Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::movers::RNA_LoopCloser Class Reference

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

#include <RNA_LoopCloser.hh>

Inheritance diagram for protocols::rna::movers::RNA_LoopCloser:
Inheritance graph
[legend]

Public Member Functions

 RNA_LoopCloser ()
 Construct the protocol object. More...
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void apply (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections)
 Apply the loop-rebuild protocol to the input pose. More...
 
core::Real apply (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections, core::Size const &cutpoint)
 Apply the loop-rebuild protocol to the input pose. More...
 
core::Real apply (core::pose::Pose &pose, core::Size const &cutpoint)
 Apply the loop-rebuild protocol to the input pose. More...
 
void apply (core::pose::Pose &pose, utility::vector1< core::Size > const &cutpoints)
 Apply the loop-rebuild protocol to the input pose. More...
 
void fast_scan (bool const &setting)
 
bool check_closure (core::pose::Pose const &pose, core::Size const i, core::Real ccd_tolerance=-1.0)
 
bool check_closure (core::pose::Pose const &pose, core::Real ccd_tolerance=-1.0)
 
core::Real get_dist_err (core::pose::Pose const &pose, core::Size const cutpoint) const
 
void set_verbose (bool const setting)
 
void set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapCOP setting)
 
utility::vector1< core::Sizeget_cutpoints_closed (core::pose::Pose const &pose) const
 
- 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 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

bool passes_fast_scan (core::pose::Pose &pose, core::Size const i) const
 
core::Real rna_ccd_close (core::pose::Pose &pose, std::map< core::Size, core::Size > const &connections, core::Size const &cutpoint) const
 
core::Real get_chainbreak_xyz (core::pose::Pose const &pose, core::Size const cutpoint, utility::vector1< core::Vector > &upstream_xyzs, utility::vector1< core::Vector > &downstream_xyzs, core::Size const cutpoint_next_input=0) const
 
core::Real get_gap_distance (core::pose::Pose &pose, core::Size const cutpoint) const
 

Private Attributes

bool verbose_
 
core::Size NUM_ROUNDS_
 
bool check_tolerance_
 
core::Real ccd_tolerance_
 
core::Real absolute_ccd_tolerance_
 
core::Real attempt_closure_cutoff_
 
core::Real gap_distance_cutoff_
 
bool fast_scan_
 
core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map_
 

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::movers::RNA_LoopCloser::RNA_LoopCloser ( )

Construct the protocol object.

Member Function Documentation

void protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose )
overridevirtual
void protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose pose,
std::map< core::Size, core::Size > const &  connections 
)

Apply the loop-rebuild protocol to the input pose.

Apply the RNA loop closer

References apply(), fast_scan_, get_cutpoints_closed(), and passes_fast_scan().

Real protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose pose,
std::map< core::Size, core::Size > const &  connections,
core::Size const &  cutpoint 
)

Apply the loop-rebuild protocol to the input pose.

References rna_ccd_close(), protocols::rna::movers::TR(), and verbose_.

Real protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose pose,
core::Size const &  cutpoint 
)

Apply the loop-rebuild protocol to the input pose.

References rna_ccd_close(), protocols::rna::movers::TR(), and verbose_.

void protocols::rna::movers::RNA_LoopCloser::apply ( core::pose::Pose pose,
utility::vector1< core::Size > const &  cutpoints 
)

Apply the loop-rebuild protocol to the input pose.

References apply().

bool protocols::rna::movers::RNA_LoopCloser::check_closure ( core::pose::Pose const &  pose,
core::Size const  i,
core::Real  ccd_tolerance = -1.0 
)
bool protocols::rna::movers::RNA_LoopCloser::check_closure ( core::pose::Pose const &  pose,
core::Real  ccd_tolerance = -1.0 
)
protocols::moves::MoverOP protocols::rna::movers::RNA_LoopCloser::clone ( ) const
inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

void protocols::rna::movers::RNA_LoopCloser::fast_scan ( bool const &  setting)
inline

References fast_scan_.

Real protocols::rna::movers::RNA_LoopCloser::get_chainbreak_xyz ( core::pose::Pose const &  pose,
core::Size const  cutpoint,
utility::vector1< core::Vector > &  upstream_xyzs,
utility::vector1< core::Vector > &  downstream_xyzs,
core::Size const  cutpoint_next_input = 0 
) const
private
utility::vector1< core::Size > protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed ( core::pose::Pose const &  pose) const
Real protocols::rna::movers::RNA_LoopCloser::get_dist_err ( core::pose::Pose const &  pose,
core::Size const  cutpoint 
) const

References get_chainbreak_xyz().

Referenced by check_closure(), and passes_fast_scan().

Real protocols::rna::movers::RNA_LoopCloser::get_gap_distance ( core::pose::Pose pose,
core::Size const  cutpoint 
) const
private
std::string protocols::rna::movers::RNA_LoopCloser::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::rna::movers::RNA_LoopCloser::passes_fast_scan ( core::pose::Pose pose,
core::Size const  i 
) const
private
Real protocols::rna::movers::RNA_LoopCloser::rna_ccd_close ( core::pose::Pose pose,
std::map< core::Size, core::Size > const &  connections,
core::Size const &  cutpoint 
) const
private
void protocols::rna::movers::RNA_LoopCloser::set_atom_level_domain_map ( core::pose::toolbox::AtomLevelDomainMapCOP  setting)
inline
void protocols::rna::movers::RNA_LoopCloser::set_verbose ( bool const  setting)
inline

References verbose_.

Member Data Documentation

core::Real protocols::rna::movers::RNA_LoopCloser::absolute_ccd_tolerance_
private

Referenced by check_closure(), and passes_fast_scan().

core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::movers::RNA_LoopCloser::atom_level_domain_map_
private
core::Real protocols::rna::movers::RNA_LoopCloser::attempt_closure_cutoff_
private

Referenced by passes_fast_scan().

core::Real protocols::rna::movers::RNA_LoopCloser::ccd_tolerance_
private

Referenced by rna_ccd_close().

bool protocols::rna::movers::RNA_LoopCloser::check_tolerance_
private

Referenced by rna_ccd_close().

bool protocols::rna::movers::RNA_LoopCloser::fast_scan_
private

Referenced by apply(), and fast_scan().

core::Real protocols::rna::movers::RNA_LoopCloser::gap_distance_cutoff_
private

Referenced by passes_fast_scan().

core::Size protocols::rna::movers::RNA_LoopCloser::NUM_ROUNDS_
private

Referenced by rna_ccd_close().

bool protocols::rna::movers::RNA_LoopCloser::verbose_
private

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