemented

Member Function Documentation

void protocols::match::Matcher::add_external_geometry_samples_for_constraint	(	Size	cst_id,
		core::chemical::ResidueTypeCOP	restype,
		utility::vector1< std::string > const &	upstream_launch_atoms,
		utility::vector1< core::id::AtomID > const &	downstream_3atoms,
		toolbox::match_enzdes_util::ExternalGeomSampler const &	exgeom,
		Size const	exgeom_id,
		bool	enumerate_ligand_rotamers = `false`,
		bool	catalytic_bond = `false`,
		bool	build_round1_hits_twice = `false`
	)

Referenced by initialize_from_file().

void protocols::match::Matcher::add_secondary_downstream_match_geometry_for_constraint	(	Size	geom_cst_id,
		core::chemical::ResidueTypeCOP	candidate_restype,
		core::chemical::ResidueTypeCOP	downstream_restype,
		utility::vector1< Size > const &	candidate_atids,
		utility::vector1< Size > const &	target_atids,
		toolbox::match_enzdes_util::MatchConstraintFileInfoCOP	mcfi,
		std::string	SecMatchStr,
		core::pose::Pose const &	upstream_pose,
		bool	catalytic_bond
	)

References protocols::match::downstream::SecondaryMatcherToDownstreamResidue::add_evaluator(), all_downstream_algorithms_, build_set_id_for_restype_, downstream_algorithms_, end, representative_downstream_algorithm_, runtime_assert, upstream_builders_, and upstream_pose_.

Referenced by initialize_from_file().

void protocols::match::Matcher::add_secondary_upstream_match_geometry_for_constraint	(	Size	geom_cst_id,
		Size	target_geom_cst_id,
		core::chemical::ResidueTypeCOP	candidate_restype,
		core::chemical::ResidueTypeCOP	target_restype,
		utility::vector1< Size > const &	candidate_atids,
		utility::vector1< Size > const &	target_atids,
		toolbox::match_enzdes_util::MatchConstraintFileInfoCOP	mcfi,
		std::string	sec_match_str,
		core::pose::Pose const &	upstream_pose
	)

Initialize a secondary matcher object based on the geometry from the upstream to the downstream residue types.

References protocols::match::downstream::SecondaryMatcherToUpstreamResidue::add_evaluator_for_target_restype(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::add_target_restype(), all_downstream_algorithms_, build_set_id_for_restype_, downstream_algorithms_, end, representative_downstream_algorithm_, runtime_assert, and upstream_builders_.

Referenced by initialize_from_file().

void protocols::match::Matcher::add_upstream_restype_for_constraint	(	Size	cst_id,
		core::chemical::ResidueTypeCOP	restype
	)

References core::chemical::aa_gly, build_set_id_for_restype_, end, core::chemical::num_canonical_aas, runtime_assert, protocols::match::upstream::BuildSet::set_residue_type(), upstream_builders_, and use_input_sc_.

Referenced by initialize_from_file().

upstream::ScaffoldBuildPointCOP protocols::match::Matcher::build_point ( Size index ) const

References all_build_points_.

Referenced by subsample_hits().

upstream::ScaffoldBuildPointOP protocols::match::Matcher::build_point ( Size index )

Non-const access.

References all_build_points_.

bool protocols::match::Matcher::check_downstream_hit_incompatibility	(	match const &	m,
		utility::LexicographicalIterator &	lex
	)		const

private

very similar to above function, the difference being that in checks whether all the downstream builders agree that their hits are compatible with each other flo sep'13 there was a problem with this in that for secondary downstream matching the mather doesn't have downstream builders i.e., compatibility can't be checked. bugfix is to also as the downstream algorithm for its dsbuilder another potential fix could be to set the dsbuilders in the matcher itself when the algorithms are created, but i'm not sure if this would interfere with other things?

References begin, utility::LexicographicalIterator::continue_at_dimension(), downstream_builders_, geomcst_is_upstream_only_, n_geometric_constraints_, representative_downstream_algorithm_, and size().

Referenced by process_matches_all_hit_combos_for_hit_subsets().

bool protocols::match::Matcher::check_non_upstream_only_hit_incompatibility	(	match_dspos1 const &	m1,
		utility::LexicographicalIterator &	lex,
		output::MatchProcessor const &	processor
	)		const

private

Returns false if all non-upstream-only hits are compatible. Returns true if any non-upstream-only hits are incompatible, and increments the lexicographical iterator at the most-significant dimension possible.

References all_build_points_, utility::LexicographicalIterator::continue_at_dimension(), protocols::match::fake_hit(), geomcst_is_upstream_only_, n_geometric_constraints_, protocols::match::output::MatchProcessor::up_coll_filt(), upstream_builders_, and protocols::match::match_dspos1::upstream_hits.

Referenced by process_matches_all_hit_combos_for_hit_subsets(), and process_matches_where_one_geomcst_defines_downstream_location().

downstream::DownstreamBuilderOP protocols::match::Matcher::create_ds_builder	(	Size const	cst_id,
		core::chemical::ResidueTypeCOP	restype,
		utility::vector1< std::string > const &	upstream_launch_atoms,
		utility::vector1< core::id::AtomID > const &	downstream_3atoms,
		bool	enumerate_ligand_rotamers,
		bool	catalytic_bond
	)

private

References all_downstream_builders_, core::chemical::ResidueType::atom_index(), build_set_id_for_restype_, downstream_builders_, downstream_orientation_atoms_, downstream_pose_, end, protocols::match::upstream::BuildSet::has_restype(), core::conformation::Residue::natoms(), relevant_downstream_atoms_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::match::upstream::BuildSet::restype(), runtime_assert, core::scoring::etable::count_pair::CountPairGeneric::set_crossover(), core::pose::Pose::total_residue(), and upstream_builders_.

Referenced by add_external_geometry_samples_for_constraint().

void protocols::match::Matcher::desymmeterize_upstream_restype_for_constraint ( Size cst_id )

References utility::to_string(), upstream_builders_, and utility_exit_with_message.

Referenced by initialize_from_file().

std::list< downstream::DownstreamAlgorithmCOP > protocols::match::Matcher::downstream_algorithms ( Size cst_id ) const

References begin, downstream_algorithms_, and end.

downstream::DownstreamBuilderCOP protocols::match::Matcher::downstream_builder ( Size cst_id ) const

Return const access to a representative downstream builder for a particular geometric constraint. All downstream builders for a single geometric constraint are required to behave the same when reconstructing the coordinates of the downstream partner from a hit; therefore, a single representative is sufficient to recover hit coordinates for any hit from a particular geometric constraint.

References downstream_builders_, and empty.

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_for_geomcst().

downstream::DownstreamBuilderOP protocols::match::Matcher::downstream_builder ( Size cst_id )

Return non-const access to a representative downstream builder for a particular geometric constraint.

References downstream_builders_, empty, and runtime_assert.

std::list< downstream::DownstreamBuilderOP > const & protocols::match::Matcher::downstream_builders ( Size cst_id ) const

Return non-const access to all of the downstream builders for a particular geometric constraint.

References downstream_builders_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::build_hits_at_all_positions().

core::pose::PoseCOP protocols::match::Matcher::downstream_pose ( ) const

References downstream_pose_.

void protocols::match::Matcher::erase_hit	(	downstream::DownstreamAlgorithm const &	dsalg,
		Size	geom_cst_id_for_hit,
		HitListIterator const &	iter
	)

To be invoked by a downstream algorithm. Downstream algorithms may prune their old, inviable hits, through this method – they should pass themselves in as an argument – and they may also prune this hits for other rounds. If the should prune other-round hits, then they will trigger an update to the hit_lists_with_primary_modificiations_ list, leading to an additional pass over the geometric constraints in a primary/peripheral pattern.

References protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), hits_, note_primary_change_to_geom_csts_hitlist(), and runtime_assert.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_peripheral_hitlist_change(), and protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_primary_hitlist_change().

bool protocols::match::Matcher::find_hits ( )

Main worker function.

References generate_hits(), initialize_active_site_grid(), initialize_bump_grids(), initialize_downstream_algorithms(), initialize_occupied_space_hash(), and initialize_scaffold_build_points().

bool protocols::match::Matcher::finish_hit_generation_for_constraint ( Size cst_id )

private

References all_downstream_builders_, build_round1_hits_twice_, geom_cst_has_primary_modification_, geom_csts_with_primary_hitlist_modificiations_, hits_, n_geometric_constraints_, occ_space_hash_, regenerate_round1_hits(), representative_downstream_algorithm_, size(), and protocols::match::TR.

Referenced by generate_hits().

bool protocols::match::Matcher::generate_hits ( )

private

References finish_hit_generation_for_constraint(), generate_hits_for_constraint(), n_geometric_constraints_, and prepare_for_hit_generation_for_constraint().

Referenced by find_hits().

void protocols::match::Matcher::generate_hits_for_constraint ( Size cst_id )

private

References end, hits(), hits_, note_primary_change_to_geom_csts_hitlist(), and representative_downstream_algorithm_.

Referenced by generate_hits().

utility::vector1< core::Size > const & protocols::match::Matcher::get_pose_build_resids ( ) const

References pose_build_resids_.

Referenced by protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation().

bool protocols::match::Matcher::has_upstream_only_geomcsts ( ) const

References geomcst_is_upstream_only_, and n_geometric_constraints_.

Matcher::HitListIterator protocols::match::Matcher::hit_list_begin ( Size geom_cst_id )

Return a non-constant iterator to a HitList for a particular geometric constraint. DANGER DANGER DANGER. This access is intended to allow a DownstreamAlgorithm to delete its own non-viable hits and also to allow a DownstreamAlgorithm to delete another algorithm's non-viable hits; Actual deletion requires invoking the method Matcher::erase_hit(). This non-const access is not intended for any other class.

References hits_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_peripheral_hitlist_change(), and protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_primary_hitlist_change().

Matcher::HitListIterator protocols::match::Matcher::hit_list_end ( Size geom_cst_id )

Return a non-constant iterator to the end position for a HitList for a particular geometric constraint. See comments for hit_list_begin()

References hits_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_peripheral_hitlist_change(), and protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_primary_hitlist_change().

Matcher::HitList const & protocols::match::Matcher::hits ( Size cst_id ) const

References hits_.

bool protocols::match::Matcher::increment_upstream_only_hit_combination	(	utility::vector1< HitPtrListCOP > const &	upstream_only_hits,
		Size	starting_point,
		utility::vector1< std::list< Hit const * >::const_iterator > &	upstream_only_hit_iterators,
		Size &	last_upstream_only_geomcst_advanced
	)		const

private

returns true if more upstream-only hit combinations remain, and false if there are no upstream-only hit cominbations remaining

References end, and geomcst_is_upstream_only_.

Referenced by process_matches_all_hit_combos_for_hit_subsets(), and process_matches_where_one_geomcst_defines_downstream_location().

void protocols::match::Matcher::initialize_active_site_grid ( )

private

References active_site_grid_, all_downstream_algorithms_, all_downstream_builders_, downstream_atoms_required_inside_active_site_, gridlig_fname_, read_gridlig_file_, core::pose::Pose::residue(), runtime_assert, core::pose::Pose::total_residue(), upstream_pose_, and upstream_resids_and_radii_defining_active_site_.

Referenced by find_hits().

void protocols::match::Matcher::initialize_bump_grids ( )

private

References all_downstream_algorithms_, all_downstream_builders_, bb_grid_, protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), utility::pointer::owning_ptr< T >::get(), original_scaffold_residue_bump_grids_, core::pose::Pose::residue(), runtime_assert, core::pose::Pose::total_residue(), protocols::match::TR, upstream_builders_, and upstream_pose_.

Referenced by find_hits().

void protocols::match::Matcher::initialize_downstream_algorithms ( )

private

References geomcst_is_upstream_only_, n_geometric_constraints_, and representative_downstream_algorithm_.

Referenced by find_hits().

void protocols::match::Matcher::initialize_from_file	(	toolbox::match_enzdes_util::EnzConstraintIO const &	enz_data,
		MatcherTask const &	mtask
	)

Intialize the geometric constraints from the EnzConstraionIO object.

Inside the CST::BEGIN blocks, The following ALGORITHM_INFO:: match input data may be provided to give additional data to the matcher. Rotamer building instructions for particular geometric constraints may be given. Here is an example of the kinds of geometric data. Each CHI_STRATEGY line is appropriate on it's own, but they are not appropriate together. Lines beginning with "#" are comments describing the meaning of each of the lines.

ALGORITHM_INFO:: match

If your upstream residue includes a proton chi (e.g. SER/THR/TYR) but the geometry

of the downstream partner does not depend on the location of the proton, then

use the following line to avoid enumerating rotamers that differ only in their proton coordinate.

IGNORE_UPSTREAM_PROTON_CHI

Secondary Matching:

You can activate secondary matching, a continuous version of the classic discrete algorithm,

by adding the line

SECONDARY_MATCH: DOWNSTREAM

#or SECONDARY_MATCH: UPSTREAM_CST 2

which instead of building its own hits and hashing them examines the hits generated in

previous rounds for compatibility with the geometry that you're seeking.

When performing secondary matching, it is not required that you specify all 6 degrees

of freedom. If you specify only a subset the geometry of only the subset you've specified

will be examined (e.g. if you don't care about torsion_AB, don't specify it

in the CST::BEGIN/CST::END block.

You can perform secondary matching to the ligand (the downstream target) or to an upstream

residue whose geometry was constructed by an earlier geometric constraint. In the example

above, the geometric constraint pointed to is #2.

The first geometric constraint cannot use secondary matching, it must always use the discrete

classic match algorithm. (A later geometric constraint may of course perform secondary

matching to the hits produced by the first geometric constraint. At that point the first

constraint is playing the same role in upstream matching as the ligand plays in downstream matching)

END Secondary Matching comments.

Below: chi sample strategies – "1" is for chi-1

These are the traditional ex?level options ( ? == 1, 2, 3 or 4 )

CHI_STRATEGY:: CHI 1 EX_ONE_STDDEV CHI_STRATEGY:: CHI 1 EX_ONE_HALF_STEP_STDDEV CHI_STRATEGY:: CHI 1 EX_TWO_FULL_STEP_STDDEVS CHI_STRATEGY:: CHI 1 EX_TWO_HALF_STEP_STDDEVS CHI_STRATEGY:: CHI 1 EX_FOUR_HALF_STEP_STDDEVS CHI_STRATEGY:: CHI 1 EX_THREE_THIRD_STEP_STDDEVS CHI_STRATEGY:: CHI 1 EX_SIX_QUARTER_STEP_STDDEVS

Below: The "AA" field, followed by the 3-letter AA code gives the sub-specification for

a block that contains multiple amino acids. If this block allowed both an ASN and a GLN, then

the first line would apply to GLN rotamers only and the second line to ASN rotamers only.

"AA" fields may be included with

any of the CHI_STRATEGY options listed here.

CHI_STRATEGY:: AA GLN CHI 2 EX_SIX_QUARTER_STEP_STDDEVS CHI_STRATEGY:: AA ASN CHI 2 EX_ONE_STDDEV

Everything below: additional chi sample strategies unique to the matcher.

CHI_STRATEGY:: CHI 1 STEP_WITHIN_SD_RANGE STEP 3.0

the above line says "step by 3 degrees within a single standard deviation</h1> <h1>to the left and right of the mean for chi 1"

CHI_STRATEGY:: CHI 1 STEP_WITHIN_SD_RANGE STEP 3.0 SD_RANGE 2.5

the above line says "step by 3 degrees within 2.5 standard deviations to</h1> <h1>the left and the right of the mean for chi 1"

CHI_STRATEGY:: CHI 2 AA HIS NON_ROTAMERIC_CHI_EXPANSION N_SAMPLES 3 REQUISIT_PROBABILITY 0.10

the line above says that "for histidine chi 2 (which is non-rotameric in the 2010 Dunbrak library)

take 3 extra samples to the left and right of the median chi value inside the non-rotameric chi well

for rotamer wells that have a probability at least 0.1". The 2010 Dunbrack library must be active.

(the -dun10 flag should be on the command line).

CHI_STRATEGY:: CHI 2 AA HIS NON_ROTAMERIC_CHI_EXPANSION N_SAMPLES 3

the line above is similar for the previous command, but leaves off the REQUISIT_PROBABILITY

which sets a default REQUISIT_PROBABILITY of 2 / #chi-bins. For HIS, this is

2 / 36th, since there are 12 bins for chi 2 and 3 bins for chi1 (36 chi bins total).

#or DESYMMETERIZE

the line above instructs the DunbrackSCSampler to expand the sampling for the symmetric amino acids

around the final (symmetric) chi angle for ASP/GLU/PHE/TYR. For example, it would treat ASP's sampling

as if there's a difference between OD1 and OD2.

ALGORITHM_INFO::END

References core::chemical::aa_from_name(), add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), add_upstream_restype_for_constraint(), utility::LexicographicalIterator::at_end(), protocols::match::MatcherTask::build_round1_hits_twice(), cutoff, desymmeterize_upstream_restype_for_constraint(), downstream_pose_, protocols::match::MatcherTask::enumerate_ligand_rotamers(), utility::pointer::access_ptr< T >::get(), utility::pointer::owning_ptr< T >::get(), core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::task::is_rot_sample_name(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_list(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_size(), n_geometric_constraints_, nn, protocols::match::upstream::no_samples, protocols::match::upstream::nonrotameric_chi_sample_wi_nrchi_bin, protocols::sic_dock::range(), core::pack::task::rot_sample_from_name(), protocols::match::upstream::rotameric_chi_mimic_EX_flags, protocols::match::upstream::rotameric_chi_step_wi_sd_range, runtime_assert, set_fa_dun_cutoff_for_constraint(), set_n_geometric_constraints(), protocols::match::upstream::SampleStrategyData::set_sample_level(), set_sample_startegy_for_constraint(), protocols::match::upstream::SampleStrategyData::set_sd_range(), protocols::match::upstream::SampleStrategyData::set_step_size(), protocols::match::upstream::SampleStrategyData::set_strategy(), size(), utility::to_string(), protocols::match::TR, upstream_pose_, and utility_exit_with_message.

Referenced by initialize_from_task().

void protocols::match::Matcher::initialize_from_task ( MatcherTask const & task )

The primary way to initialize a Matcher is through a MatcherTask.

void protocols::match::Matcher::initialize_occupied_space_hash ( )

private

References euclidean_bin_widths_, euler_bin_widths_, occ_space_bounding_box_, and occ_space_hash_.

Referenced by find_hits().

bool protocols::match::Matcher::initialize_scaffold_build_points ( )

private

this function returns false in case there are no build points for a certain cst. this can happen if MPMs in the MatcherTask ruled out all user defined build points

References all_build_points_, utility::pointer::owning_ptr< T >::get(), core::pose::Pose::n_residue(), per_cst_build_resids_, pose_build_resids_, core::pose::Pose::residue(), runtime_assert, runtime_assert_msg, same_build_resids_for_all_csts_, size(), protocols::match::TR, and upstream_pose_.

Referenced by find_hits().

Size protocols::match::Matcher::n_geometric_constraints ( ) const

inline

References n_geometric_constraints_.

std::list< downstream::DownstreamAlgorithmOP > const & protocols::match::Matcher::nonconst_downstream_algorithms ( Size cst_id )

Non-const access to the set of downstream algorithms for a particular geometric constraint – note that the list containing these algorithms is itself const.

References downstream_algorithms_.

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation_at_target_build_point(), and protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_for_geomcst().

void protocols::match::Matcher::note_primary_change_to_geom_csts_hitlist ( Size geom_cst_id )

private

Note that a change has occurred for a particular hit list.

References geom_cst_has_primary_modification_, and geom_csts_with_primary_hitlist_modificiations_.

Referenced by erase_hit(), and generate_hits_for_constraint().

OccupiedSpaceHashCOP protocols::match::Matcher::occ_space_hash ( ) const

References occ_space_hash_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::build_and_discard_first_round_hits_at_all_positions(), protocols::match::downstream::ClassicMatchAlgorithm::build_hits_at_all_positions(), protocols::match::downstream::ClassicMatchAlgorithm::respond_to_peripheral_hitlist_change(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_peripheral_hitlist_change(), protocols::match::downstream::ClassicMatchAlgorithm::respond_to_primary_hitlist_change(), and protocols::match::downstream::SecondaryMatcherToDownstreamResidue::respond_to_primary_hitlist_change().

OccupiedSpaceHashOP protocols::match::Matcher::occ_space_hash ( )

References occ_space_hash_.

Matcher const& protocols::match::Matcher::operator= ( Matcher const & rhs )

private

utility::vector1< upstream::ScaffoldBuildPointCOP > const & protocols::match::Matcher::per_constraint_build_points ( Size cst_id ) const

References per_constraint_build_points_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::build_and_discard_first_round_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build_hits_at_all_positions(), and protocols::match::downstream::DownstreamAlgorithm::default_build_hits_at_all_positions().

Matcher::Size protocols::match::Matcher::predict_n_matches_for_hit_subsets	(	Vector const &	euclidean_bin_widths,
		Vector const &	euler_bin_widths,
		utility::vector1< std::list< Hit const * > > const &	neighbor_hits,
		Size	accuracy_threshold
	)		const

private

References protocols::match::MatchCounter::add_hits(), protocols::match::MatchCounter::count_n_matches(), empty, geomcst_is_upstream_only_, protocols::match::MatchCounter::initialize(), n_geometric_constraints_, occ_space_bounding_box_, protocols::match::MatchCounter::set_bounding_box(), protocols::match::MatchCounter::set_euler_bin_widths(), protocols::match::MatchCounter::set_n_geometric_constraints(), protocols::match::MatchCounter::set_xyz_bin_widths(), size(), and protocols::match::TR.

Referenced by refine_grid_and_subsample_for_hit_subsets().

void protocols::match::Matcher::prepare_for_hit_generation_for_constraint ( Size cst_id )

private

Update the per_constraint_build_points_ array for the given constraint before beginning hit generation. This follows one of two paths depending on whether same_build_resids_for_all_csts_ is active or not. I cannot see any reason that this function could not be called earlier than immediately before hit generation for a particular constraint.

References all_build_points_, per_constraint_build_points_, per_cst_build_resids_, pose_build_resids_, same_build_resids_for_all_csts_, and size().

Referenced by generate_hits().

void protocols::match::Matcher::process_matches ( output::MatchProcessor & processor ) const

After find_hits completes, use this function to have the Matcher enerate the hit-combinations (matches) and send those matches to the specified match-processor. The match processor may do what it pleases with the matches.

References all_downstream_builders_, protocols::match::output::MatchProcessor::begin_processing(), check_potential_dsbuilder_incompatibility_, protocols::match::output::MatchProcessor::end_processing(), n_geometric_constraints_, output_matches_as_singular_downstream_positioning_, process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), representative_downstream_algorithm_, and protocols::match::TR.

MatcherOutputStats protocols::match::Matcher::process_matches_all_hit_combos_for_hit_subsets	(	output::MatchProcessor &	processor,
		HitHasher &	hit_hasher,
		utility::vector1< std::list< Hit const * > > const &	neighbor_hits
	)		const

private

This loop iterates across all 64 origin definitions (loop "ii"), inserts the "neighbor hits" into each of the hashes. It then iterates across all the bins in the hash map (loop "iter"), and then enumerates all combinations of hits (loop "lex") for the non-upstream-only geometric constraints. For each combination of hits (a partial match if there are any upstream-only geometric constraints), it then retrieves all upstream-only hits, and iterates across all cominbations of upstream-only hits for this match (loop "true"). Then, for every fully-constructed match,

Referenced by process_matches_main_loop_enumerating_all_hit_combos().

void protocols::match::Matcher::process_matches_main_loop_enumerating_all_hit_combos ( output::MatchProcessor & processor ) const

private

This needs a major refactoring.

Referenced by process_matches().

void protocols::match::Matcher::process_matches_where_one_geomcst_defines_downstream_location ( output::MatchProcessor & processor ) const

private

Referenced by process_matches().

utility::vector1< std::list< Hit const * > > protocols::match::Matcher::refine_grid_and_subsample_for_hit_subsets	(	Vector &	good_euclidean_bin_widths,
		Vector &	good_euler_bin_widths,
		utility::vector1< std::list< Hit const * > > const &	neighbor_hits
	)		const

private

References euclidean_bin_widths_, euler_bin_widths_, predict_n_matches_for_hit_subsets(), subsample_hits(), and protocols::match::TR.

Referenced by process_matches_main_loop_enumerating_all_hit_combos().

void protocols::match::Matcher::regenerate_round1_hits ( )

private

just like generate_hits_for_constraint, but without calling not_primary_change_to_geom_csts_hitlist. Used with the "build round-1 hits twice" scheme.

References end, hits(), hits_, and representative_downstream_algorithm_.

Referenced by finish_hit_generation_for_constraint().

downstream::DownstreamAlgorithmCOP protocols::match::Matcher::representative_downstream_algorithm ( Size cst_id ) const

References representative_downstream_algorithm_.

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build_hits_at_all_positions().

void protocols::match::Matcher::select_hit_representatives	(	utility::vector1< utility::vector1< Hit const * > > const &	hit_vectors,
		utility::vector1< Size > &	n_hits_per_geomcst,
		utility::vector1< utility::vector1< Size > > &	reps
	)		const

private

Selects a subset of all possible hit combinations (e.g. by clustering hits) for a particular bin. Useful if there are too many matches found.

Subsample all the available hits for a single voxel in 6D to select 10 or fewer hits for each geometric constraint. If there are already 10 or fewer hits for geom-cst ii, then it takes them all. Otherwise, it selects 10 representatives for each upstream conformation. For example, if all the hits in this voxel come from a single rotamer of the upsteram hit, then exactly 10 upstream hits will be chosen. The purpose of this code is to speed up match enumeration when it might otherwise get very bogged down by the combinatorics

References dynamic_grid_refinement_, and n_geometric_constraints_.

Referenced by process_matches_all_hit_combos_for_hit_subsets().

void protocols::match::Matcher::set_bump_tolerance ( Real permitted_overlap )

References bb_grid_, protocols::match::bump_grid_to_enclose_pose(), utility::pointer::owning_ptr< T >::get(), runtime_assert, and upstream_pose_.

Referenced by initialize_from_task().

void protocols::match::Matcher::set_downstream_pose	(	core::pose::Pose const &	pose,
		utility::vector1< core::id::AtomID >	orientation_atoms
	)

References downstream_orientation_atoms_, downstream_pose_, and runtime_assert.

Referenced by initialize_from_task().

void protocols::match::Matcher::set_fa_dun_cutoff_for_constraint	(	Size	cst_id,
		core::chemical::ResidueTypeCOP	restype,
		core::Real	fa_dun_cutoff
	)

References build_set_id_for_restype_, end, protocols::match::upstream::BuildSet::set_fa_dun_cutoff(), and upstream_builders_.

Referenced by initialize_from_file().

void protocols::match::Matcher::set_hash_euclidean_bin_width ( Real width )

References euclidean_bin_widths_.

void protocols::match::Matcher::set_hash_euclidean_bin_widths ( Vector widths )

References euclidean_bin_widths_.

Referenced by initialize_from_task().

void protocols::match::Matcher::set_hash_euler_bin_width ( Real width )

References euler_bin_widths_.

void protocols::match::Matcher::set_hash_euler_bin_widths ( Vector widths )

References euler_bin_widths_.

Referenced by initialize_from_task().

void protocols::match::Matcher::set_n_geometric_constraints ( Size n_constraints )

References build_set_id_for_restype_, downstream_algorithms_, downstream_builders_, geom_cst_has_primary_modification_, geomcst_is_upstream_only_, hits_, n_geometric_constraints_, per_constraint_build_points_, representative_downstream_algorithm_, and upstream_builders_.

Referenced by initialize_from_file().

void protocols::match::Matcher::set_occupied_space_bounding_box ( BoundingBox const & bb )

References numeric::geometry::BoundingBox< class >::lower(), occ_space_bounding_box_, protocols::match::TR, and numeric::geometry::BoundingBox< class >::upper().

Referenced by initialize_from_task().

void protocols::match::Matcher::set_original_scaffold_build_points ( utility::vector1< Size > const & resids )

References per_cst_build_resids_, pose_build_resids_, and same_build_resids_for_all_csts_.

void protocols::match::Matcher::set_original_scaffold_build_points_for_constraint	(	Size	cst_id,
		utility::vector1< Size > const &	resids
	)

References begin, end, n_geometric_constraints_, per_cst_build_resids_, pose_build_resids_, runtime_assert, and same_build_resids_for_all_csts_.

Referenced by initialize_from_task().

void protocols::match::Matcher::set_sample_startegy_for_constraint	(	Size	cst_id,
		core::chemical::ResidueTypeCOP	restype,
		Size	chi,
		upstream::SampleStrategyData const &	strat
	)

References build_set_id_for_restype_, end, runtime_assert, protocols::match::upstream::BuildSet::set_sample_strategy_for_chi(), and upstream_builders_.

Referenced by initialize_from_file().

void protocols::match::Matcher::set_upstream_pose ( core::pose::Pose const & pose )

Setup.

References upstream_pose_.

Referenced by initialize_from_task().

utility::vector1< std::list< Hit const * > > protocols::match::Matcher::subsample_hits	(	Vector const &	euclidean_bin_widths,
		Vector const &	euler_bin_widths,
		utility::vector1< std::list< Hit const * > > const &	neighbor_hits
	)		const

private

Referenced by refine_grid_and_subsample_for_hit_subsets().

bool protocols::match::Matcher::test_upstream_only_hit_incompatibility	(	match const &	m,
		utility::vector1< HitPtrListCOP > const &	upstream_only_hits,
		utility::vector1< std::list< Hit const * >::const_iterator > &	upstream_only_hit_iterators,
		Size &	last_upstream_only_geomcst_advanced,
		output::MatchProcessor const &	processor
	)		const

private

returns false if all upstream-only hits in a particular combination are compatible with each other and with the non-upstream-only hits. Returns true if any are incompatible. Ignores compatibility between non-upstream-only hits. If there is an incompatibility, the upstream_only_hit_iterators are advanced. In the event that this increment beyond the incompatible upstream-only-hit combinations advance the most-significant upstream-only geometric-constraint's iterator to its list end, then this function sets the value of last_upstream_only_geomcst_advanced to zero. update flo nov 10: this function now also checks whether upstream only csts clash with any of the downstream objects. it's faster to do this here than in the filters

References all_build_points_, geomcst_is_upstream_only_, n_geometric_constraints_, representative_downstream_algorithm_, protocols::match::output::MatchProcessor::up_coll_filt(), protocols::match::output::MatchProcessor::up_down_filt(), and upstream_builders_.

Referenced by process_matches_all_hit_combos_for_hit_subsets(), and process_matches_where_one_geomcst_defines_downstream_location().

bool protocols::match::Matcher::test_upstream_only_hit_incompatibility	(	match_dspos1 const &	m1,
		utility::vector1< HitPtrListCOP > const &	upstream_only_hits,
		utility::vector1< std::list< Hit const * >::const_iterator > &	upstream_only_hit_iterators,
		Size &	last_upstream_only_geomcst_advanced,
		output::MatchProcessor const &	processor
	)		const

private

same as above

References all_build_points_, protocols::match::fake_hit(), protocols::match::full_hit(), geomcst_is_upstream_only_, n_geometric_constraints_, protocols::match::match_dspos1::originating_geom_cst_for_dspos, protocols::match::output::MatchProcessor::up_coll_filt(), protocols::match::output::MatchProcessor::up_down_filt(), upstream_builders_, and protocols::match::match_dspos1::upstream_hits.

upstream::UpstreamBuilderCOP protocols::match::Matcher::upstream_builder ( Size cst_id ) const

References upstream_builders_.

Referenced by protocols::match::downstream::ClassicMatchAlgorithm::build_and_discard_first_round_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build_hits_at_all_positions(), protocols::match::downstream::DownstreamAlgorithm::default_build_hits_at_all_positions(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation(), and protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation_at_target_build_point().

upstream::UpstreamBuilderOP protocols::match::Matcher::upstream_builder ( Size cst_id )

References upstream_builders_.

core::pose::PoseCOP protocols::match::Matcher::upstream_pose ( ) const

Data accessors.

References upstream_pose_.

Member Data Documentation

downstream::ActiveSiteGridOP protocols::match::Matcher::active_site_grid_

private

Referenced by initialize_active_site_grid().

utility::vector1< upstream::ScaffoldBuildPointOP > protocols::match::Matcher::all_build_points_

private

Referenced by build_point(), check_non_upstream_only_hit_incompatibility(), initialize_scaffold_build_points(), prepare_for_hit_generation_for_constraint(), and test_upstream_only_hit_incompatibility().

std::list< downstream::DownstreamAlgorithmOP > protocols::match::Matcher::all_downstream_algorithms_

private

Referenced by add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), initialize_active_site_grid(), and initialize_bump_grids().

std::list< downstream::DownstreamBuilderOP > protocols::match::Matcher::all_downstream_builders_

private

Referenced by create_ds_builder(), finish_hit_generation_for_constraint(), initialize_active_site_grid(), initialize_bump_grids(), and process_matches().

BumpGridOP protocols::match::Matcher::bb_grid_

private

Referenced by initialize_bump_grids(), and set_bump_tolerance().

bool protocols::match::Matcher::build_round1_hits_twice_

private

Referenced by finish_hit_generation_for_constraint(), and initialize_from_task().

utility::vector1< std::map< std::string, Size > > protocols::match::Matcher::build_set_id_for_restype_

private

Referenced by add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), add_upstream_restype_for_constraint(), create_ds_builder(), set_fa_dun_cutoff_for_constraint(), set_n_geometric_constraints(), and set_sample_startegy_for_constraint().

bool protocols::match::Matcher::check_potential_dsbuilder_incompatibility_

mutableprivate

Referenced by process_matches(), and process_matches_all_hit_combos_for_hit_subsets().

utility::vector1< std::list< downstream::DownstreamAlgorithmOP > > protocols::match::Matcher::downstream_algorithms_

private

Referenced by add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), downstream_algorithms(), nonconst_downstream_algorithms(), and set_n_geometric_constraints().

std::list< core::id::AtomID > protocols::match::Matcher::downstream_atoms_required_inside_active_site_

private

Referenced by initialize_active_site_grid(), and initialize_from_task().

utility::vector1< std::list< downstream::DownstreamBuilderOP > > protocols::match::Matcher::downstream_builders_

private

Referenced by check_downstream_hit_incompatibility(), create_ds_builder(), downstream_builder(), downstream_builders(), and set_n_geometric_constraints().

utility::vector1< core::id::AtomID > protocols::match::Matcher::downstream_orientation_atoms_

private

Referenced by create_ds_builder(), and set_downstream_pose().

core::pose::PoseOP protocols::match::Matcher::downstream_pose_

private

Referenced by create_ds_builder(), downstream_pose(), initialize_from_file(), and set_downstream_pose().

bool protocols::match::Matcher::dynamic_grid_refinement_

private

Referenced by initialize_from_task(), process_matches_main_loop_enumerating_all_hit_combos(), and select_hit_representatives().

Vector protocols::match::Matcher::euclidean_bin_widths_

private

Referenced by initialize_occupied_space_hash(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), refine_grid_and_subsample_for_hit_subsets(), set_hash_euclidean_bin_width(), and set_hash_euclidean_bin_widths().

Vector protocols::match::Matcher::euler_bin_widths_

private

Referenced by initialize_occupied_space_hash(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), refine_grid_and_subsample_for_hit_subsets(), set_hash_euler_bin_width(), and set_hash_euler_bin_widths().

utility::vector1< bool > protocols::match::Matcher::geom_cst_has_primary_modification_

private

Referenced by finish_hit_generation_for_constraint(), note_primary_change_to_geom_csts_hitlist(), and set_n_geometric_constraints().

std::list< Size > protocols::match::Matcher::geom_csts_with_primary_hitlist_modificiations_

private

Referenced by finish_hit_generation_for_constraint(), and note_primary_change_to_geom_csts_hitlist().

utility::vector1< bool > protocols::match::Matcher::geomcst_is_upstream_only_

private

Does the downstream algorithm want the 6D coordinate stored in hit.second() to be hashed?

Referenced by check_downstream_hit_incompatibility(), check_non_upstream_only_hit_incompatibility(), has_upstream_only_geomcsts(), increment_upstream_only_hit_combination(), initialize_downstream_algorithms(), predict_n_matches_for_hit_subsets(), process_matches_all_hit_combos_for_hit_subsets(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), set_n_geometric_constraints(), subsample_hits(), and test_upstream_only_hit_incompatibility().

std::string protocols::match::Matcher::gridlig_fname_

private

Referenced by initialize_active_site_grid(), and initialize_from_task().

utility::vector1< HitList > protocols::match::Matcher::hits_

private

Referenced by erase_hit(), finish_hit_generation_for_constraint(), generate_hits_for_constraint(), hit_list_begin(), hit_list_end(), hits(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), regenerate_round1_hits(), and set_n_geometric_constraints().

Size protocols::match::Matcher::n_geometric_constraints_

private

Referenced by check_downstream_hit_incompatibility(), check_non_upstream_only_hit_incompatibility(), finish_hit_generation_for_constraint(), generate_hits(), has_upstream_only_geomcsts(), initialize_downstream_algorithms(), initialize_from_file(), initialize_from_task(), n_geometric_constraints(), predict_n_matches_for_hit_subsets(), process_matches(), process_matches_all_hit_combos_for_hit_subsets(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), select_hit_representatives(), set_n_geometric_constraints(), set_original_scaffold_build_points_for_constraint(), subsample_hits(), and test_upstream_only_hit_incompatibility().

BoundingBox protocols::match::Matcher::occ_space_bounding_box_

private

Referenced by initialize_occupied_space_hash(), predict_n_matches_for_hit_subsets(), process_matches_main_loop_enumerating_all_hit_combos(), process_matches_where_one_geomcst_defines_downstream_location(), set_occupied_space_bounding_box(), and subsample_hits().

OccupiedSpaceHashOP protocols::match::Matcher::occ_space_hash_

private

Referenced by finish_hit_generation_for_constraint(), initialize_occupied_space_hash(), and occ_space_hash().

utility::vector1< BumpGridOP > protocols::match::Matcher::original_scaffold_residue_bump_grids_

private

Referenced by initialize_bump_grids().

utility::vector1< bool > protocols::match::Matcher::output_match_dspos1_for_geomcst_

private

Referenced by initialize_from_task(), and process_matches_where_one_geomcst_defines_downstream_location().

bool protocols::match::Matcher::output_matches_as_singular_downstream_positioning_

private

Referenced by initialize_from_task(), and process_matches().

utility::vector1< utility::vector1< upstream::ScaffoldBuildPointCOP > > protocols::match::Matcher::per_constraint_build_points_

private

Referenced by per_constraint_build_points(), prepare_for_hit_generation_for_constraint(), and set_n_geometric_constraints().

utility::vector1< utility::vector1< Size > > protocols::match::Matcher::per_cst_build_resids_

private

Referenced by initialize_scaffold_build_points(), prepare_for_hit_generation_for_constraint(), set_original_scaffold_build_points(), and set_original_scaffold_build_points_for_constraint().

utility::vector1< Size > protocols::match::Matcher::pose_build_resids_

private

Referenced by get_pose_build_resids(), initialize_scaffold_build_points(), prepare_for_hit_generation_for_constraint(), set_original_scaffold_build_points(), and set_original_scaffold_build_points_for_constraint().

bool protocols::match::Matcher::read_gridlig_file_

private

Referenced by initialize_active_site_grid(), and initialize_from_task().

utility::vector1< core::id::AtomID > protocols::match::Matcher::relevant_downstream_atoms_

private

Referenced by create_ds_builder(), initialize_from_task(), and Matcher().

utility::vector1< downstream::DownstreamAlgorithmOP > protocols::match::Matcher::representative_downstream_algorithm_

private

Referenced by add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), check_downstream_hit_incompatibility(), finish_hit_generation_for_constraint(), generate_hits_for_constraint(), initialize_downstream_algorithms(), process_matches(), process_matches_all_hit_combos_for_hit_subsets(), process_matches_where_one_geomcst_defines_downstream_location(), regenerate_round1_hits(), representative_downstream_algorithm(), set_n_geometric_constraints(), and test_upstream_only_hit_incompatibility().

bool protocols::match::Matcher::same_build_resids_for_all_csts_

private

Referenced by initialize_scaffold_build_points(), prepare_for_hit_generation_for_constraint(), set_original_scaffold_build_points(), and set_original_scaffold_build_points_for_constraint().

utility::vector1< upstream::UpstreamBuilderOP > protocols::match::Matcher::upstream_builders_

private

Referenced by add_external_geometry_samples_for_constraint(), add_secondary_downstream_match_geometry_for_constraint(), add_secondary_upstream_match_geometry_for_constraint(), add_upstream_restype_for_constraint(), check_non_upstream_only_hit_incompatibility(), create_ds_builder(), desymmeterize_upstream_restype_for_constraint(), initialize_bump_grids(), initialize_from_task(), set_fa_dun_cutoff_for_constraint(), set_n_geometric_constraints(), set_sample_startegy_for_constraint(), test_upstream_only_hit_incompatibility(), and upstream_builder().

core::pose::PoseOP protocols::match::Matcher::upstream_pose_

private

Referenced by add_secondary_downstream_match_geometry_for_constraint(), initialize_active_site_grid(), initialize_bump_grids(), initialize_from_file(), initialize_scaffold_build_points(), set_bump_tolerance(), set_upstream_pose(), and upstream_pose().

std::list< std::pair< Size, Real > > protocols::match::Matcher::upstream_resids_and_radii_defining_active_site_

private

Referenced by initialize_active_site_grid(), and initialize_from_task().

bool protocols::match::Matcher::use_input_sc_

private

Referenced by add_upstream_restype_for_constraint(), and initialize_from_task().

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

src/protocols/match/Matcher.hh
src/protocols/match/Matcher.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

If your upstream residue includes a proton chi (e.g. SER/THR/TYR) but the geometry

of the downstream partner does not depend on the location of the proton, then

use the following line to avoid enumerating rotamers that differ only in their proton coordinate.

Secondary Matching:

You can activate secondary matching, a continuous version of the classic discrete algorithm,

by adding the line

which instead of building its own hits and hashing them examines the hits generated in

previous rounds for compatibility with the geometry that you're seeking.

When performing secondary matching, it is not required that you specify all 6 degrees

of freedom. If you specify only a subset the geometry of only the subset you've specified

will be examined (e.g. if you don't care about torsion_AB, don't specify it

in the CST::BEGIN/CST::END block.

You can perform secondary matching to the ligand (the downstream target) or to an upstream

residue whose geometry was constructed by an earlier geometric constraint. In the example

above, the geometric constraint pointed to is #2.

The first geometric constraint cannot use secondary matching, it must always use the discrete

classic match algorithm. (A later geometric constraint may of course perform secondary

matching to the hits produced by the first geometric constraint. At that point the first

constraint is playing the same role in upstream matching as the ligand plays in downstream matching)

END Secondary Matching comments.

Below: chi sample strategies – "1" is for chi-1

These are the traditional ex?level options ( ? == 1, 2, 3 or 4 )

Below: The "AA" field, followed by the 3-letter AA code gives the sub-specification for

a block that contains multiple amino acids. If this block allowed both an ASN and a GLN, then

the first line would apply to GLN rotamers only and the second line to ASN rotamers only.

"AA" fields may be included with

any of the CHI_STRATEGY options listed here.

Everything below: additional chi sample strategies unique to the matcher.

the above line says "step by 3 degrees within a single standard deviation</h1> <h1>to the left and right of the mean for chi 1"

the above line says "step by 3 degrees within 2.5 standard deviations to</h1> <h1>the left and the right of the mean for chi 1"

the line above says that "for histidine chi 2 (which is non-rotameric in the 2010 Dunbrak library)

take 3 extra samples to the left and right of the median chi value inside the non-rotameric chi well

for rotamer wells that have a probability at least 0.1". The 2010 Dunbrack library must be active.

(the -dun10 flag should be on the command line).

the line above is similar for the previous command, but leaves off the REQUISIT_PROBABILITY

which sets a default REQUISIT_PROBABILITY of 2 / #chi-bins. For HIS, this is

2 / 36th, since there are 12 bins for chi 2 and 3 bins for chi1 (36 chi bins total).

the line above instructs the DunbrackSCSampler to expand the sampling for the symmetric amino acids

around the final (symmetric) chi angle for ASP/GLU/PHE/TYR. For example, it would treat ASP's sampling

as if there's a difference between OD1 and OD2.

Member Data Documentation