A base class for all scoring methods that need atom coordinates. More...

#include <AtomBasedConstraintsScore.hh>

Inheritance diagram for protocols::frag_picker::scores::AtomBasedConstraintsScore:

Public Member Functions
	AtomBasedConstraintsScore (core::Size, core::Real, bool, core::Size, utility::vector1< std::string >, std::string)
	Prepare an atom-based score that utilizes some user-defined atoms. More...

	AtomBasedConstraintsScore (core::Size, core::Real, bool, core::Size, std::string)
	Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB. More...

void	do_caching (VallChunkOP) override
	In this case caching means copying coordinates of relevant atoms from a chunk's pose. More...

void	clean_up () override
	Erases the internal array of coordinates. More...

bool	has_atom (core::Size residue_id, core::Size atom_id)
	Returns true if a given atom has been successfully cached and one can use its coordinates. More...

numeric::xyzVector< core::Real >	get_atom_coordinates (core::Size residue_id, core::Size atom_id)
	Returns coordinates for a given atom. More...

std::map< std::string, core::Size >	get_constrainable_atoms_map ()
	Returns a map that defines all constrained atoms used by this scoring method. More...

core::Size	get_constrained_atom_id (std::string atom_name)
	returns an internal ID assigned to a given atom name More...

std::string	get_constrained_atom_name (core::Size atom_id)
	returns a name of a constrained atom when its internal ID is known More...

core::Size	get_query_size ()
	provides an access to the size of the length of a query sequence More...

Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)

virtual bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)

bool	score (FragmentCandidateOP, FragmentScoreMapOP) override

Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
	FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)

std::string &	get_score_name ()
	Returns a name of this scoring method. More...

core::Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...

void	set_id (core::Size id)
	Sets a new integer index for this scoring method. More...

core::Size	get_priority ()
	Returns a priority of this scoring method. More...

core::Real	get_min_allowed_score ()
	Returns the lowest acceptable score value for this scoring method. More...

bool	get_use_lowest ()
	Returns the boolean choice on using the above lowest acceptable score value. More...

void	set_min_allowed_score (core::Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Private Member Functions
core::Size	get_atom_type (std::string atom_name)

Private Attributes
core::Size	query_size_

utility::vector1 < utility::vector1 < numeric::xyzVector < core::Real > > >	chunk_atoms_xyz_

utility::vector1 < utility::vector1< bool > >	atom_flags_

std::map< std::string, core::Size >	constrainable_atoms_

Additional Inherited Members
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
core::Size	id_

core::Size	priority_

std::string	name_

core::Real	lowest_acceptable_value_

bool	use_lowest_

Detailed Description

A base class for all scoring methods that need atom coordinates.

The base class provides an access to atom coordinates from the current chunk It takes care of caching proper atoms from the pose for fast access.

Constructor & Destructor Documentation

protocols::frag_picker::scores::AtomBasedConstraintsScore::AtomBasedConstraintsScore	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::Size	query_size,
		utility::vector1< std::string >	constrainable_atoms,
		std::string	score_name
	)

Prepare an atom-based score that utilizes some user-defined atoms.

User may provide names of atoms that will be cached when a new chunk is considered (i.e. at every do_caching() call)

Parameters

priority	- the priority for this scoring method. The lower the priority, the later the score will be evaluated Because a fragment may be discarded when a score is too low, the most accurate and meaningful scores should have the highest priority
lowest_acceptable_value	- a fragment for which this score is below a certain threshold will be discarded
query_size	- the number of residues in the query sequence
constrainable_atoms	- a vector of strings providing names of constrained atoms. On every do_cahing() event these and only these atoms will be cached from a chunk's pose
score_name	- name assigned to this scoring term; this string must show up in scores config file if the score is to be evaluated during picking

References constrainable_atoms_, and query_size_.

protocols::frag_picker::scores::AtomBasedConstraintsScore::AtomBasedConstraintsScore	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::Size	query_size,
		std::string	score_name
	)

Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB.

These atoms that will be cached when a new chunk is considered (i.e. at every do_caching() call)

Parameters

priority	- the priority for this scoring method. The lower the priority, the later the score will be evaluated Because a fragment may be discarded when a score is too low, the most accurate and meaningful scores should have the highest priority
lowest_acceptable_value	- a fragment for which this score is below a certain threshold will be discarded
query_size	- the number of residues in the query sequence
score_name	- name assigned to this scoring term; this string must show up in scores config file if the score is to be evaluated during picking

References constrainable_atoms_, and query_size_.

Member Function Documentation

void protocols::frag_picker::scores::AtomBasedConstraintsScore::clean_up ( )

overridevirtual

Erases the internal array of coordinates.

Implements protocols::frag_picker::scores::CachingScoringMethod.

References atom_flags_, and chunk_atoms_xyz_.

void protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching ( VallChunkOP chunk )

overridevirtual

In this case caching means copying coordinates of relevant atoms from a chunk's pose.

Implements protocols::frag_picker::scores::CachingScoringMethod.

References atom_flags_, chunk_atoms_xyz_, constrainable_atoms_, core::chemical::ResidueType::has(), protocols::frag_picker::scores::trAtomBasedConstraintsScore(), and protocols::kinmatch::xyz().

numeric::xyzVector<core::Real> protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates	(	core::Size	residue_id,
		core::Size	atom_id
	)

inline

Returns coordinates for a given atom.

Parameters

residue_id	the residue order number. The first is 1, the last one depends on the size of a pose i.e. the size of the current chunk
atom_id	the residue order number, the first is 1

References chunk_atoms_xyz_.

Referenced by protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), and protocols::frag_picker::scores::DihedralConstraintsScore::cached_score().

core::Size protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_type ( std::string atom_name )

private

std::map<std::string, core::Size> protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map ( )

inline

Returns a map that defines all constrained atoms used by this scoring method.

Returned map defines the order of atoms as they are stored inside this object. Indexes defined y this map can be used as arguments for has_atom() and get_atom_coordinates() methods.

References constrainable_atoms_.

Referenced by protocols::frag_picker::scores::AtomPairConstraintsScore::read_constraints(), protocols::frag_picker::scores::InterbondAngleScore::read_constraints(), and protocols::frag_picker::scores::DihedralConstraintsScore::read_constraints().

core::Size protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_id ( std::string atom_name )

inline

returns an internal ID assigned to a given atom name

this ID remains the same for all residues

References constrainable_atoms_.

std::string protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrained_atom_name ( core::Size atom_id )

returns a name of a constrained atom when its internal ID is known

this is the oposite to get_constrained_atom_id(std::string)

References constrainable_atoms_.

core::Size protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size ( )

inline

provides an access to the size of the length of a query sequence

References query_size_.

Referenced by protocols::frag_picker::scores::AtomPairConstraintsScore::AtomPairConstraintsScore(), protocols::frag_picker::scores::DihedralConstraintsScore::DihedralConstraintsScore(), protocols::frag_picker::scores::InterbondAngleScore::InterbondAngleScore(), and protocols::frag_picker::scores::AtomPairConstraintsScore::read_constraints().

bool protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom	(	core::Size	residue_id,
		core::Size	atom_id
	)

inline

Returns true if a given atom has been successfully cached and one can use its coordinates.

Parameters

residue_id	the residue order number. The first is 1, the last one depends on the size of a pose i.e. the size of the current chunk
atom_id	the residue order number, the first is 1

References atom_flags_.

Referenced by protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::frag_picker::scores::InterbondAngleScore::cached_score(), and protocols::frag_picker::scores::DihedralConstraintsScore::cached_score().

Member Data Documentation

utility::vector1<utility::vector1<bool> > protocols::frag_picker::scores::AtomBasedConstraintsScore::atom_flags_

private

Referenced by clean_up(), do_caching(), and has_atom().

utility::vector1<utility::vector1<numeric::xyzVector<core::Real> > > protocols::frag_picker::scores::AtomBasedConstraintsScore::chunk_atoms_xyz_

private

Referenced by clean_up(), do_caching(), and get_atom_coordinates().

std::map<std::string, core::Size> protocols::frag_picker::scores::AtomBasedConstraintsScore::constrainable_atoms_

private

Referenced by AtomBasedConstraintsScore(), do_caching(), get_constrainable_atoms_map(), get_constrained_atom_id(), and get_constrained_atom_name().

core::Size protocols::frag_picker::scores::AtomBasedConstraintsScore::query_size_

private

Referenced by AtomBasedConstraintsScore(), and get_query_size().

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

src/protocols/frag_picker/scores/AtomBasedConstraintsScore.hh
src/protocols/frag_picker/scores/AtomBasedConstraintsScore.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation