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protocols::enzdes::GenerateStoredRBConfs Class Reference

generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used More...

#include <ModifyStoredLigandRBConfsMovers.hh>

Inheritance diagram for protocols::enzdes::GenerateStoredRBConfs:
Inheritance graph

Public Types

typedef ModifyStoredRBConfs parent
- Public Types inherited from protocols::enzdes::ModifyStoredRBConfs
typedef core::Size Size
typedef core::Real Real
typedef protocols::moves::Mover parent
typedef utility::vector1
< utility::vector1
< core::conformation::ResidueCOP > > 
- 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

Public Member Functions

 GenerateStoredRBConfs (core::Size num_total_rbconfs, bool include_metals)
 ~GenerateStoredRBConfs () override
void apply (core::pose::Pose &pose) override
 two things happen: More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::enzdes::ModifyStoredRBConfs
 ModifyStoredRBConfs (std::string const &name)
 ~ModifyStoredRBConfs () override
void swap_coordinates_in_pose (core::pose::Pose &pose, core::conformation::Residue &rescoords) const
 helper function to exchange coordinates in a pose this function doesn't actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa More...
utility::vector1< Realclosest_orient_atoms_msd (core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueCOP > const &confs) const
 calculates the closest orient atom (i.e. atoms used in rotamer placement msd between every conf and the confs coming before it in the pose or in the vector 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes

core::Size num_total_rbconfs_
bool include_metals_

Additional Inherited Members

- 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::enzdes::ModifyStoredRBConfs
RBConfLists get_rigid_body_confs (core::pose::Pose const &pose) const
 this function is the function that all derived classes should call to get access to pose stored additional rb confs. right now it only returns the confs in the proper format, but in the future some logic might be added as to for which seqpos to return the stored confs More...
void set_rigid_body_confs (RBConfLists rbs, core::pose::Pose &pose) const
 same as for above function. all derived classes should use this function to communicate new/changed rigid body confs back to the pose/enzdes cacheable observer More...
void set_rigid_body_confs_for_seqpos (core::Size seqpos, utility::vector1< core::conformation::ResidueCOP > &confs, core::pose::Pose &pose) const
 see comments for set_rigid_body_confs 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

generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::enzdes::GenerateStoredRBConfs::GenerateStoredRBConfs ( core::Size  num_total_rbconfs,
bool  include_metals 
protocols::enzdes::GenerateStoredRBConfs::~GenerateStoredRBConfs ( )

Member Function Documentation

void protocols::enzdes::GenerateStoredRBConfs::apply ( core::pose::Pose pose)
std::string protocols::enzdes::GenerateStoredRBConfs::get_name ( ) const

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

Reimplemented from protocols::enzdes::ModifyStoredRBConfs.

Member Data Documentation

bool protocols::enzdes::GenerateStoredRBConfs::include_metals_

Referenced by apply().

core::Size protocols::enzdes::GenerateStoredRBConfs::num_total_rbconfs_

Referenced by apply().

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