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protocols::enzdes::PredesignPerturbMover Class Reference

#include <EnzdesMovers.hh>

Inheritance diagram for protocols::enzdes::PredesignPerturbMover:
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Public Member Functions

 PredesignPerturbMover ()
 
 ~PredesignPerturbMover ()
 
void set_docking_pose (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task)
 
void reinstate_pose (core::pose::Pose &pose, core::pose::Pose const &old_Pose)
 
void find_constraints_to_ligand (core::pose::Pose const &pose)
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_ligand (core::Size res_no)
 
utility::vector1< core::Size >
const & 
get_constrained_lig_atoms () const
 Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to the ligand. More...
 
core::Vector find_rotation_center (core::pose::Pose const &pose)
 
core::Vector find_geometric_center_for_constrained_lig_atoms (core::pose::Pose const &pose)
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &datamap, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
protocols::moves::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...
 
- Public Member Functions inherited from protocols::rigid::RigidBodyPerturbMover
 RigidBodyPerturbMover ()
 
 RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in, utility::vector1< bool > ok_for_centroid_calculation)
 
 RigidBodyPerturbMover (core::pose::Pose const &pose_in, core::kinematics::MoveMap const &mm, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (RigidBodyPerturbMover const &)
 
virtual ~RigidBodyPerturbMover ()
 
void rot_magnitude (core::Real const magnitude)
 
void trans_magnitude (core::Real const magnitude)
 
core::Size get_trans_mag () const
 
core::Size get_rot_mag () const
 
void rot_center (core::Vector const )
 Manual override of rotation center. More...
 
- Public Member Functions inherited from protocols::rigid::RigidBodyMover
 RigidBodyMover ()
 
 RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)
 
 RigidBodyMover (RigidBodyMover const &src)
 
virtual ~RigidBodyMover ()
 
void rot_center (core::Vector const rot_center_in)
 Manual override of rotation center. More...
 
virtual bool preserve_detailed_balance () const
 get whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...
 
virtual void set_preserve_detailed_balance (bool)
 set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...
 
virtual utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &pose)
 get the TorsionIDs perturbed by the mover during moves, along with their ranges More...
 
int rb_jump () const
 
void rb_jump (int jump_id)
 
void unfreeze ()
 
void freeze ()
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 
virtual ~ThermodynamicMover ()
 
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 callback executed before any Monte Carlo trials More...
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback executed after the Metropolis criterion is evaluated More...
 
virtual core::Real last_proposal_density_ratio ()
 callback for proposal density ratio of last apply method More...
 
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback executed after all Monte Carlo trials More...
 
virtual bool is_multi_trial ()
 determine whether the move performs multiple trials on a single apply More...
 
virtual core::Real last_inner_score_temperature_delta ()
 get change in internal score/temperature for last apply method of multiple trial movers More...
 
virtual
protocols::canonical_sampling::MetropolisHastingsMoverAP 
metropolis_hastings_mover ()
 get the MetropolisHastingsMover for multiple trial movers More...
 
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 set the MetropolisHastingsMover for multiple trial movers More...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 get the DOF_IDs perturbed by the mover during moves (not including those returned by torsion_id_ranges(), along with their ranges 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...
 
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)
 
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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

EnzdesConstraintReporter constraint_reporter_
 
utility::vector1< core::Sizepositions_to_replace_
 
core::Size dock_trials_
 
core::pack::task::TaskFactoryOP task_factory_
 

Additional Inherited Members

- Public Types inherited from protocols::rigid::RigidBodyPerturbMover
typedef RigidBodyMover parent
 
- 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::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...
 
- Protected Attributes inherited from protocols::rigid::RigidBodyPerturbMover
core::Real rot_mag_
 perturbation magnitudes (rotational and translational) More...
 
core::Real trans_mag_
 
utility::vector1< core::Realrb_delta_
 

Constructor & Destructor Documentation

protocols::enzdes::PredesignPerturbMover::PredesignPerturbMover ( )
protocols::enzdes::PredesignPerturbMover::~PredesignPerturbMover ( )

Member Function Documentation

void protocols::enzdes::PredesignPerturbMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::enzdes::PredesignPerturbMover::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References PredesignPerturbMover().

void protocols::enzdes::PredesignPerturbMover::find_constraints_to_ligand ( core::pose::Pose const &  pose)
core::Vector protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms ( core::pose::Pose const &  pose)
core::Vector protocols::enzdes::PredesignPerturbMover::find_rotation_center ( core::pose::Pose const &  pose)
protocols::moves::MoverOP protocols::enzdes::PredesignPerturbMover::fresh_instance ( ) const
virtual

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

utility::vector1< core::Size > const& protocols::enzdes::PredesignPerturbMover::get_constrained_lig_atoms ( ) const
inline

Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to the ligand.

References protocols::enzdes::EnzdesConstraintReporter::constrained_lig_atoms(), and constraint_reporter_.

std::string protocols::enzdes::PredesignPerturbMover::get_name ( ) const
virtual

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

Reimplemented from protocols::rigid::RigidBodyPerturbMover.

void protocols::enzdes::PredesignPerturbMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References constraint_reporter_, dock_trials_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::enzdes::EnzdesConstraintReporter::ligand_resno(), core::pose::Pose::num_jump(), protocols::rosetta_scripts::parse_task_operations(), protocols::rigid::RigidBodyPerturbMover::rot_magnitude(), task_factory_, and protocols::rigid::RigidBodyPerturbMover::trans_magnitude().

void protocols::enzdes::PredesignPerturbMover::reinstate_pose ( core::pose::Pose pose,
core::pose::Pose const &  old_Pose 
)
void protocols::enzdes::PredesignPerturbMover::set_docking_pose ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task 
)
void protocols::enzdes::PredesignPerturbMover::set_ligand ( core::Size  res_no)

Member Data Documentation

EnzdesConstraintReporter protocols::enzdes::PredesignPerturbMover::constraint_reporter_
private
core::Size protocols::enzdes::PredesignPerturbMover::dock_trials_
private
utility::vector1< core::Size > protocols::enzdes::PredesignPerturbMover::positions_to_replace_
private

Referenced by reinstate_pose(), and set_docking_pose().

core::pack::task::TaskFactoryOP protocols::enzdes::PredesignPerturbMover::task_factory_
private

Referenced by apply(), and parse_my_tag().


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