#include <StepWiseProteinModeler.hh>

Public Member Functions
	StepWiseProteinModeler (scoring::ScoreFunctionOP scorefxn)

	StepWiseProteinModeler (core::scoring::ScoreFunctionOP scorefxn, utility::vector1< Size > const &moving_res_list)

	StepWiseProteinModeler (StepWiseProteinModeler const &src)

	~StepWiseProteinModeler ()

StepWiseProteinModelerOP	clone_modeler () const
	clone the conformation More...

StepWiseProteinModeler &	operator= (StepWiseProteinModeler const &src)

virtual void	apply (pose::Pose &pose)

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

void	set_moving_res_and_reset (Size const moving_res)

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

void	set_skip_modeler (bool const &setting)

options::StepWiseModelerOptionsCOP	options ()

void	set_options (options::StepWiseModelerOptionsCOP options)

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

void	set_working_parameters (stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)

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

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

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

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

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

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
void	reinitialize ()

void	initialize_working_parameters_and_root (pose::Pose &pose)

void	do_residue_modeler (core::pose::Pose &pose, utility::vector1< pose::PoseOP > &pose_list)

void	do_minimizing (core::pose::Pose &pose, utility::vector1< pose::PoseOP > &pose_list)

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP	setup_working_parameters_for_stepwise_with_full_model_info (core::pose::Pose &pose)

void	figure_out_moving_res_list (pose::Pose const &pose)

void	figure_out_protein_moving_res_list_from_most_distal_res (pose::Pose const &pose, Size const moving_res)

bool	modeler_successful (utility::vector1< pose::PoseOP > &pose_list)

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	pack_scorefxn_

utility::vector1< Size >	moving_res_list_

Size	moving_res_

bool	full_optimize_

bool	do_ccd_

options::StepWiseModelerOptionsCOP	options_

stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP	working_parameters_

utility::vector1 < InputStreamWithResidueInfoOP >	input_streams_

utility::vector1< Size >	bridge_res_

utility::vector1< Size >	working_minimize_res_

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 protocols::filters::Filters_map	Filters_map

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

protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::StepWiseProteinModeler ( scoring::ScoreFunctionOP scorefxn )

Referenced by clone_modeler().

protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::StepWiseProteinModeler	(	core::scoring::ScoreFunctionOP	scorefxn,
		utility::vector1< Size > const &	moving_res_list
	)

protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::StepWiseProteinModeler ( StepWiseProteinModeler const & src )

protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::~StepWiseProteinModeler ( )

Member Function Documentation

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::apply ( pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References do_minimizing(), do_residue_modeler(), initialize_working_parameters_and_root(), modeler_successful(), reinitialize(), and core::pose::Pose::remove_constraints().

StepWiseProteinModelerOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::clone_modeler ( ) const

clone the conformation

References StepWiseProteinModeler().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::do_minimizing	(	core::pose::Pose &	pose,
		utility::vector1< pose::PoseOP > &	pose_list
	)

private

References atom_pair_constraint, cart_bonded, protocols::stepwise::modeler::check_scorefxn_has_constraint_terms_if_pose_has_constraints(), core::scoring::ScoreFunction::clone(), core::pose::Pose::clone(), coordinate_constraint, elec_dens_atomwise, full_optimize_, protocols::stepwise::modeler::get_file_name(), protocols::moves::Mover::get_native_pose(), linear_chainbreak, make_vector1(), moving_res_list_, options_, protocols::stepwise::legacy::modeler::protein::output_silent_struct(), scorefxn_, tag, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::do_residue_modeler	(	core::pose::Pose &	pose,
		utility::vector1< pose::PoseOP > &	pose_list
	)

private

References protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::apply(), do_ccd_, full_optimize_, protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::get_pose_list(), input_streams_, moving_res_list_, options_, pack_scorefxn_, protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::set_input_streams(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::set_options(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::set_scorefxn(), and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::figure_out_moving_res_list ( pose::Pose const & pose )

private

References figure_out_protein_moving_res_list_from_most_distal_res(), moving_res_, and moving_res_list_.

Referenced by initialize_working_parameters_and_root().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::figure_out_protein_moving_res_list_from_most_distal_res	(	pose::Pose const &	pose,
		Size const	moving_res
	)

private

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

Referenced by figure_out_moving_res_list().

virtual std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::initialize_working_parameters_and_root ( pose::Pose & pose )

private

References protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), figure_out_moving_res_list(), protocols::moves::Mover::get_native_pose(), moving_res_list_, options_, protocols::stepwise::modeler::revise_root_and_moving_res_list(), setup_working_parameters_for_stepwise_with_full_model_info(), and working_parameters_.

Referenced by apply().

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::modeler_successful ( utility::vector1< pose::PoseOP > & pose_list )

private

References options_, and protocols::TR.

Referenced by apply().

StepWiseProteinModeler & protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::operator= ( StepWiseProteinModeler const & src )

References bridge_res_, do_ccd_, full_optimize_, input_streams_, moving_res_, moving_res_list_, options_, pack_scorefxn_, scorefxn_, working_minimize_res_, and working_parameters_.

options::StepWiseModelerOptionsCOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::options ( )

References options_.

Referenced by set_options().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::reinitialize ( )

private

References bridge_res_, do_ccd_, moving_res_list_, working_minimize_res_, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_bridge_res ( utility::vector1< Size > const & setting )

inline

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

References input_streams_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_moving_res_and_reset ( Size const moving_res )

References moving_res_, and moving_res_list_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_moving_res_list ( utility::vector1< Size > const & setting )

inline

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_options ( options::StepWiseModelerOptionsCOP options )

References options(), and options_.

Referenced by set_skip_modeler().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_skip_modeler ( bool const & setting )

References options_, and set_options().

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_working_minimize_res ( utility::vector1< Size > const & setting )

inline

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::set_working_parameters ( stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters )

References working_parameters_.

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::setup_working_parameters_for_stepwise_with_full_model_info ( core::pose::Pose & pose )

private

References bridge_res_, protocols::moves::Mover::get_native_pose(), moving_res_list_, protocols::stepwise::legacy::modeler::protein::setup_protein_working_parameters_for_swa(), and working_minimize_res_.

Referenced by initialize_working_parameters_and_root().

Member Data Documentation

utility::vector1< Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::bridge_res_

private

Referenced by figure_out_protein_moving_res_list_from_most_distal_res(), operator=(), reinitialize(), and setup_working_parameters_for_stepwise_with_full_model_info().

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::do_ccd_

private

Referenced by do_residue_modeler(), figure_out_protein_moving_res_list_from_most_distal_res(), operator=(), and reinitialize().

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::full_optimize_

private

Referenced by do_minimizing(), do_residue_modeler(), and operator=().

utility::vector1< InputStreamWithResidueInfoOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::input_streams_

private

Referenced by do_residue_modeler(), operator=(), and set_input_streams().

Size protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::moving_res_

private

Referenced by figure_out_moving_res_list(), operator=(), and set_moving_res_and_reset().

utility::vector1< Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::moving_res_list_

private

Referenced by do_minimizing(), do_residue_modeler(), figure_out_moving_res_list(), figure_out_protein_moving_res_list_from_most_distal_res(), initialize_working_parameters_and_root(), operator=(), reinitialize(), set_moving_res_and_reset(), and setup_working_parameters_for_stepwise_with_full_model_info().

options::StepWiseModelerOptionsCOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::options_

private

Referenced by do_minimizing(), do_residue_modeler(), initialize_working_parameters_and_root(), modeler_successful(), operator=(), options(), set_options(), and set_skip_modeler().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::pack_scorefxn_

private

Referenced by do_residue_modeler(), and operator=().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::scorefxn_

private

Referenced by do_minimizing(), and operator=().

utility::vector1< Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::working_minimize_res_

private

Referenced by operator=(), reinitialize(), and setup_working_parameters_for_stepwise_with_full_model_info().

stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler::working_parameters_

private

Referenced by do_minimizing(), do_residue_modeler(), initialize_working_parameters_and_root(), operator=(), reinitialize(), and set_working_parameters().

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

src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinModeler.hh
src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinModeler.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation