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

#include <FragmentCrmsd.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentCrmsd:

Public Member Functions
	FragmentCrmsd (core::Size, core::Real, bool, core::pose::PoseOP)
	creates a crmsd-based scoring function. More...

	FragmentCrmsd (core::Size, core::Real, bool, utility::vector1< utility::vector1< core::Real > >)
	creates a crmsd-based scoring function. More...

	~FragmentCrmsd () override

void	set_pose (core::pose::PoseOP const &pose)
	Update pose/coordinates for rescoring (useful for RosettaScripts implementation of the FragmentPicker). More...

void	do_caching (VallChunkOP) override

void	clean_up () override

bool	score (FragmentCandidateOP, FragmentScoreMapOP) override

bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override

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)

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	fill_CA_coords (core::pose::Pose const &, ObjexxFCL::FArray2_double &, core::Size)

Private Attributes
std::string	cached_scores_id_

core::Size	n_atoms_

core::pose::PoseOP	reference_pose_

ObjexxFCL::FArray2D_double	reference_coordinates_

ObjexxFCL::FArray2D_double	chunk_coordinates_

ObjexxFCL::FArray2D_double	fragment_coordinates_

ObjexxFCL::FArray2D_double	frag_pos_coordinates_

ObjexxFCL::FArray1D_double	weights_

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 by its crmsd to the given reference structure

Constructor & Destructor Documentation

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

creates a crmsd-based scoring function.

fragments will be compared to a given pose, which should have the same number of residues a the query sequence

References fill_CA_coords(), n_atoms_, reference_coordinates_, reference_pose_, and weights_.

protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		utility::vector1< utility::vector1< core::Real > >	xyz
	)

creates a crmsd-based scoring function.

fragments will be compared to given coordinates, which should have the same number of residues a the query sequence

References n_atoms_, reference_coordinates_, protocols::frag_picker::scores::trRmsScore(), weights_, and protocols::kinmatch::xyz().

protocols::frag_picker::scores::FragmentCrmsd::~FragmentCrmsd ( )

overridedefault

Member Function Documentation

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

overridevirtual

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

References cached_scores_id_, chunk_coordinates_, do_caching(), frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

overridevirtual

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

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

overridevirtual

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

References chunk_coordinates_.

Referenced by cached_score().

void protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords	(	core::pose::Pose const &	,
		ObjexxFCL::FArray2_double &	,
		core::Size
	)

private

References protocols::simple_filters::coords(), core::chemical::ResidueType::has(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::frag_picker::scores::trRmsScore(), core::conformation::Residue::type(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

Referenced by FragmentCrmsd(), and set_pose().

bool protocols::frag_picker::scores::FragmentCrmsd::score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map
	)

overridevirtual

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

References frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd().

void protocols::frag_picker::scores::FragmentCrmsd::set_pose ( core::pose::PoseOP const & pose )

Update pose/coordinates for rescoring (useful for RosettaScripts implementation of the FragmentPicker).

References fill_CA_coords(), n_atoms_, reference_coordinates_, reference_pose_, and weights_.

Referenced by protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd().

Member Data Documentation

std::string protocols::frag_picker::scores::FragmentCrmsd::cached_scores_id_

private

Referenced by cached_score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::chunk_coordinates_

private

Referenced by cached_score(), and do_caching().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::frag_pos_coordinates_

private

Referenced by cached_score(), and score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::fragment_coordinates_

private

Referenced by cached_score(), and score().

core::Size protocols::frag_picker::scores::FragmentCrmsd::n_atoms_

private

Referenced by FragmentCrmsd(), and set_pose().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::reference_coordinates_

private

Referenced by cached_score(), FragmentCrmsd(), score(), and set_pose().

core::pose::PoseOP protocols::frag_picker::scores::FragmentCrmsd::reference_pose_

private

Referenced by FragmentCrmsd(), and set_pose().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::FragmentCrmsd::weights_

private

Referenced by FragmentCrmsd(), and set_pose().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation