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protocols::star::StarAbinitio Class Reference

#include <StarAbinitio.hh>

Inheritance diagram for protocols::star::StarAbinitio:
Inheritance graph
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Public Member Functions

 StarAbinitio ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
protocols::moves::MoverOP clone () const override
 Uses the copy constructor to create a new instance More...
 
protocols::moves::MoverOP fresh_instance () const override
 Uses the no-argument constructor to create a new instance More...
 
std::string get_name () const override
 Returns the name of this mover 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 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...
 
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 setup_kinematics (const protocols::loops::Loops &aligned, const utility::vector1< unsigned > &interior_cuts, core::pose::Pose &pose) const
 
void tear_down_kinematics (core::pose::Pose &pose) const
 Removes virtual residue, cutpoint variants and restores simple kinematics More...
 

Private Attributes

core::fragment::FragSetOP fragments_lg_
 
core::fragment::FragSetOP fragments_sm_
 
core::fragment::SecondaryStructureOP pred_ss_
 
protocols::minimization_packing::SaneMinMoverOP minimizer_
 

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...
 

Constructor & Destructor Documentation

protocols::star::StarAbinitio::StarAbinitio ( )

Member Function Documentation

void protocols::star::StarAbinitio::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::star::StarAbinitio::clone ( ) const
overridevirtual

Uses the copy constructor to create a new instance

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::star::StarAbinitio::fresh_instance ( ) const
overridevirtual

Uses the no-argument constructor to create a new instance

Reimplemented from protocols::moves::Mover.

std::string protocols::star::StarAbinitio::get_name ( ) const
overridevirtual

Returns the name of this mover

Implements protocols::moves::Mover.

void protocols::star::StarAbinitio::setup_kinematics ( const protocols::loops::Loops aligned,
const utility::vector1< unsigned > &  interior_cuts,
core::pose::Pose pose 
) const
private

Sets up kinematics to keep the orientation of the aligned regions fixed with respect to one another. A virtual residue is placed at the aligned regions' center of mass. A jump from the virtual residue to the midpoint of each region is added. Interior cutpoints (i.e. those between consecutive aligned regions) are retrieved from the input parameter.

References core::pose::addVirtualResAsRoot(), core::conformation::membrane::center, protocols::loops::Loops::center_of_mass(), core::pose::correctly_add_cutpoint_variants(), core::pose::Pose::fold_tree(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::loops::Loops::num_loop(), core::pose::Pose::size(), protocols::star::TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

void protocols::star::StarAbinitio::tear_down_kinematics ( core::pose::Pose pose) const
private

Member Data Documentation

core::fragment::FragSetOP protocols::star::StarAbinitio::fragments_lg_
private
core::fragment::FragSetOP protocols::star::StarAbinitio::fragments_sm_
private
protocols::minimization_packing::SaneMinMoverOP protocols::star::StarAbinitio::minimizer_
private
core::fragment::SecondaryStructureOP protocols::star::StarAbinitio::pred_ss_
private

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