#include <StepWiseModeler.hh>

Inheritance diagram for protocols::stepwise::modeler::StepWiseModeler:

[legend]

Public Member Functions
	StepWiseModeler (core::Size const moving_res, core::scoring::ScoreFunctionCOP scorefxn)

	StepWiseModeler (core::scoring::ScoreFunctionCOP scorefxn)

	~StepWiseModeler () override

	StepWiseModeler (StepWiseModeler const &src)

virtual StepWiseModelerOP	clone_modeler () const

StepWiseModeler &	operator= (StepWiseModeler const &src)

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

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

void	set_moving_res_and_reset (core::Size const moving_res)

void	set_working_prepack_res (utility::vector1< core::Size > const &setting)

void	set_working_minimize_res (utility::vector1< core::Size > const &setting)

void	set_figure_out_prepack_res (bool const setting)

void	set_working_parameters (working_parameters::StepWiseWorkingParametersCOP working_parameters)

working_parameters::StepWiseWorkingParametersCOP	working_parameters ()

void	set_options (options::StepWiseModelerOptionsCOP options)

options::StepWiseModelerOptionsCOP	options ()

void	set_precomputed_library_mover (precomputed::PrecomputedLibraryMoverCOP precomputed_library_mover)

precomputed::PrecomputedLibraryMoverCOP	precomputed_library_mover ()

core::Size	get_num_sampled ()

void	set_input_streams (utility::vector1< protein::InputStreamWithResidueInfoOP > const &input_streams)

void	set_moving_res_list (utility::vector1< core::Size > const &setting)

core::scoring::ScoreFunctionCOP	scorefxn ()

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

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

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...

Private Member Functions
void	initialize (core::pose::Pose &pose)

void	reinitialize (core::pose::Pose &pose)

void	initialize_working_parameters_and_root (core::pose::Pose &pose)

void	initialize_scorefunctions (core::pose::Pose const &pose)

void	initialize_constraints (core::pose::Pose &pose)

void	do_prepacking (core::pose::Pose &pose)

void	do_sampling (core::pose::Pose &pose)

void	do_minimizing (core::pose::Pose &pose)

void	do_stepwise_lores (core::pose::Pose &pose)

void	figure_out_moving_res_list (core::pose::Pose const &pose)

void	figure_out_moving_res_list_from_most_distal_res (core::pose::Pose const &pose, core::Size const moving_res)

bool	sampling_successful ()

void	look_for_precompute_move (core::pose::Pose &pose)

Private Attributes
core::Size	moving_res_

utility::vector1< core::Size >	moving_res_list_

utility::vector1< core::Size >	working_minimize_res_

utility::vector1< core::Size >	working_prepack_res_

working_parameters::StepWiseWorkingParametersCOP	working_parameters_

options::StepWiseModelerOptionsCOP	options_

core::scoring::ScoreFunctionCOP	scorefxn_

core::scoring::ScoreFunctionCOP	sample_scorefxn_

core::scoring::ScoreFunctionCOP	pack_scorefxn_

utility::vector1< protein::InputStreamWithResidueInfoOP >	input_streams_

utility::vector1< core::pose::PoseOP >	pose_list_

bool	figure_out_prepack_res_

bool	prepack_res_was_inputted_

packer::StepWiseMasterPackerOP	master_packer_

core::scoring::constraints::ConstraintSetOP	cst_set_

precomputed::PrecomputedLibraryMoverCOP	precomputed_library_mover_

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

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...

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...

Constructor & Destructor Documentation

◆ StepWiseModeler() [1/3]

protocols::stepwise::modeler::StepWiseModeler::StepWiseModeler	(	core::Size const	moving_res,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

References set_moving_res_and_reset().

◆ StepWiseModeler() [2/3]

protocols::stepwise::modeler::StepWiseModeler::StepWiseModeler ( core::scoring::ScoreFunctionCOP scorefxn )

◆ ~StepWiseModeler()

protocols::stepwise::modeler::StepWiseModeler::~StepWiseModeler ( )

overridedefault

◆ StepWiseModeler() [3/3]

protocols::stepwise::modeler::StepWiseModeler::StepWiseModeler ( StepWiseModeler const & src )

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::StepWiseModeler::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References do_minimizing(), do_prepacking(), do_sampling(), do_stepwise_lores(), initialize(), options_, reinitialize(), and sampling_successful().

◆ clone_modeler()

StepWiseModelerOP protocols::stepwise::modeler::StepWiseModeler::clone_modeler ( ) const

virtual

◆ do_minimizing()

void protocols::stepwise::modeler::StepWiseModeler::do_minimizing ( core::pose::Pose & pose )

private

References master_packer_, options_, pose_list_, scorefxn_, and working_parameters_.

Referenced by apply().

◆ do_prepacking()

void protocols::stepwise::modeler::StepWiseModeler::do_prepacking ( core::pose::Pose & pose )

private

References master_packer_, options_, pack_scorefxn_, working_parameters_, and working_prepack_res_.

Referenced by apply().

◆ do_sampling()

void protocols::stepwise::modeler::StepWiseModeler::do_sampling ( core::pose::Pose & pose )

private

References protocols::stepwise::modeler::StepWiseConnectionSampler::apply(), protocols::stepwise::modeler::StepWiseConnectionSampler::get_pose_list(), input_streams_, master_packer_, options_, pose_list_, sample_scorefxn_, protocols::stepwise::modeler::StepWiseConnectionSampler::set_input_streams(), protocols::stepwise::modeler::StepWiseConnectionSampler::set_master_packer(), protocols::stepwise::modeler::StepWiseConnectionSampler::set_options(), protocols::stepwise::modeler::StepWiseConnectionSampler::set_scorefxn(), and working_parameters_.

Referenced by apply().

◆ do_stepwise_lores()

void protocols::stepwise::modeler::StepWiseModeler::do_stepwise_lores ( core::pose::Pose & pose )

private

References protocols::rna::movers::RNA_DeNovoOptimizer::apply(), core::pose::Pose::clone(), pose_list_, core::pose::remove_variant_type_from_pose_residue(), scorefxn_, core::pose::Pose::size(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by apply().

◆ figure_out_moving_res_list()

void protocols::stepwise::modeler::StepWiseModeler::figure_out_moving_res_list ( core::pose::Pose const & pose )

private

References figure_out_moving_res_list_from_most_distal_res(), moving_res_, and moving_res_list_.

Referenced by initialize_working_parameters_and_root().

◆ figure_out_moving_res_list_from_most_distal_res()

void protocols::stepwise::modeler::StepWiseModeler::figure_out_moving_res_list_from_most_distal_res	(	core::pose::Pose const &	pose,
		core::Size const	moving_res
	)

private

References protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), and moving_res_list_.

Referenced by figure_out_moving_res_list().

◆ get_name()

std::string protocols::stepwise::modeler::StepWiseModeler::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ get_num_sampled()

core::Size protocols::stepwise::modeler::StepWiseModeler::get_num_sampled ( )

inline

References pose_list_.

◆ initialize()

void protocols::stepwise::modeler::StepWiseModeler::initialize ( core::pose::Pose & pose )

private

References figure_out_prepack_res_, initialize_scorefunctions(), initialize_working_parameters_and_root(), moving_res_list_, pose_list_, and prepack_res_was_inputted_.

Referenced by apply().

◆ initialize_constraints()

void protocols::stepwise::modeler::StepWiseModeler::initialize_constraints ( core::pose::Pose & pose )

private

References core::pose::full_model_info::const_full_model_info(), and core::pose::Pose::constraint_set().

Referenced by initialize_working_parameters_and_root().

◆ initialize_scorefunctions()

void protocols::stepwise::modeler::StepWiseModeler::initialize_scorefunctions ( core::pose::Pose const & pose )

private

References protocols::stepwise::modeler::initialize_pack_scorefxn(), protocols::stepwise::modeler::initialize_sample_scorefxn(), options_, pack_scorefxn_, sample_scorefxn_, and scorefxn_.

Referenced by initialize().

◆ initialize_working_parameters_and_root()

void protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root ( core::pose::Pose & pose )

private

References protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), core::pose::Pose::constraint_set(), cst_set_, figure_out_moving_res_list(), figure_out_prepack_res_, protocols::stepwise::modeler::packer::figure_out_working_interface_res(), core::pose::fix_up_residue_type_variants(), protocols::stepwise::modeler::get_all_working_moving_res(), protocols::moves::Mover::get_native_pose(), initialize_constraints(), look_for_precompute_move(), core::pose::full_model_info::make_sure_full_model_info_is_setup(), moving_res_list_, options_, protocols::stepwise::modeler::revise_root_and_moving_res_list(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), working_minimize_res_, working_parameters_, and working_prepack_res_.

Referenced by initialize().

◆ look_for_precompute_move()

void protocols::stepwise::modeler::StepWiseModeler::look_for_precompute_move ( core::pose::Pose & pose )

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::get_moving_res_from_full_model_info(), moving_res_, precomputed_library_mover_, set_moving_res_and_reset(), set_working_minimize_res(), and set_working_prepack_res().

Referenced by initialize_working_parameters_and_root().

◆ operator=()

StepWiseModeler & protocols::stepwise::modeler::StepWiseModeler::operator= ( StepWiseModeler const & src )

References figure_out_prepack_res_, input_streams_, moving_res_, moving_res_list_, options_, precomputed_library_mover_, prepack_res_was_inputted_, scorefxn_, working_minimize_res_, and working_prepack_res_.

◆ options()

options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseModeler::options ( )

inline

References options_.

Referenced by set_options().

◆ precomputed_library_mover()

precomputed::PrecomputedLibraryMoverCOP protocols::stepwise::modeler::StepWiseModeler::precomputed_library_mover ( )

inline

References precomputed_library_mover_.

Referenced by set_precomputed_library_mover().

◆ reinitialize()

void protocols::stepwise::modeler::StepWiseModeler::reinitialize ( core::pose::Pose & pose )

private

References core::pose::Pose::constraint_set(), cst_set_, figure_out_prepack_res_, moving_res_list_, prepack_res_was_inputted_, working_minimize_res_, working_parameters_, and working_prepack_res_.

Referenced by apply().

◆ sampling_successful()

bool protocols::stepwise::modeler::StepWiseModeler::sampling_successful ( )

private

References options_, pose_list_, and protocols::TR().

Referenced by apply().

◆ scorefxn()

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseModeler::scorefxn ( )

inline

References scorefxn_.

◆ set_figure_out_prepack_res()

void protocols::stepwise::modeler::StepWiseModeler::set_figure_out_prepack_res ( bool const setting )

inline

References figure_out_prepack_res_.

◆ set_input_streams()

void protocols::stepwise::modeler::StepWiseModeler::set_input_streams ( utility::vector1< protein::InputStreamWithResidueInfoOP > const & input_streams )

References input_streams_.

◆ set_moving_res_and_reset()

void protocols::stepwise::modeler::StepWiseModeler::set_moving_res_and_reset ( core::Size const moving_res )

References moving_res_, and working_parameters_.

Referenced by look_for_precompute_move(), and StepWiseModeler().

◆ set_moving_res_list()

void protocols::stepwise::modeler::StepWiseModeler::set_moving_res_list ( utility::vector1< core::Size > const & setting )

inline

References moving_res_list_.

◆ set_options()

void protocols::stepwise::modeler::StepWiseModeler::set_options ( options::StepWiseModelerOptionsCOP options )

inline

References options(), and options_.

◆ set_precomputed_library_mover()

void protocols::stepwise::modeler::StepWiseModeler::set_precomputed_library_mover ( precomputed::PrecomputedLibraryMoverCOP precomputed_library_mover )

inline

References precomputed_library_mover(), and precomputed_library_mover_.