protocols::frag_picker::scores::InterbondAngleScore Class Reference

Scores a fragment with a set of Dihedral constraints. More...

#include <InterbondAngleScore.hh>

Inheritance diagram for protocols::frag_picker::scores::InterbondAngleScore:

Collaboration diagram for protocols::frag_picker::scores::InterbondAngleScore:

Public Member Functions
	InterbondAngleScore (Size, Real, bool, std::string, Size, utility::vector1< std::string >)
	Prepare an atom-based score that utilizes some user-defined atoms. More...
	InterbondAngleScore (Size, Real, bool, std::string, Size)
	Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB. More...
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
	Calculates the score. More...
Public Member Functions inherited from protocols::frag_picker::scores::AtomBasedConstraintsScore
	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	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
void	read_constraints (std::string)
Size	get_atom_type (std::string atom_name)

Private Attributes
utility::vector1 < utility::vector1 < FourAtomsConstraintDataOP > >	data_
core::scoring::constraints::FuncFactory	factory_

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

Scores a fragment with a set of Dihedral constraints.

Constructor & Destructor Documentation

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

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)

References core::scoring::constraints::FuncFactory::add_type(), data_, factory_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

protocols::frag_picker::scores::InterbondAngleScore::InterbondAngleScore	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		std::string	constraints_file_name,
		Size	query_size
	)

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)

References core::scoring::constraints::FuncFactory::add_type(), data_, factory_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

Member Function Documentation

bool protocols::frag_picker::scores::InterbondAngleScore::cached_score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

virtual

Calculates the score.

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References core::pack::dunbrack::c, data_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(), protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, core::scoring::total_score, protocols::frag_picker::scores::trInterbondAngleScore(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

private

void protocols::frag_picker::scores::InterbondAngleScore::read_constraints ( std::string  constraints_file_name)

private

References core::pack::dunbrack::c, data_, factory_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_constrainable_atoms_map(), core::scoring::constraints::FuncFactory::new_func(), and protocols::frag_picker::scores::trInterbondAngleScore().

Referenced by InterbondAngleScore().

Member Data Documentation

utility::vector1<utility::vector1<FourAtomsConstraintDataOP> > protocols::frag_picker::scores::InterbondAngleScore::data_

private

Referenced by cached_score(), InterbondAngleScore(), and read_constraints().

core::scoring::constraints::FuncFactory protocols::frag_picker::scores::InterbondAngleScore::factory_

private

Referenced by InterbondAngleScore(), and read_constraints().

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

• src/protocols/frag_picker/scores/InterbondAngleScore.hh
• src/protocols/frag_picker/scores/InterbondAngleScore.cc