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protocols::rna::RNA_HelixAssembler Class Reference

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

#include <RNA_HelixAssembler.hh>

Inheritance diagram for protocols::rna::RNA_HelixAssembler:
Inheritance graph
Collaboration diagram for protocols::rna::RNA_HelixAssembler:
Collaboration graph

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)
Moveroperator= (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 Stringsinfo ()
 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 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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rna::RNA_HelixAssembler::RNA_HelixAssembler ( )

Construct the protocol object.

References core::scoring::atom_pair_constraint, core::scoring::rna_torsion, and scorefxn.

Referenced by clone().

Member Function Documentation

void protocols::rna::RNA_HelixAssembler::apply ( core::pose::Pose pose)

Apply the RNA HelixAssembler

Implements protocols::moves::Mover.

References core::pose::Pose::sequence().

void protocols::rna::RNA_HelixAssembler::apply ( core::pose::Pose pose,
std::string const &  sequence 
void protocols::rna::RNA_HelixAssembler::build_on_base_pair ( core::pose::Pose pose,
Size const &  n,
char const &  seq1,
char const &  seq2 
protocols::moves::MoverOP protocols::rna::RNA_HelixAssembler::clone ( ) const

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_HelixAssembler().

std::string protocols::rna::RNA_HelixAssembler::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs ( core::pose::Pose pose)
void protocols::rna::RNA_HelixAssembler::minimize_base_step ( core::pose::Pose pose,
Size const  n 
void protocols::rna::RNA_HelixAssembler::put_constraints_on_base_step ( core::pose::Pose pose,
Size const &  n 
void protocols::rna::RNA_HelixAssembler::random_perturbation ( bool const &  setting)

References random_perturbation_.

void protocols::rna::RNA_HelixAssembler::set_Aform_torsions ( core::pose::Pose pose,
Size const &  n 
void protocols::rna::RNA_HelixAssembler::set_minimize_all ( bool const &  setting)

References minimize_all_.

void protocols::rna::RNA_HelixAssembler::set_model_and_remove_capping_residues ( bool  setting)
void protocols::rna::RNA_HelixAssembler::set_scorefxn ( core::scoring::ScoreFunctionOP  setting)

References scorefxn.

void protocols::rna::RNA_HelixAssembler::use_phenix_geo ( bool const  setting)

Member Data Documentation

core::Real const protocols::rna::RNA_HelixAssembler::ALPHA_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::BETA_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::CHI_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::DELTA_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::EPSILON_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::GAMMA_A_FORM
protocols::rna::RNA_IdealCoord protocols::rna::RNA_HelixAssembler::ideal_coord_
std::string const protocols::rna::RNA_HelixAssembler::ideal_jump

Referenced by apply().

bool protocols::rna::RNA_HelixAssembler::minimize_all_
bool protocols::rna::RNA_HelixAssembler::model_and_remove_capping_residues_
core::Real const protocols::rna::RNA_HelixAssembler::NU1_A_FORM
core::Real const protocols::rna::RNA_HelixAssembler::NU2_A_FORM
core::Real protocols::rna::RNA_HelixAssembler::perturb_amplitude_

Referenced by build_on_base_pair().

bool protocols::rna::RNA_HelixAssembler::random_perturbation_
core::chemical::ResidueTypeSetCAP protocols::rna::RNA_HelixAssembler::rsd_set
core::scoring::ScoreFunctionOP protocols::rna::RNA_HelixAssembler::scorefxn
bool protocols::rna::RNA_HelixAssembler::use_phenix_geo_
bool protocols::rna::RNA_HelixAssembler::verbose_

Referenced by apply().

core::Real const protocols::rna::RNA_HelixAssembler::ZETA_A_FORM

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