#include <Hasher.hh>

Inheritance diagram for protocols::legacy_sewing::Hasher:

Public Member Functions
	Hasher ()
	default constructor More...

ScoreResult	score_one (Model const &m1, SewResidue const &m1_basis, Model const &m2, SewResidue const &m2_basis, core::Size box_length)

void	insert (Model const &model)
	Insert this model into the hash table. More...

ScoreResults	score (Model const &model, core::Size num_segment_matches, core::Size min_segment_score, core::Size max_clash_score, std::set< core::Size > const &score_segments, bool store_atoms, core::Size box_length) const

ScoreResults	score (Model const &model, core::Size num_segment_matches, core::Size min_segment_score, core::Size max_clash_score, bool store_atoms, core::Size box_length) const
	Score the given model against the models in the hash table. More...

void	score_basis (ScoreResults &alignment_scores, Model const &transformed_model, SewResidue const &basis_residue, bool store_atoms) const

void	score_basis_125 (ScoreResults &alignment_scores, Model const &transformed_model, SewResidue const &basis_residue, bool store_atoms) const

void	trim_scores (ScoreResults &scores, core::Size num_segment_matches, core::Size min_segment_score, core::Size max_clash_score) const
	Trim the ScoreResults to remove weak hits. More...

ScoreResults	remove_duplicates (ScoreResults const &scores) const
	keep only best scoring alignment between two models More...

void	remove_connection_inconsistencies (std::map< int, Model > const &models, ScoreResults &scores) const
	remove edges between segments that both have 'next' or 'previous' segments More...

HashMap const &	hash_map () const
	const accessor to the underlying hash map More...

void	neighborhood_lookup (HashKey const &key, utility::fixedsizearray1< HashMap::const_iterator, 27 > &hit_its) const
	retrive hits from the bin corresponding to the key (3D voxel) and all neighboring quarter-angstrom bins More...

void	neighborhood_lookup_125 (HashKey const &key, utility::fixedsizearray1< HashMap::const_iterator, 125 > &hit_its) const
	retrive hits from the bin corresponding to the key (3D voxel) and all neighboring quarter-angstrom bins More...

Model	transform_model (Model const &model, SewResidue const &basis_residue) const
	Transform all features to the local coordinate frame of the basis set. More...

void	hash_model (Model const &transformed_model, SewResidue const &basis_residue)
	Hash the transformed residues into the HashMap. More...

HashKey	generate_key (SewAtom const &atom) const
	Create the HashKey from a SewAtom. More...

void	write_to_disk (std::string filename) const
	Serialize hash table to disk. More...

void	read_from_disk (std::string filename)
	Populate the hash table from one on disk. More...

Private Attributes
HashMap	hash_map_

Constructor & Destructor Documentation

protocols::legacy_sewing::Hasher::Hasher ( )

default constructor

References hash_map_.

Member Function Documentation

HashKey protocols::legacy_sewing::Hasher::generate_key ( SewAtom const & atom ) const

Create the HashKey from a SewAtom.

References protocols::legacy_sewing::SewAtom::coords_.

Referenced by hash_model(), score_basis(), and score_basis_125().

HashMap const & protocols::legacy_sewing::Hasher::hash_map ( ) const

const accessor to the underlying hash map

References hash_map_.

void protocols::legacy_sewing::Hasher::hash_model	(	Model const &	transformed_model,
		SewResidue const &	basis_residue
	)

Hash the transformed residues into the HashMap.

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

Referenced by insert(), and score_one().

void protocols::legacy_sewing::Hasher::insert ( Model const & model )

Insert this model into the hash table.

Insert the features into the HashMap. This is done by iterating through all possible basis sets (coordinate frames defined by atom positions), and for each set transform all features to the corresponding local coordinates and then insert then into the hash table. The complexity of this operation should be O(m^4) where m is the number of features. The total size of the HashMap should be O(N * m^4) where N is the number of hashed objects.

References protocols::legacy_sewing::SewResidue::basis_atoms_, hash_model(), protocols::legacy_sewing::Model::segments_, and transform_model().

Referenced by protocols::legacy_sewing::LegacyAppendAssemblyMover::hash_pdb_model().

void protocols::legacy_sewing::Hasher::neighborhood_lookup	(	HashKey const &	key,
		utility::fixedsizearray1< HashMap::const_iterator, 27 > &	hit_its
	)		const

retrive hits from the bin corresponding to the key (3D voxel) and all neighboring quarter-angstrom bins

when doing a lookup, look in each of the quarter angstrom bins surrounding the query key. This should prevent issues of close matches being missed due to being across bin boundaries.

References hash_map_.

Referenced by score_basis().

void protocols::legacy_sewing::Hasher::neighborhood_lookup_125	(	HashKey const &	key,
		utility::fixedsizearray1< HashMap::const_iterator, 125 > &	hit_its
	)		const

retrive hits from the bin corresponding to the key (3D voxel) and all neighboring quarter-angstrom bins

when doing a lookup, look in each of the quarter angstrom bins surrounding the query key. This should prevent issues of close matches being missed due to being across bin boundaries.

References hash_map_.

Referenced by score_basis_125().

void protocols::legacy_sewing::Hasher::read_from_disk ( std::string filename )

Populate the hash table from one on disk.

read the hash table from disk. This function clears the contents of the hash map

References protocols::legacy_sewing::HashValue::atomno, protocols::legacy_sewing::HashValue::basis_resnum, hash_map_, protocols::legacy_sewing::HashValue::model_id, protocols::legacy_sewing::HashValue::resnum, and protocols::legacy_sewing::HashValue::segment_id.

void protocols::legacy_sewing::Hasher::remove_connection_inconsistencies	(	std::map< int, Model > const &	models,
		ScoreResults &	scores
	)		const

remove edges between segments that both have 'next' or 'previous' segments

References protocols::legacy_sewing::SegmentGraph::has_next(), protocols::legacy_sewing::SegmentGraph::has_previous(), protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::TR().

ScoreResults protocols::legacy_sewing::Hasher::remove_duplicates ( ScoreResults const & scores ) const

keep only best scoring alignment between two models

Keep only the segment matches between two models that has the most aligned atoms.

References protocols::legacy_sewing::TR().

Referenced by score().

ScoreResults protocols::legacy_sewing::Hasher::score	(	Model const &	model,
		core::Size	num_segment_matches,
		core::Size	min_segment_score,
		core::Size	max_clash_score,
		std::set< core::Size > const &	score_segments,
		bool	store_atoms,
		core::Size	box_length
	)		const

Tally the score of each model/basis_set in the HashMap against the input pose. This is very similar to the insert function, but instead of populating the hash with the transformed features, you tally the number of HashMap hits corresponding to each structure/basis_set pair.

References protocols::legacy_sewing::Model::model_id_, remove_duplicates(), score_basis(), score_basis_125(), protocols::legacy_sewing::Model::segments_, protocols::legacy_sewing::TR(), transform_model(), and trim_scores().

Referenced by protocols::legacy_sewing::LegacyAppendAssemblyMover::hash_pdb_model(), and score().

ScoreResults protocols::legacy_sewing::Hasher::score	(	Model const &	model,
		core::Size	num_segment_matches,
		core::Size	min_segment_score,
		core::Size	max_clash_score,
		bool	store_atoms,
		core::Size	box_length
	)		const

Score the given model against the models in the hash table.

References score(), protocols::legacy_sewing::Model::segments_, and protocols::legacy_sewing::TR().

void protocols::legacy_sewing::Hasher::score_basis	(	ScoreResults &	alignment_scores,
		Model const &	transformed_model,
		SewResidue const &	basis_residue,
		bool	store_atoms
	)		const

Referenced by score(), and score_one().

void protocols::legacy_sewing::Hasher::score_basis_125	(	ScoreResults &	alignment_scores,
		Model const &	transformed_model,
		SewResidue const &	basis_residue,
		bool	store_atoms
	)		const

References protocols::legacy_sewing::ModelConstIterator< T >::atom(), protocols::legacy_sewing::SewAtom::atomno_, generate_key(), hash_map_, protocols::legacy_sewing::Model::model_begin(), protocols::legacy_sewing::Model::model_end(), protocols::legacy_sewing::Model::model_id_, neighborhood_lookup_125(), protocols::legacy_sewing::ModelConstIterator< T >::residue(), protocols::legacy_sewing::SewResidue::resnum_, and protocols::legacy_sewing::ModelConstIterator< T >::segment().

Referenced by score(), and score_one().

ScoreResult protocols::legacy_sewing::Hasher::score_one	(	Model const &	m1,
		SewResidue const &	m1_basis,
		Model const &	m2,
		SewResidue const &	m2_basis,
		core::Size	box_length
	)

References hash_model(), protocols::legacy_sewing::Model::model_id_, protocols::legacy_sewing::SewResidue::resnum_, score_basis(), score_basis_125(), protocols::legacy_sewing::TR(), and transform_model().

Referenced by protocols::legacy_sewing::Assembly::follow_edge(), and protocols::legacy_sewing::Assembly::get_score_result().

Model protocols::legacy_sewing::Hasher::transform_model	(	Model const &	model_in,
		SewResidue const &	basis_residue
	)		const

Transform all features to the local coordinate frame of the basis set.

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

References protocols::legacy_sewing::ModelIterator< T >::atom(), protocols::legacy_sewing::SewResidue::basis_atoms_, protocols::legacy_sewing::Model::model_begin(), protocols::legacy_sewing::Model::model_end(), protocols::legacy_sewing::ModelIterator< T >::residue(), protocols::legacy_sewing::SewResidue::resnum_, protocols::legacy_sewing::ModelIterator< T >::segment(), and protocols::legacy_sewing::ModelIterator< T >::segment_valid().

Referenced by insert(), score(), and score_one().

void protocols::legacy_sewing::Hasher::trim_scores	(	ScoreResults &	scores,
		core::Size	num_segment_matches,
		core::Size	min_segment_score,
		core::Size	max_clash_score
	)		const

Trim the ScoreResults to remove weak hits.

trim the given ScoreResults based on the number of segments that match between two models, the number of atom matches for each of these segments, and the clash score (number of hits between atoms of different atom_types)

References protocols::legacy_sewing::TR().

Referenced by score().

void protocols::legacy_sewing::Hasher::write_to_disk ( std::string filename ) const

Serialize hash table to disk.

write the hash table to disk!

References hash_map_.

Member Data Documentation

HashMap protocols::legacy_sewing::Hasher::hash_map_

private

Referenced by hash_map(), hash_model(), Hasher(), neighborhood_lookup(), neighborhood_lookup_125(), read_from_disk(), score_basis(), score_basis_125(), and write_to_disk().

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

src/protocols/legacy_sewing/hashing/Hasher.hh
src/protocols/legacy_sewing/hashing/Hasher.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation