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protocols::enzdes::MinimizeStoredRBConfs Class Reference

rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization More...

#include <ModifyStoredLigandRBConfsMovers.hh>

Inheritance diagram for protocols::enzdes::MinimizeStoredRBConfs:
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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 > > 
RBConfLists
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 MinimizeStoredRBConfs (core::scoring::ScoreFunctionCOP sfxn)
 
 ~MinimizeStoredRBConfs ()
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void rb_minimize_all_confs (core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueCOP > &confs) const
 
- Public Member Functions inherited from protocols::enzdes::ModifyStoredRBConfs
 ModifyStoredRBConfs (std::string const name)
 
 ~ModifyStoredRBConfs ()
 
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 ~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 MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
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 Attributes

core::scoring::ScoreFunctionCOP sfxn_
 
Real min_rms_
 

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. 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::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...
 

Detailed Description

rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::enzdes::MinimizeStoredRBConfs::MinimizeStoredRBConfs ( core::scoring::ScoreFunctionCOP  sfxn)
protocols::enzdes::MinimizeStoredRBConfs::~MinimizeStoredRBConfs ( )

Member Function Documentation

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

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

Reimplemented from protocols::enzdes::ModifyStoredRBConfs.

void protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs ( core::pose::Pose const &  pose,
utility::vector1< core::conformation::ResidueCOP > &  confs 
) const

Member Data Documentation

Real protocols::enzdes::MinimizeStoredRBConfs::min_rms_
private

Referenced by rb_minimize_all_confs().

core::scoring::ScoreFunctionCOP protocols::enzdes::MinimizeStoredRBConfs::sfxn_
private

Referenced by rb_minimize_all_confs().


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