protocols::comparative_modeling::Align_RmsdEvaluator Class Reference

#include <Align_RmsdEvaluator.hh>

Inheritance diagram for protocols::comparative_modeling::Align_RmsdEvaluator:

Public Member Functions
	Align_RmsdEvaluator (core::pose::PoseCOP native_pose, std::string tag="", bool calc_gdt=true, core::sequence::SequenceAlignmentOP aln=nullptr, bool gdt_by_TM=false)
	~Align_RmsdEvaluator () override
void	apply (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &ss) const override
	evaluate pose and store values in Silent_Struct More...
core::Real	apply (core::pose::Pose &) const override
	evaluate pose More...
void	report_gdt_components (bool const setting)
bool	report_gdt_components () const
void	calc_gdt (bool const setting)
bool	calc_gdt () const
void	gdt_by_TM (bool const setting)
bool	gdt_by_TM () const
Public Member Functions inherited from protocols::evaluation::AlignEvaluator
	AlignEvaluator (core::pose::PoseCOP native_pose, std::string tag="", bool report_aln_components=true, core::sequence::SequenceAlignmentOP aln=nullptr)
	~AlignEvaluator () override
core::Real	apply (core::pose::Pose &) const override
	outdated method - don't use! More...
core::sequence::SequenceAlignmentOP	get_alignment (core::pose::Pose const &pose) const
void	report_aln_components (bool const setting)
bool	report_aln_components () const
std::string	tag () const
core::pose::PoseCOP	native_pose () const
Public Member Functions inherited from protocols::evaluation::SingleValuePoseEvaluator< core::Real >
	SingleValuePoseEvaluator (std::string const &name="UNSPECIFIED_SingleValuePoseEvaluator")
void	apply (core::pose::Pose &, std::string tag, core::io::silent::SilentStruct &pss) const override
	evaluate pose and store values in Silent_Struct why is this specific to a specific type of SilentStruct? that seems needlessly pointless and overly constraining. More...
virtual void	apply (core::pose::Pose &, std::string tag, core::io::silent::SilentStruct &pss) const =0
	evaluate pose and store values in Silent_Struct More...
virtual void	apply (core::io::silent::SilentStruct &pss) const
	direct application to SilentStruct... default implementation makes pose and calls "apply", you can overload if you don't need the pose-step More...
bool	applicable (core::pose::Pose const &) const override
core::Size	size () const override
std::string	name (core::Size) const override
Public Member Functions inherited from protocols::evaluation::PoseEvaluator
	PoseEvaluator ()
	~PoseEvaluator () override=default
virtual void	apply (core::io::silent::SilentStruct &pss) const
	direct application to SilentStruct... default implementation makes pose and calls "apply", you can overload if you don't need the pose-step More...

Private Attributes
bool	calc_gdt_
bool	gdt_by_TM_
bool	report_gdt_components_

Constructor & Destructor Documentation

Align_RmsdEvaluator()

protocols::comparative_modeling::Align_RmsdEvaluator::Align_RmsdEvaluator	(	core::pose::PoseCOP	native_pose,
		std::string	tag = "",
		bool	calc_gdt = true,
		core::sequence::SequenceAlignmentOP	aln = nullptr,
		bool	gdt_by_TM = false
	)

~Align_RmsdEvaluator()

protocols::comparative_modeling::Align_RmsdEvaluator::~Align_RmsdEvaluator ( )

overridedefault

Member Function Documentation

apply() [1/2]

core::Real protocols::comparative_modeling::Align_RmsdEvaluator::apply ( core::pose::Pose &  ) const

inlineoverridevirtual

evaluate pose

Implements protocols::evaluation::SingleValuePoseEvaluator< core::Real >.

apply() [2/2]

void protocols::comparative_modeling::Align_RmsdEvaluator::apply ( core::pose::Pose &  , std::string  tag, core::io::silent::SilentStruct &  pss  ) const

overridevirtual

evaluate pose and store values in Silent_Struct

Implements protocols::evaluation::AlignEvaluator.

References core::io::silent::SilentStruct::add_energy(), calc_gdt(), protocols::comparative_modeling::gather_coords(), gdt_by_TM(), core::scoring::gdtha(), core::scoring::gdtsc(), protocols::evaluation::AlignEvaluator::get_alignment(), protocols::evaluation::AlignEvaluator::native_pose(), protocols::evaluation::AlignEvaluator::report_aln_components(), report_gdt_components(), protocols::evaluation::SingleValuePoseEvaluator< core::Real >::size(), core::id::SequenceMapping::size1(), protocols::evaluation::AlignEvaluator::tag(), protocols::comparative_modeling::tr(), core::scoring::xyz_gdtmm(), core::scoring::xyz_gdttm(), and core::scoring::xyz_maxsub().

calc_gdt() [1/2]

bool protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt ( ) const

inline

References calc_gdt_.

Referenced by apply(), and report_gdt_components().

calc_gdt() [2/2]

void protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt ( bool const  setting )

inline

References calc_gdt_.

gdt_by_TM() [1/2]

bool protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM ( ) const

inline

References gdt_by_TM_.

Referenced by apply().

gdt_by_TM() [2/2]

void protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM ( bool const  setting )

inline

References gdt_by_TM_.

report_gdt_components() [1/2]

bool protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components ( ) const

inline

References report_gdt_components_.

Referenced by apply().

report_gdt_components() [2/2]

void protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components ( bool const  setting )

inline

References calc_gdt(), and report_gdt_components_.

Member Data Documentation

calc_gdt_

bool protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt_

private

Referenced by calc_gdt().

gdt_by_TM_

bool protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM_

private

Referenced by gdt_by_TM().

report_gdt_components_

bool protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components_

private

Referenced by report_gdt_components().

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

• src/protocols/comparative_modeling/Align_RmsdEvaluator.hh
• src/protocols/comparative_modeling/Align_RmsdEvaluator.cc