The RNA de novo structure modeling protocol. More...

#include <RNA_HelixAssembler.hh>

Inheritance diagram for protocols::rna::RNA_HelixAssembler:

Collaboration diagram for protocols::rna::RNA_HelixAssembler:

Public Member Functions
	RNA_HelixAssembler ()
	Construct the protocol object. More...

virtual protocols::moves::MoverOP	clone () const
	Clone this object. More...

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

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

void	apply (core::pose::Pose &pose, std::string const &sequence)
	Apply the loop-rebuild protocol to the input pose. More...

void	random_perturbation (bool const &setting)

void	set_minimize_all (bool const &setting)

void	set_scorefxn (core::scoring::ScoreFunctionOP setting)

void	use_phenix_geo (bool const setting)

void	set_model_and_remove_capping_residues (bool 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

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 (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	set_Aform_torsions (core::pose::Pose &pose, Size const &n)

void	build_on_base_pair (core::pose::Pose &pose, Size const &n, char const &seq1, char const &seq2)

void	minimize_base_step (core::pose::Pose &pose, Size const n)

void	put_constraints_on_base_step (core::pose::Pose &pose, Size const &n)

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

Private Attributes
bool	verbose_

bool	random_perturbation_

bool	minimize_all_

bool	use_phenix_geo_

std::string const	ideal_jump

core::chemical::ResidueTypeSetCAP	rsd_set

core::Real const	ALPHA_A_FORM

core::Real const	BETA_A_FORM

core::Real const	GAMMA_A_FORM

core::Real const	DELTA_A_FORM

core::Real const	EPSILON_A_FORM

core::Real const	ZETA_A_FORM

core::Real const	CHI_A_FORM

core::Real const	NU2_A_FORM

core::Real const	NU1_A_FORM

core::Real	perturb_amplitude_

core::scoring::ScoreFunctionOP	scorefxn

protocols::rna::RNA_IdealCoord	ideal_coord_

bool	model_and_remove_capping_residues_

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...