protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler Class Reference

#include <MultiPhosphateSampler.hh>

Public Member Functions
	MultiPhosphateSampler (pose::Pose &pose_to_prepack, Size const moving_res)
	MultiPhosphateSampler (pose::Pose const &reference_pose)
	~MultiPhosphateSampler ()
MultiPhosphateSamplerOP	clone_sampler () const
virtual moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
void	apply (core::pose::Pose &pose)
std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	sample_phosphates ()
void	sample_phosphates (pose::PoseOP &viewer_pose_op)
void	copy_phosphates (pose::Pose &mod_pose) const
void	reset_to_original_pose ()
void	set_screen_all (bool const &setting)
bool	screen_all () const
bool	instantiated_some_phosphate () const
void	set_moving_partition_res (utility::vector1< Size > const &setting)
void	set_five_prime_phosphate_res (utility::vector1< Size > const &setting)
void	set_three_prime_phosphate_res (utility::vector1< Size > const &setting)
pose::Pose &	pose ()
void	set_scorefxn (scoring::ScoreFunctionOP scorefxn)
utility::vector1< PhosphateMove >	phosphate_move_list () const
void	set_phosphate_move_list (utility::vector1< PhosphateMove > const &setting)
utility::vector1< Size > const &	moving_partition_res ()
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
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 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	initialize_parameters ()
void	initialize_by_prepack (pose::Pose &pose, Size const moving_res)
utility::vector1< PhosphateMove >	initialize_phosphate_move_list (pose::Pose &pose)
utility::vector1< PhosphateMove >	check_moved (utility::vector1< PhosphateMove > phosphate_move_list, pose::Pose const &pose) const
void	find_phosphate_contacts_other_partition (utility::vector1< Size > const &partition_res1, utility::vector1< Size > const &partition_res2, pose::Pose const &pose, utility::vector1< PhosphateMove > const &phosphate_move_list, utility::vector1< PhosphateMove > &actual_phosphate_move_list) const
bool	check_other_partition_for_contact (pose::Pose const &pose, utility::vector1< Size > const &other_partition_res, Vector const &takeoff_xyz) const

Private Attributes
pose::PoseCOP	pose_with_original_phosphates_
pose::PoseOP	phosphate_sample_pose_
scoring::ScoreFunctionOP	scorefxn_
Real	phosphate_takeoff_donor_distance_cutoff2_
bool	screen_all_
utility::vector1< Size >	moving_partition_res_
utility::vector1< Size >	five_prime_phosphate_res_input_
utility::vector1< Size >	three_prime_phosphate_res_input_
utility::vector1< PhosphateMove >	phosphate_move_list_
utility::vector1< PhosphateMove >	actual_phosphate_move_list_
bool	instantiated_some_phosphate_
bool	prepacked_

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::sampling::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler	(	pose::Pose &	pose_to_prepack,
		Size const	moving_res
	)

References initialize_by_prepack(), initialize_parameters(), and prepacked_.

Referenced by clone_sampler().

protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler

(

pose::Pose const &

reference_pose

)

References clone(), initialize_parameters(), and prepacked_.

protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::~MultiPhosphateSampler

(

)

Member Function Documentation

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::apply ( core::pose::Pose &  pose )

inlinevirtual

Implements protocols::moves::Mover.

utility::vector1< PhosphateMove > protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::check_moved ( utility::vector1< PhosphateMove >  phosphate_move_list, pose::Pose const &  pose  ) const

private

References find_phosphate_contacts_other_partition(), utility::vector1< T, class >::has_value(), core::conformation::Residue::is_RNA(), moving_partition_res_, pose_with_original_phosphates_, prepacked_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by sample_phosphates().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact ( pose::Pose const &  pose, utility::vector1< Size > const &  other_partition_res, Vector const &  takeoff_xyz  ) const

private

References core::chemical::ResidueType::Hpos_polar(), phosphate_takeoff_donor_distance_cutoff2_, q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by find_phosphate_contacts_other_partition().

virtual moves::MoverOP protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::clone ( ) const

inlinevirtual

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.

MultiPhosphateSamplerOP protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::clone_sampler

(

)

const

References MultiPhosphateSampler(), phosphate_move_list_, pose_with_original_phosphates_, and screen_all_.

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::copy_phosphates

(

pose::Pose &

mod_pose

)

const

References protocols::stepwise::sampling::rna::phosphate::copy_over_phosphate_variants(), phosphate_move_list_, and phosphate_sample_pose_.

Referenced by protocols::stepwise::monte_carlo::rna::DeleteMover::minimize_after_delete().

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::find_phosphate_contacts_other_partition ( utility::vector1< Size > const &  partition_res1, utility::vector1< Size > const &  partition_res2, pose::Pose const &  pose, utility::vector1< PhosphateMove > const &  phosphate_move_list, utility::vector1< PhosphateMove > &  actual_phosphate_move_list  ) const

private

References check_other_partition_for_contact(), protocols::stepwise::sampling::rna::phosphate::FIVE_PRIME_PHOSPHATE, utility::vector1< T, class >::has_value(), core::pose::Pose::residue(), protocols::stepwise::sampling::rna::phosphate::PhosphateMove::rsd(), protocols::stepwise::sampling::rna::phosphate::PhosphateMove::terminus(), and core::conformation::Residue::xyz().

Referenced by check_moved().

std::string protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack ( pose::Pose &  pose, Size const  moving_res  )

private

References core::pose::Pose::clone(), protocols::stepwise::sampling::rna::phosphate::copy_over_phosphate_variants(), protocols::stepwise::figure_out_moving_partition_res_for_jump(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), jump_nr, moving_partition_res_, phosphate_move_list_, phosphate_sample_pose_, pose_with_original_phosphates_, core::pose::Pose::remove_constraints(), sample_phosphates(), and protocols::stepwise::split_pose().

Referenced by MultiPhosphateSampler().

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::initialize_parameters ( )

private

References phosphate_takeoff_donor_distance_cutoff2_, scorefxn_, and screen_all_.

Referenced by MultiPhosphateSampler().

utility::vector1< PhosphateMove > protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list ( pose::Pose &  pose )

private

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), protocols::stepwise::sampling::rna::phosphate::FIVE_PRIME_PHOSPHATE, five_prime_phosphate_res_input_, core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), phosphate_move_list(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), screen_all_, core::pose::full_model_info::FullModelInfo::size(), protocols::stepwise::sampling::rna::phosphate::THREE_PRIME_PHOSPHATE, three_prime_phosphate_res_input_, and core::pose::Pose::total_residue().

Referenced by sample_phosphates().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate ( ) const

inline

utility::vector1< Size > const& protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::moving_partition_res ( )

inline

utility::vector1< PhosphateMove> protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::phosphate_move_list ( ) const

inline

Referenced by initialize_phosphate_move_list().

pose::Pose & protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::pose

(

)

References phosphate_sample_pose_.

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::reset_to_original_pose

(

)

References phosphate_sample_pose_, and pose_with_original_phosphates_.

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::sample_phosphates

(

)

References actual_phosphate_move_list_, protocols::stepwise::sampling::rna::phosphate::PhosphateMover::apply(), check_moved(), protocols::stepwise::sampling::rna::phosphate::copy_over_phosphate_variants(), initialize_phosphate_move_list(), protocols::stepwise::sampling::rna::phosphate::PhosphateMover::instantiated_phosphate(), instantiated_some_phosphate_, phosphate_move_list_, phosphate_sample_pose_, pose_with_original_phosphates_, and scorefxn_.

Referenced by initialize_by_prepack(), protocols::stepwise::monte_carlo::rna::DeleteMover::minimize_after_delete(), and sample_phosphates().

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::sample_phosphates

(

pose::PoseOP &

viewer_pose_op

)

References phosphate_sample_pose_, and sample_phosphates().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::screen_all ( ) const

inline

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_five_prime_phosphate_res ( utility::vector1< Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_moving_partition_res ( utility::vector1< Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_phosphate_move_list ( utility::vector1< PhosphateMove > const &  setting )

inline

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_scorefxn

(

scoring::ScoreFunctionOP

scorefxn

)

References scorefxn_.

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_screen_all ( bool const &  setting )

inline

void protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::set_three_prime_phosphate_res ( utility::vector1< Size > const &  setting )

inline

Member Data Documentation

utility::vector1< PhosphateMove> protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::actual_phosphate_move_list_

private

Referenced by sample_phosphates().

utility::vector1< Size > protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::five_prime_phosphate_res_input_

private

Referenced by initialize_phosphate_move_list().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate_

private

Referenced by sample_phosphates().

utility::vector1< Size > protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::moving_partition_res_

private

Referenced by check_moved(), and initialize_by_prepack().

utility::vector1< PhosphateMove> protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::phosphate_move_list_

private

Referenced by clone_sampler(), copy_phosphates(), initialize_by_prepack(), and sample_phosphates().

pose::PoseOP protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::phosphate_sample_pose_

private

Referenced by copy_phosphates(), initialize_by_prepack(), pose(), reset_to_original_pose(), and sample_phosphates().

Real protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::phosphate_takeoff_donor_distance_cutoff2_

private

Referenced by check_other_partition_for_contact(), and initialize_parameters().

pose::PoseCOP protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::pose_with_original_phosphates_

private

Referenced by check_moved(), clone_sampler(), initialize_by_prepack(), reset_to_original_pose(), and sample_phosphates().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::prepacked_

private

Referenced by check_moved(), and MultiPhosphateSampler().

scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::scorefxn_

private

Referenced by initialize_parameters(), sample_phosphates(), and set_scorefxn().

bool protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::screen_all_

private

Referenced by clone_sampler(), initialize_parameters(), and initialize_phosphate_move_list().

utility::vector1< Size > protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::three_prime_phosphate_res_input_

private

Referenced by initialize_phosphate_move_list().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/phosphate/MultiPhosphateSampler.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/phosphate/MultiPhosphateSampler.cc