Use LoopHash to generate low-resolution alternate conformations for the given pose. More...

#include <LoopHashDiversifier.hh>

Inheritance diagram for protocols::loophash::LoopHashDiversifier:

[legend]

Public Member Functions
	LoopHashDiversifier ()

	LoopHashDiversifier (LoopHashLibraryOP library, core::Real min_inter_ss_bbrms, core::Real max_inter_ss_bbrms, core::Real min_intra_ss_bbrms, core::Real max_intra_ss_bbrms, core::Real min_rms, core::Real max_rms, std::string const &start_res, std::string const &stop_res, core::Size window_size, core::Size max_radius, core::Size max_struct, core::Size num_iterations, core::Size num_try_div, bool diversify_loop_only, bool ideal, bool filter_by_phipsi, protocols::filters::FilterOP cenfilter, protocols::filters::FilterOP ranking_cenfilter, core::scoring::ScoreFunctionOP scorefxn_cen_cst, core::scoring::ScoreFunctionOP scorefxn_rama_cst)

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

	~LoopHashDiversifier () override
	‍**Creator Methods**‍/// More...

core::Real	min_inter_ss_bbrms () const

void	min_inter_ss_bbrms (core::Real const min_inter_ss_bbrms)

core::Real	max_inter_ss_bbrms () const

void	max_inter_ss_bbrms (core::Real const max_inter_ss_bbrms)

core::Real	min_intra_ss_bbrms () const

void	min_intra_ss_bbrms (core::Real const min_intra_ss_bbrms)

core::Real	max_intra_ss_bbrms () const

void	max_intra_ss_bbrms (core::Real const max_intra_ss_bbrms)

core::Real	min_rms () const

void	min_rms (core::Real const min_rms)

core::Real	max_rms () const

void	max_rms (core::Real const max_rms)

core::Size	num_iterations () const

void	num_iterations (core::Size const num_iterations)

core::Size	num_try_div () const

void	num_try_div (core::Size const num_try_div)

utility::vector1< core::Size >	loop_sizes () const

void	add_loop_size (core::Size const loop_size)

void	cenfilter (protocols::filters::FilterOP cenfilter)

void	ranking_cenfilter (protocols::filters::FilterOP filter)

protocols::filters::FilterOP	ranking_cenfilter () const

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Attributes
utility::vector1< core::Size >	loop_sizes_

LoopHashLibraryOP	library_

core::Real	min_inter_ss_bbrms_

core::Real	max_inter_ss_bbrms_

core::Real	min_intra_ss_bbrms_

core::Real	max_intra_ss_bbrms_

core::Real	min_rms_

core::Real	max_rms_

std::string	start_res_

std::string	stop_res_

core::Size	window_size_

core::Size	max_radius_

core::Size	max_struct_

core::Size	num_iterations_

core::Size	num_try_div_

bool	diversify_loop_only_

bool	ideal_

bool	filter_by_phipsi_

protocols::filters::FilterOP	cenfilter_

protocols::filters::FilterOP	ranking_cenfilter_

core::scoring::ScoreFunctionOP	scorefxn_cen_cst_

core::scoring::ScoreFunctionOP	scorefxn_rama_cst_

std::vector< std::pair< core::Real, core::io::silent::SilentStructOP > >	all_structs_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Use LoopHash to generate low-resolution alternate conformations for the given pose.

It's possible to limit the amount of movement based on the secondary structure, such that secondary structure elements either move less than loops or don't move at all. The algorithm in pseudo-code:

Convert the pose to centroid mode.
For num_iterations():
- Randomly pick a window to diversify with LoopHash.
- If diversify_loop_only_ is \t true and there are no loops in the window, skip the rest of the iteration.
- Set the amount of backbone movement to allow (i.e. minimum and maximum allowed RMSD of backbone segments) based on whether or not the secondary structure changes within the window.
- Keep all the insertions that pass a filter.
Convert the best-scoring diversified pose to full-atom mode and apply it.

Constructor & Destructor Documentation

◆ LoopHashDiversifier() [1/2]

protocols::loophash::LoopHashDiversifier::LoopHashDiversifier ( )

References loop_sizes_, and window_size_.

◆ LoopHashDiversifier() [2/2]

protocols::loophash::LoopHashDiversifier::LoopHashDiversifier	(	LoopHashLibraryOP	library,
		core::Real	min_inter_ss_bbrms,
		core::Real	max_inter_ss_bbrms,
		core::Real	min_intra_ss_bbrms,
		core::Real	max_intra_ss_bbrms,
		core::Real	min_rms,
		core::Real	max_rms,
		std::string const &	start_res,
		std::string const &	stop_res,
		core::Size	window_size,
		core::Size	max_radius,
		core::Size	max_struct,
		core::Size	num_iterations,
		core::Size	num_try_div,
		bool	diversify_loop_only,
		bool	ideal,
		bool	filter_by_phipsi,
		protocols::filters::FilterOP	cenfilter,
		protocols::filters::FilterOP	ranking_cenfilter,
		core::scoring::ScoreFunctionOP	scorefxn_cen_cst,
		core::scoring::ScoreFunctionOP	scorefxn_rama_cst
	)

References loop_sizes_, and window_size_.

◆ ~LoopHashDiversifier()

protocols::loophash::LoopHashDiversifier::~LoopHashDiversifier ( )

overridedefault

‍****Creator Methods****‍///

‍****End Creator Methods****‍///

Member Function Documentation

◆ add_loop_size()

void protocols::loophash::LoopHashDiversifier::add_loop_size ( core::Size const loop_size )

References loop_sizes_.

Referenced by parse_my_tag().

◆ apply()

void protocols::loophash::LoopHashDiversifier::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ cenfilter()

void protocols::loophash::LoopHashDiversifier::cenfilter ( protocols::filters::FilterOP cenfilter )

References cenfilter_.

Referenced by parse_my_tag().

◆ clone()

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::loophash::LoopHashDiversifier::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ loop_sizes()

utility::vector1< core::Size > protocols::loophash::LoopHashDiversifier::loop_sizes ( ) const

References loop_sizes_.

Referenced by apply(), and parse_my_tag().

◆ max_inter_ss_bbrms() [1/2]

Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( ) const

References max_inter_ss_bbrms_.

Referenced by apply(), and max_inter_ss_bbrms().

◆ max_inter_ss_bbrms() [2/2]

void protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( core::Real const max_inter_ss_bbrms )

References max_inter_ss_bbrms(), and max_inter_ss_bbrms_.

◆ max_intra_ss_bbrms() [1/2]

Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( ) const

References max_intra_ss_bbrms_.

Referenced by apply(), and max_intra_ss_bbrms().

◆ max_intra_ss_bbrms() [2/2]

void protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( core::Real const max_intra_ss_bbrms )

References max_intra_ss_bbrms(), and max_intra_ss_bbrms_.

◆ max_rms() [1/2]

Real protocols::loophash::LoopHashDiversifier::max_rms ( ) const

References max_rms_.

Referenced by apply(), and max_rms().

◆ max_rms() [2/2]

void protocols::loophash::LoopHashDiversifier::max_rms ( core::Real const max_rms )

References max_rms(), and max_rms_.

◆ min_inter_ss_bbrms() [1/2]

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( ) const

References min_inter_ss_bbrms_.

Referenced by apply(), and min_inter_ss_bbrms().

◆ min_inter_ss_bbrms() [2/2]

void protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( core::Real const min_inter_ss_bbrms )

References min_inter_ss_bbrms(), and min_inter_ss_bbrms_.

◆ min_intra_ss_bbrms() [1/2]

Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( ) const

References min_intra_ss_bbrms_.

Referenced by apply(), and min_intra_ss_bbrms().

◆ min_intra_ss_bbrms() [2/2]

void protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( core::Real const min_intra_ss_bbrms )

References min_intra_ss_bbrms(), and min_intra_ss_bbrms_.

◆ min_rms() [1/2]

Real protocols::loophash::LoopHashDiversifier::min_rms ( ) const

References min_rms_.

Referenced by apply(), and min_rms().

◆ min_rms() [2/2]

void protocols::loophash::LoopHashDiversifier::min_rms ( core::Real const min_rms )

References min_rms(), and min_rms_.

◆ mover_name()

std::string protocols::loophash::LoopHashDiversifier::mover_name ( )

static

Referenced by get_name(), protocols::loophash::LoopHashDiversifierCreator::keyname(), and provide_xml_schema().

◆ num_iterations() [1/2]

Size protocols::loophash::LoopHashDiversifier::num_iterations ( ) const

References num_iterations_.

Referenced by num_iterations().

◆ num_iterations() [2/2]

void protocols::loophash::LoopHashDiversifier::num_iterations ( core::Size const num_iterations )

References num_iterations(), and num_iterations_.

◆ num_try_div() [1/2]

Size protocols::loophash::LoopHashDiversifier::num_try_div ( ) const

References num_try_div_.

Referenced by num_try_div().

◆ num_try_div() [2/2]

void protocols::loophash::LoopHashDiversifier::num_try_div ( core::Size const num_try_div )

References num_try_div(), and num_try_div_.

◆ parse_my_tag()

void protocols::loophash::LoopHashDiversifier::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_loop_size(), cenfilter(), diversify_loop_only_, filter_by_phipsi_, core::pose::get_resnum_string(), ideal_, library_, loop_sizes(), max_inter_ss_bbrms_, max_intra_ss_bbrms_, max_radius_, max_rms_, max_struct_, min_inter_ss_bbrms_, min_intra_ss_bbrms_, min_rms_, num_iterations_, num_try_div_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_filter_or_null(), ranking_cenfilter(), scorefxn_cen_cst_, scorefxn_rama_cst_, start_res_, stop_res_, and window_size_.