scores a fragment by its crmsd to the given reference structure More...

#include <RDCScore.hh>

Inheritance diagram for protocols::frag_picker::scores::RDCScore:

Collaboration diagram for protocols::frag_picker::scores::RDCScore:

Public Member Functions
	RDCScore (Size, Real, bool)
	creates a RDC-based scoring function. 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	cached_score (FragmentCandidateOP, FragmentScoreMapOP)

bool	score (FragmentCandidateOP, FragmentScoreMapOP)

	RDCScore (Size, Real, bool, Size)
	Prepare the scoring method. 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	score (FragmentCandidateOP, FragmentScoreMapOP)
	Evaluate 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...

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)

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
utility::vector1< std::string > &	rdc_atoms ()

void	read_RDC_file (std::string const &, Size)

Real	sqr (Real x) const

Real	iprod (const Real a[3], const Real b[3]) const

void	mvmul (Real a[3][3], const Real src[3], Real dest[3]) const

void	jacobi (Real a[5][5], Real d[], Real v[5][5], int *nrot)

int	m_inv_gen (Real m[5][5], int n, Real minv[5][5])

Private Attributes
core::scoring::ResidualDipolarCouplingOP	rdc_file_

core::scoring::ResidualDipolarCoupling::RDC_lines	rdc_raw_data_

utility::vector1 < core::scoring::RDC >	rdc_data_

utility::vector1< std::string >	rdc_atoms_

utility::vector1< std::string >	rdc_atom_names_

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 by its crmsd to the given reference structure

Calculates a score for a fragment based on RDC experimental data.

Definition at line 36 of file RDCScore.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::RDCScore::RDCScore	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest
	)

creates a RDC-based scoring function.

Definition at line 54 of file RDCScore.cc.

References rdc_file_, and rdc_raw_data_.

protocols::frag_picker::scores::RDCScore::RDCScore	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		Size	query_size
	)

Prepare the scoring method.

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
rdc_file_name	- from this file RDC data will be obtained
query_size	- the number of residues in the query sequence

Definition at line 65 of file RDCScore_Gront.cc.

Member Function Documentation

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

virtual

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

Definition at line 76 of file RDCScore.cc.

References score().

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

virtual

Erases the internal array of coordinates.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

Definition at line 83 of file RDCScore.cc.

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

virtual

Erases the internal array of coordinates.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

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

virtual

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

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

Definition at line 69 of file RDCScore.cc.

void protocols::frag_picker::scores::RDCScore::do_caching ( VallChunkOP )

virtual

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

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

Real protocols::frag_picker::scores::RDCScore::iprod	(	const Real	a[3],
		const Real	b[3]
	)		const

inlineprivate

Definition at line 69 of file RDCScore_Gront.hh.

void protocols::frag_picker::scores::RDCScore::jacobi	(	Real	a[5][5],
		Real	d[],
		Real	v[5][5],
		int *	nrot
	)

private

Definition at line 160 of file RDCScore_Gront.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, ROTATE, and core::scoring::hbonds::t().

Referenced by m_inv_gen().

int protocols::frag_picker::scores::RDCScore::m_inv_gen	(	Real	m[5][5],
		int	n,
		Real	minv[5][5]
	)

private

Definition at line 124 of file RDCScore_Gront.cc.

References jacobi().

void protocols::frag_picker::scores::RDCScore::mvmul	(	Real	a[3][3],
		const Real	src[3],
		Real	dest[3]
	)		const

inlineprivate

Definition at line 72 of file RDCScore_Gront.hh.

utility::vector1< std::string > & protocols::frag_picker::scores::RDCScore::rdc_atoms ( )

private

Definition at line 46 of file RDCScore_Gront.cc.

References rdc_atoms_.

void protocols::frag_picker::scores::RDCScore::read_RDC_file	(	std::string const &	filename,
		Size	exp_id = `1`
	)

private

Definition at line 79 of file RDCScore_Gront.cc.

References rdc_data_, and protocols::frag_picker::scores::trRDCScore().

bool protocols::frag_picker::scores::RDCScore::score	(	FragmentCandidateOP	fragment,
		FragmentScoreMapOP	empty_map
	)

virtual

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

Definition at line 86 of file RDCScore.cc.

References core::chemical::ChemicalManager::get_instance(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, core::pose::make_pose_from_sequence(), rdc_raw_data_, core::chemical::ChemicalManager::residue_type_set(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::scoring::store_RDC_in_pose(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by cached_score().

bool protocols::frag_picker::scores::RDCScore::score	(	FragmentCandidateOP	,
		FragmentScoreMapOP
	)

virtual

Evaluate the score.

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

Real protocols::frag_picker::scores::RDCScore::sqr ( Real x) const

inlineprivate

Definition at line 66 of file RDCScore_Gront.hh.

Member Data Documentation

utility::vector1<std::string> protocols::frag_picker::scores::RDCScore::rdc_atom_names_

private

Definition at line 63 of file RDCScore_Gront.hh.

utility::vector1<std::string> protocols::frag_picker::scores::RDCScore::rdc_atoms_

private

Definition at line 59 of file RDCScore_Gront.hh.

Referenced by rdc_atoms().

utility::vector1<core::scoring::RDC> protocols::frag_picker::scores::RDCScore::rdc_data_

private

Definition at line 58 of file RDCScore_Gront.hh.

Referenced by read_RDC_file().

core::scoring::ResidualDipolarCouplingOP protocols::frag_picker::scores::RDCScore::rdc_file_

private

Definition at line 48 of file RDCScore.hh.

Referenced by RDCScore().

core::scoring::ResidualDipolarCoupling::RDC_lines protocols::frag_picker::scores::RDCScore::rdc_raw_data_

private

Definition at line 49 of file RDCScore.hh.

Referenced by RDCScore(), and score().

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

src/protocols/frag_picker/scores/RDCScore.hh
src/protocols/frag_picker/scores/RDCScore_Gront.hh
src/protocols/frag_picker/scores/RDCScore.cc
src/protocols/frag_picker/scores/RDCScore_Gront.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation