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

#include <AtomPairConstraintsScore.hh>

Inheritance diagram for protocols::frag_picker::scores::AtomPairConstraintsScore:

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

	AtomPairConstraintsScore (core::Size, core::Real, bool, std::string, core::Size)
	Prepare an AtomPair constraint - based score that utilizes N, C, CA, O && CB atoms. More...

bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
	Calculates a score for a given fragment. More...

Public Member Functions inherited from protocols::frag_picker::scores::AtomBasedConstraintsScore
	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)

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
void	read_constraints (std::string)

core::Size	get_atom_type (std::string atom_name)

Private Attributes
utility::vector1 < utility::vector1 < AtomPairConstraintsDataOP > >	data_

core::scoring::func::FuncFactory	factory_

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

Scores a fragment with a set of AtomPair constraints.

Constructor & Destructor Documentation

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

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

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 && meaningful scores should have the highest priority
lowest_acceptable_value	- a fragment for which this score is below a certain threshold will be discarded
constraints_file_name	- from this file AtomPair constraints will be obtained
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 && only these atoms will be cached from a chunk's pose

References data_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

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

Prepare an AtomPair constraint - based score that utilizes N, C, CA, O && CB atoms.

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 && meaningful scores should have the highest priority
lowest_acceptable_value	- a fragment for which this score is below a certain threshold will be discarded
constraints_file_name	- from this file AtomPair constraints will be obtained
query_size	- the number of residues in the query sequence

References data_, protocols::frag_picker::scores::AtomBasedConstraintsScore::get_query_size(), and read_constraints().

Member Function Documentation

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

overridevirtual

Calculates a score for a given fragment.

Resulting value is written into a given score map.

Parameters

fragment	- fragment to be scored
scores	- resulting score will be stored here

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::trAtomPairConstraintsScore(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

private

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

private

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

Referenced by AtomPairConstraintsScore().

Member Data Documentation

utility::vector1<utility::vector1<AtomPairConstraintsDataOP> > protocols::frag_picker::scores::AtomPairConstraintsScore::data_

private

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

core::scoring::func::FuncFactory protocols::frag_picker::scores::AtomPairConstraintsScore::factory_

private

Referenced by read_constraints().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation