#include <PhosphateMover.hh>

Public Member Functions
	PhosphateMover (Size const sample_res, PhosphateTerminus which_terminus_, scoring::ScoreFunctionCOP scorefxn)

	PhosphateMover (PhosphateMove const phosphate_move, scoring::ScoreFunctionCOP scorefxn)

	~PhosphateMover ()

virtual void	apply (core::pose::Pose &pose_to_visualize)

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

void	screen_phosphate (pose::Pose &pose)

bool	instantiated_phosphate () const

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	initialize_variables ()

void	setup_variants_and_free_pose_for_terminal_phosphate (pose::Pose &pose)

void	setup_variants_and_free_pose_for_five_prime_phosphate (pose::Pose &pose)

void	setup_variants_and_free_pose_for_three_prime_phosphate (pose::Pose &pose)

void	screen_five_prime_phosphate (pose::Pose &pose)

void	screen_three_prime_phosphate (pose::Pose &pose)

void	setup_atom_and_neighbor_list (pose::Pose &pose)

bool	check_phosphate_contacts_donor (pose::Pose &pose) const

bool	pass_clash_check (std::string const atom_name, Size const n, pose::Pose &pose)

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::modeler::rna::phosphate::PhosphateMover::PhosphateMover	(	Size const	sample_res,
		PhosphateTerminus	which_terminus_,
		scoring::ScoreFunctionCOP	scorefxn
	)

References initialize_variables().

protocols::stepwise::modeler::rna::phosphate::PhosphateMover::PhosphateMover	(	PhosphateMove const	phosphate_move,
		scoring::ScoreFunctionCOP	scorefxn
	)

References initialize_variables().

protocols::stepwise::modeler::rna::phosphate::PhosphateMover::~PhosphateMover ( )

Member Function Documentation

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply ( core::pose::Pose & pose_to_visualize )

virtual

Implements protocols::moves::Mover.

References do_screening_, screen_phosphate(), and setup_variants_and_free_pose_for_terminal_phosphate().

Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor ( pose::Pose & pose ) const

private

References cos_of(), donor_atom_xyz_list_, donor_base_atom_xyz_list_, op1_atom_idx_, op2_atom_idx_, phosphate_move_, core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), and core::conformation::Residue::xyz().

Referenced by screen_five_prime_phosphate(), and screen_three_prime_phosphate().

std::string protocols::stepwise::modeler::rna::phosphate::PhosphateMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::initialize_variables ( )

private

References do_screening_, force_phosphate_instantiation_, instantiated_phosphate_, number_score_calls_, and screen_for_donor_contact_.

Referenced by PhosphateMover().

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::instantiated_phosphate ( ) const

inline

Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check	(	std::string const	atom_name,
		Size const	n,
		pose::Pose &	pose
	)

private

References core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_type(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), neighbor_copy_dofs_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by screen_five_prime_phosphate(), and screen_three_prime_phosphate().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate ( pose::Pose & pose )

private

References ALPHA, BB, BETA, check_phosphate_contacts_donor(), force_phosphate_instantiation_, GAMMA, get_full_torsions(), instantiated_phosphate_, number_score_calls_, pass_clash_check(), phosphate_move_, pose_free_, protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), score, screen_for_donor_contact_, and core::pose::Pose::set_torsion().

Referenced by screen_phosphate().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_phosphate ( pose::Pose & pose )

References protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, instantiated_phosphate_, number_score_calls_, phosphate_move_, runtime_assert, screen_five_prime_phosphate(), screen_three_prime_phosphate(), setup_atom_and_neighbor_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.

Referenced by apply().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate ( pose::Pose & pose )

private

References BB, check_phosphate_contacts_donor(), core::pose::Pose::delta(), EPSILON, force_phosphate_instantiation_, get_epsilon_torsions(), get_full_torsions(), instantiated_phosphate_, number_score_calls_, pass_clash_check(), phosphate_move_, pose_free_, protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), score, screen_for_donor_contact_, core::pose::Pose::set_torsion(), and ZETA.

Referenced by screen_phosphate().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list ( pose::Pose & pose )

private

References core::chemical::ResidueType::atom_base(), core::conformation::Residue::atom_index(), donor_atom_xyz_list_, donor_base_atom_xyz_list_, protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, core::chemical::ResidueType::Hpos_polar(), core::conformation::Residue::nbr_atom_xyz(), neighbor_copy_dofs_, op1_atom_idx_, op2_atom_idx_, phosphate_move_, q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by screen_phosphate().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate ( pose::Pose & pose )

private

References add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), core::pose::Pose::clone(), protocols::stepwise::modeler::rna::phosphate::correctly_position_five_prime_phosphate(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), phosphate_move_, pose_free_, remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), runtime_assert, and sample_res.

Referenced by setup_variants_and_free_pose_for_terminal_phosphate().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_terminal_phosphate ( pose::Pose & pose )

private

References protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, phosphate_move_, runtime_assert, setup_variants_and_free_pose_for_five_prime_phosphate(), setup_variants_and_free_pose_for_three_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.

Referenced by apply().

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_three_prime_phosphate ( pose::Pose & pose )

private

References add_variant_type_to_pose_residue(), core::pose::Pose::clone(), phosphate_move_, pose_free_, remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), and sample_res.

Referenced by setup_variants_and_free_pose_for_terminal_phosphate().

Member Data Documentation

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::do_screening_

private

Referenced by apply(), and initialize_variables().

utility::vector1< Vector > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::donor_atom_xyz_list_

private

Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().

utility::vector1< Vector > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::donor_base_atom_xyz_list_

private

Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::force_phosphate_instantiation_

private

Referenced by initialize_variables(), screen_five_prime_phosphate(), and screen_three_prime_phosphate().

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::instantiated_phosphate_

private

Referenced by initialize_variables(), screen_five_prime_phosphate(), screen_phosphate(), and screen_three_prime_phosphate().

utility::vector1< Size > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::neighbor_copy_dofs_

private

Referenced by pass_clash_check(), and setup_atom_and_neighbor_list().

Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::number_score_calls_

private

Referenced by initialize_variables(), screen_five_prime_phosphate(), screen_phosphate(), and screen_three_prime_phosphate().

Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op1_atom_idx_

private

Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().

Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op2_atom_idx_

private

Referenced by check_phosphate_contacts_donor(), and setup_atom_and_neighbor_list().

PhosphateMove const protocols::stepwise::modeler::rna::phosphate::PhosphateMover::phosphate_move_

private

Referenced by check_phosphate_contacts_donor(), screen_five_prime_phosphate(), screen_phosphate(), screen_three_prime_phosphate(), setup_atom_and_neighbor_list(), setup_variants_and_free_pose_for_five_prime_phosphate(), setup_variants_and_free_pose_for_terminal_phosphate(), and setup_variants_and_free_pose_for_three_prime_phosphate().

pose::PoseOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pose_free_

private

Referenced by screen_five_prime_phosphate(), screen_three_prime_phosphate(), setup_variants_and_free_pose_for_five_prime_phosphate(), and setup_variants_and_free_pose_for_three_prime_phosphate().

scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::scorefxn_

private

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_for_donor_contact_

private

Referenced by initialize_variables(), screen_five_prime_phosphate(), and screen_three_prime_phosphate().

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

src/protocols/stepwise/modeler/rna/phosphate/PhosphateMover.hh
src/protocols/stepwise/modeler/rna/phosphate/PhosphateMover.cc

Private Attributes
PhosphateMove const	phosphate_move_

scoring::ScoreFunctionCOP	scorefxn_

bool	do_screening_

bool	screen_for_donor_contact_

bool	instantiated_phosphate_

bool	force_phosphate_instantiation_

pose::PoseOP	pose_free_

utility::vector1< Vector >	donor_atom_xyz_list_

utility::vector1< Vector >	donor_base_atom_xyz_list_

utility::vector1< Size >	neighbor_copy_dofs_

Size	op1_atom_idx_

Size	op2_atom_idx_

Size	number_score_calls_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation