A geometric hashing class used by the SEWING protocol. More...

#include <Hasher.hh>

Inheritance diagram for protocols::sewing::hashing::Hasher:

Public Member Functions
	Hasher ()

	~Hasher () override

	Hasher (HasherSettings &hasher_settings, SegmentVectorCOP segment_vector)

	Hasher (HasherSettings &hasher_settings, SegmentVectorCOP segment_vector, std::map< core::Size, data_storage::SmartSegmentOP > pdb_segments)

	Hasher (Hasher const &src)

HasherOP	clone () const

bool	can_hash (data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2)

void	initialize_from_options ()

std::pair< utility::vector1 < std::pair< core::Size, core::Size > >::const_iterator, utility::vector1< std::pair < core::Size, core::Size > >::const_iterator >	iterate_over_basis_pairs (data_storage::SmartSegmentCOP segment_1, data_storage::SmartSegmentCOP segment_2)
	returns pair of iterators to beginning and end of all_basis_pairs between the given SewSegments More...

SegmentVectorCOP	segment_vector () const

void	segment_vector (SegmentVectorCOP segment_vector)

HasherSettings	hasher_settings () const

void	hasher_settings (HasherSettings const &hasher_settings)

std::map< core::Size, data_storage::SmartSegmentOP > &	pdb_segments ()

std::map< core::Size, data_storage::SmartSegmentOP >	const_pdb_segments () const

void	pdb_segments (std::map< core::Size, data_storage::SmartSegmentOP > &)

void	transform_segments (data_storage::Basis current_basis, bool first)
	iterates through neighbors of n_terminal segments transforms xyz coordninates into basis_residue coordinate frame. More...

void	hash_segments (data_storage::SmartSegmentOP const transformed_segment, data_storage::Basis const &basis_residue)
	adds segments to the hash_map, excluding the basis residue from being scored. More...

HashKey	generate_key (core::conformation::Atom const &atom) const
	creates key for HashMap More...

std::set< HashValue >	find_aligned_atoms (core::conformation::Atom const &start_atom) const
	Given a ModelIterator to a particular atom, returns a set of HashValues that correspond to it. More...

data_storage::SmartSegmentOP	initialize_hashmap (data_storage::BasisPair const &basis_pair)
	Returns a transformed segments that will be scored against the model currently in the HashMap. More...

bool	score_basis_pair (data_storage::BasisPair const &basis_pair)
	returns whether the basis pair meets edge requirements for max_clash and min_hash_score More...

core::Size	get_hash_map_size () const

data_storage::SmartSegmentCOP	get_seg1 () const

data_storage::SmartSegmentCOP	get_seg2 () const

Private Member Functions
void	allocate_segments ()
	iterates through all neighbors of the n_term segment and copies them into preallocated vector via the data_storage::SmartSegment become() method. More...

Private Attributes
HasherSettings	hasher_settings_

utility::vector1< std::pair < core::Size, core::Size > >	all_basis_pairs_

SegmentVectorCOP	segment_vector_

HashMap	hash_map_

data_storage::SmartSegmentOP	seg1_

data_storage::SmartSegmentOP	seg2_

utility::vector1 < data_storage::SmartSegmentOP >	seg1_substructure_

utility::vector1 < data_storage::SmartSegmentOP >	seg2_substructure_

std::map< core::Size, data_storage::SmartSegmentOP >	pdb_segments_

Detailed Description

A geometric hashing class used by the SEWING protocol.

Constructor & Destructor Documentation

protocols::sewing::hashing::Hasher::Hasher ( )

References all_basis_pairs_, and allocate_segments().

protocols::sewing::hashing::Hasher::~Hasher ( )

override

protocols::sewing::hashing::Hasher::Hasher	(	HasherSettings &	hasher_settings,
		SegmentVectorCOP	segment_vector
	)

References all_basis_pairs_, allocate_segments(), protocols::sewing::hashing::HasherSettings::boxes_per_dimension, hasher_settings(), hasher_settings_, segment_vector(), segment_vector_, and protocols::TR().

protocols::sewing::hashing::Hasher::Hasher	(	HasherSettings &	hasher_settings,
		SegmentVectorCOP	segment_vector,
		std::map< core::Size, data_storage::SmartSegmentOP >	pdb_segments
	)

References all_basis_pairs_, allocate_segments(), protocols::sewing::hashing::HasherSettings::boxes_per_dimension, hasher_settings(), hasher_settings_, pdb_segments(), pdb_segments_, segment_vector(), segment_vector_, and protocols::TR().

protocols::sewing::hashing::Hasher::Hasher ( Hasher const & src )

References all_basis_pairs_, allocate_segments(), const_pdb_segments(), hasher_settings(), hasher_settings_, pdb_segments_, segment_vector(), and segment_vector_.

Member Function Documentation

void protocols::sewing::hashing::Hasher::allocate_segments ( )

private

iterates through all neighbors of the n_term segment and copies them into preallocated vector via the data_storage::SmartSegment become() method.

initializes preallocated segments and respective neighbor vectors

References seg1_, seg1_substructure_, seg2_, and seg2_substructure_.

Referenced by Hasher().

bool protocols::sewing::hashing::Hasher::can_hash	(	data_storage::SmartSegmentCOP	seg1,
		data_storage::SmartSegmentCOP	seg2
	)

References protocols::TR().

Referenced by iterate_over_basis_pairs(), and score_basis_pair().

HasherOP protocols::sewing::hashing::Hasher::clone ( ) const

std::map< core::Size, data_storage::SmartSegmentOP > protocols::sewing::hashing::Hasher::const_pdb_segments ( ) const

References pdb_segments_.

Referenced by Hasher().

std::set< HashValue > protocols::sewing::hashing::Hasher::find_aligned_atoms ( core::conformation::Atom const & start_atom ) const

Given a ModelIterator to a particular atom, returns a set of HashValues that correspond to it.

References protocols::sewing::hashing::HasherSettings::boxes_per_dimension, generate_key(), hash_map_, and hasher_settings_.

Referenced by score_basis_pair().

HashKey protocols::sewing::hashing::Hasher::generate_key ( core::conformation::Atom const & atom ) const

creates key for HashMap

Method to generate a HashKey for a SewAtom based on its coordinates. Essentially, this discretizes the coordinates into 0.25 Angstrom bins.

References protocols::noesy_assign::round(), and core::conformation::Atom::xyz().

Referenced by find_aligned_atoms(), and hash_segments().

core::Size protocols::sewing::hashing::Hasher::get_hash_map_size ( ) const

References hash_map_.

data_storage::SmartSegmentCOP protocols::sewing::hashing::Hasher::get_seg1 ( ) const

References seg1_.

data_storage::SmartSegmentCOP protocols::sewing::hashing::Hasher::get_seg2 ( ) const

References seg2_.

void protocols::sewing::hashing::Hasher::hash_segments	(	data_storage::SmartSegmentOP const	transformed_n_term_segment,
		data_storage::Basis const &	basis_residue
	)

adds segments to the hash_map, excluding the basis residue from being scored.

For each of the transformed features, insert the appropriate key-value pair into the hash table. The key is the 3D-voxel (or bin) corresponding to the basis set. The value is the residues number for the residue that generated basis set that the transformed atom coordinates are in frame of

References protocols::sewing::hashing::HashValue::atomno, protocols::sewing::hashing::HashValue::basis_resnum, protocols::sewing::hashing::HashValue::basis_segment_id, generate_key(), hash_map_, protocols::sewing::data_storage::Basis::resnum(), protocols::sewing::hashing::HashValue::resnum, protocols::sewing::data_storage::Basis::segment_id(), protocols::sewing::hashing::HashValue::segment_id, segment_vector_, and protocols::TR().

Referenced by initialize_hashmap().

HasherSettings protocols::sewing::hashing::Hasher::hasher_settings ( ) const

References hasher_settings_.

Referenced by Hasher(), and hasher_settings().

void protocols::sewing::hashing::Hasher::hasher_settings ( HasherSettings const & hasher_settings )

References hasher_settings(), and hasher_settings_.

void protocols::sewing::hashing::Hasher::initialize_from_options ( )

References hasher_settings_.

data_storage::SmartSegmentOP protocols::sewing::hashing::Hasher::initialize_hashmap ( data_storage::BasisPair const & basis_pair )

Returns a transformed segments that will be scored against the model currently in the HashMap.

References hash_map_, hash_segments(), seg1_substructure_, seg2_substructure_, protocols::TR(), and transform_segments().

Referenced by score_basis_pair().

std::pair< utility::vector1< std::pair< core::Size, core::Size > >::const_iterator, utility::vector1< std::pair< core::Size, core::Size > >::const_iterator > protocols::sewing::hashing::Hasher::iterate_over_basis_pairs	(	data_storage::SmartSegmentCOP	segment_1,
		data_storage::SmartSegmentCOP	segment_2
	)

returns pair of iterators to beginning and end of all_basis_pairs between the given SewSegments

what this function does

References all_basis_pairs_, can_hash(), hasher_settings_, protocols::mean_field::min(), protocols::sewing::hashing::HasherSettings::min_hash_score, core::id::to_string(), and protocols::TR().

std::map< core::Size, data_storage::SmartSegmentOP > & protocols::sewing::hashing::Hasher::pdb_segments ( )

References pdb_segments_.

Referenced by Hasher().

void protocols::sewing::hashing::Hasher::pdb_segments ( std::map< core::Size, data_storage::SmartSegmentOP > & pdbsegs )

References pdb_segments_.

bool protocols::sewing::hashing::Hasher::score_basis_pair ( data_storage::BasisPair const & basis_pair )

returns whether the basis pair meets edge requirements for max_clash and min_hash_score

what this function does

References can_hash(), find_aligned_atoms(), protocols::sewing::hashing::HasherSettings::hash_between_termini, hasher_settings_, initialize_hashmap(), protocols::sewing::hashing::HasherSettings::min_hash_score, pdb_segments_, segment_vector_, and protocols::TR().

SegmentVectorCOP protocols::sewing::hashing::Hasher::segment_vector ( ) const

References segment_vector_.

Referenced by Hasher().

void protocols::sewing::hashing::Hasher::segment_vector ( SegmentVectorCOP segment_vector )

References segment_vector_.

void protocols::sewing::hashing::Hasher::transform_segments	(	data_storage::Basis	current_basis,
		bool	first
	)

iterates through neighbors of n_terminal segments transforms xyz coordninates into basis_residue coordinate frame.

Construct HomogenousTransform using the 3 points in the BasisSet. Use this HomogenousTransform to transform all features into the local coordinate frame

References protocols::sewing::data_storage::SmartSegment::become(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), protocols::sewing::data_storage::SmartSegment::link_to(), pdb_segments_, protocols::sewing::data_storage::Basis::resnum(), seg1_, seg1_substructure_, seg2_, seg2_substructure_, protocols::sewing::data_storage::Basis::segment_id(), segment_vector_, protocols::TR(), and protocols::kinmatch::xyz().