protocols::frag_picker::scores::PhiPsiRmsd Class Reference

scores a fragment by the root mean square deviation of Phi and Psi angles. More...

#include <PhiPsiRmsd.hh>

Public Member Functions
	PhiPsiRmsd (Size priority, Real lowest_acceptable_value, bool use_lowest, core::pose::PoseOP reference_pose)
	creates a Phi-Psi-based scoring function. More...
	PhiPsiRmsd (Size, Real, bool, PhiPsiTalosIO &)
void	do_caching (VallChunkOP)
void	clean_up ()
bool	score (FragmentCandidateOP, FragmentScoreMapOP)
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
bool	describe_score (FragmentCandidateOP, FragmentScoreMapOP, std::ostream &)
	Print debugging informations about a score for a given fragment. 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
void	read_talos_phi_psi (std::string const &)

Private Attributes
std::string	cached_scores_id_
Size	n_atoms_
ObjexxFCL::FArray1D_double	chunk_phi_
ObjexxFCL::FArray1D_double	chunk_psi_
ObjexxFCL::FArray1D_double	query_phi_
ObjexxFCL::FArray1D_double	query_psi_
utility::vector1< bool >	existing_data_

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 the root mean square deviation of Phi and Psi angles.

Constructor & Destructor Documentation

protocols::frag_picker::scores::PhiPsiRmsd::PhiPsiRmsd	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		core::pose::PoseOP	reference_pose
	)

creates a Phi-Psi-based scoring function.

Detailed: Phi-Psi angles from a fragment will be compared to relevant angles in a given pose, which should have the same number of residues a the query sequence

References existing_data_, n_atoms_, core::pose::Pose::phi(), core::pose::Pose::psi(), query_phi_, query_psi_, and core::pose::Pose::total_residue().

protocols::frag_picker::scores::PhiPsiRmsd::PhiPsiRmsd	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		PhiPsiTalosIO &	reader
	)

References existing_data_, protocols::frag_picker::PhiPsiTalosIO::get_entry(), protocols::frag_picker::PhiPsiTalosIO::get_sequence(), protocols::frag_picker::PhiPsiTalosIO::has_entry(), n_atoms_, query_phi_, query_psi_, and protocols::frag_picker::scores::trPhiPsiRmsd.

Member Function Documentation

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

virtual

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

References cached_scores_id_, chunk_phi_, chunk_psi_, do_caching(), existing_data_, basic::FRAGMENTPICKING_PHIPSI_SCORE, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, PROF_START, PROF_STOP, query_phi_, query_psi_, score(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by score().

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

virtual

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

bool protocols::frag_picker::scores::PhiPsiRmsd::describe_score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map,
		std::ostream &	out
	)

Print debugging informations about a score for a given fragment.

References chunk_phi_, chunk_psi_, protocols::abinitio::abscript::I, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, query_phi_, query_psi_, score(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

void protocols::frag_picker::scores::PhiPsiRmsd::do_caching ( VallChunkOP  current_chunk )

virtual

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

References protocols::frag_picker::VallChunk::at(), chunk_phi_, chunk_psi_, and protocols::frag_picker::VallChunk::size().

Referenced by cached_score().

void protocols::frag_picker::scores::PhiPsiRmsd::read_talos_phi_psi ( std::string const &  )

private

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

virtual

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

References cached_score().

Referenced by cached_score(), and describe_score().

Member Data Documentation

std::string protocols::frag_picker::scores::PhiPsiRmsd::cached_scores_id_

private

Referenced by cached_score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::chunk_phi_

private

Referenced by cached_score(), describe_score(), and do_caching().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::chunk_psi_

private

Referenced by cached_score(), describe_score(), and do_caching().

utility::vector1<bool> protocols::frag_picker::scores::PhiPsiRmsd::existing_data_

private

Referenced by cached_score(), and PhiPsiRmsd().

Size protocols::frag_picker::scores::PhiPsiRmsd::n_atoms_

private

Referenced by PhiPsiRmsd().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::query_phi_

private

Referenced by cached_score(), describe_score(), and PhiPsiRmsd().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::query_psi_

private

Referenced by cached_score(), describe_score(), and PhiPsiRmsd().

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

• symlinks/rosetta/src/protocols/frag_picker/scores/PhiPsiRmsd.hh
• symlinks/rosetta/src/protocols/frag_picker/scores/PhiPsiRmsd.cc