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

#include <AtomBasedConstraintsScore.hh>

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

	AtomBasedConstraintsScore (Size, Real, bool, 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)
	In this case caching means copying coordinates of relevant atoms from a chunk's pose. More...

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

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

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

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

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 (Size atom_id)
	returns a name of a constrained atom when its internal ID is known More...

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 (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)

virtual bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)

virtual bool	score (FragmentCandidateOP fragment, FragmentScoreMapOP scores)

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

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

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

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

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

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 (Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

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

Private Attributes
Size	query_size_

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

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

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

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

Size	priority_

std::string	name_

Real	lowest_acceptable_value_

bool	use_lowest_

Detailed Description

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

Detailed: 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	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		Size	query_size,
		utility::vector1< std::string >	constrainable_atoms,
		std::string	score_name
	)

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

Detailed: 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	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		Size	query_size,
		std::string	score_name
	)

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

Detailed: 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 ( )

virtual

Erases the internal array of coordinates.

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

Reimplemented in protocols::frag_picker::scores::RDCScore, and protocols::frag_picker::scores::RDCScore.

References atom_flags_, and chunk_atoms_xyz_.

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

virtual

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

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

Reimplemented in protocols::frag_picker::scores::RDCScore, and protocols::frag_picker::scores::RDCScore.

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

numeric::xyzVector<Real> protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates	(	Size	residue_id,
		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_, and size().

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

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

private

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

inline

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

Detailed: 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().

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

Detailed: this ID remains the same for all residues

References constrainable_atoms_.

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

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

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

References constrainable_atoms_.

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	(	Size	residue_id,
		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_, and size().

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