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protocols::rna::denovo::movers::RNP_HighResMover Class Reference

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

#include <RNP_HighResMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNP_HighResMover:
Inheritance graph
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Public Member Functions

 RNP_HighResMover (RNA_FragmentMoverOP rna_fragment_mover, protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer, core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options)
 Construct the protocol object given the RNA fragment library to use. More...
 
 ~RNP_HighResMover () override
 
void initialize (core::pose::Pose const &pose)
 
void apply (core::pose::Pose &pose) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void protein_sidechain_packing (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn) const
 
void rnp_docking (core::pose::Pose &pose) const
 

Private Attributes

RNA_FragmentMoverOP rna_fragment_mover_
 
protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer_
 
core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options_
 
core::Size const fragment_cycles_
 
core::Size const frag_size_
 
core::Real protein_sc_pack_cutoff_
 
bool is_init_
 
core::kinematics::FoldTree rnp_docking_ft_
 
protocols::rigid::RigidBodyPerturbMoverOP rnp_docking_mover_
 
bool docking_
 

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 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...
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rna::denovo::movers::RNP_HighResMover::RNP_HighResMover ( RNA_FragmentMoverOP  rna_fragment_mover,
protocols::rna::movers::RNA_LoopCloserOP  rna_loop_closer,
core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP  options 
)

Construct the protocol object given the RNA fragment library to use.

References protein_sc_pack_cutoff_.

protocols::rna::denovo::movers::RNP_HighResMover::~RNP_HighResMover ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::movers::RNP_HighResMover::apply ( core::pose::Pose pose)
overridevirtual
std::string protocols::rna::denovo::movers::RNP_HighResMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::movers::RNP_HighResMover::initialize ( core::pose::Pose const &  pose)
void protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP const &  packer_scorefxn 
) const
private
void protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking ( core::pose::Pose pose) const
private

References rnp_docking_mover_.

Referenced by apply().

Member Data Documentation

bool protocols::rna::denovo::movers::RNP_HighResMover::docking_
private

Referenced by apply(), and initialize().

core::Size const protocols::rna::denovo::movers::RNP_HighResMover::frag_size_
private

Referenced by apply().

core::Size const protocols::rna::denovo::movers::RNP_HighResMover::fragment_cycles_
private

Referenced by apply().

bool protocols::rna::denovo::movers::RNP_HighResMover::is_init_
private

Referenced by apply(), and initialize().

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP protocols::rna::denovo::movers::RNP_HighResMover::options_
private

Referenced by apply(), and initialize().

core::Real protocols::rna::denovo::movers::RNP_HighResMover::protein_sc_pack_cutoff_
private
RNA_FragmentMoverOP protocols::rna::denovo::movers::RNP_HighResMover::rna_fragment_mover_
private

Referenced by apply().

protocols::rna::movers::RNA_LoopCloserOP protocols::rna::denovo::movers::RNP_HighResMover::rna_loop_closer_
private

Referenced by apply().

core::kinematics::FoldTree protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking_ft_
private
protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking_mover_
private

Referenced by initialize(), and rnp_docking().


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