Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler Class Reference

#include <RigidBodyStepWiseSampler.hh>

Public Member Functions

 RigidBodyStepWiseSampler (pose::Pose const &pose, Size const moving_res)
 RigidBodyStepWiseSampler (Size const moving_res, core::conformation::Residue const &moving_residue_at_origin, core::kinematics::Stub const &reference_stub)
 ~RigidBodyStepWiseSampler ()
void init ()
 Initialization. More...
virtual void apply (core::pose::Pose &pose)
 Apply the current rotamer to pose. More...
virtual void apply (core::pose::Pose &pose, Size const id)
 Apply the i-th rotamer to pose. More...
void apply (core::pose::Pose &pose, core::conformation::Residue const &moving_residue_at_origin)
void apply (core::pose::Pose &pose, core::conformation::Residue const &moving_residue_at_origin, Size const id)
void apply (core::conformation::Residue &residue_initially_at_origin)
void apply (Vector &xyz_initially_at_origin, Size const seqpos)
core::kinematics::Stub const & get_stub ()
core::kinematics::Stub const & get_stub (utility::vector1< Size > const &id_list)
core::kinematics::Stub const & get_stub (Size const id)
core::kinematics::Stub const & reference_stub ()
core::conformation::Residue const & get_residue_at_origin (Size const seqpos)
core::pose::PoseCOP pose_at_origin ()
void fast_forward_to_end ()
void fast_forward_to_next_translation ()
void fast_forward_to_next_euler_gamma ()
ValueList const & get_values ()
Size const & moving_res () const
core::conformation::Residue const & moving_residue_at_origin () const
virtual StepWiseSamplerType type () const
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
Size const & reference_res () const
utility::vector1< Size > const & moving_partition_res () const
RigidBodyStepWiseSamplerValueRangevalue_range ()
void set_x_values (Real const centroid_x_min, Real const centroid_x_max, Real const centroid_x_bin)
void set_y_values (Real const centroid_y_min, Real const centroid_y_max, Real const centroid_y_bin)
void set_z_values (Real const centroid_z_min, Real const centroid_z_max, Real const centroid_z_bin)
void set_euler_alpha_values (Real const centroid_euler_alpha_min, Real const centroid_euler_alpha_max, Real const centroid_euler_alpha_bin)
void set_euler_z_values (Real const centroid_euler_z_min, Real const centroid_euler_z_max, Real const centroid_euler_z_bin)
void set_euler_gamma_values (Real const centroid_euler_gamma_min, Real const centroid_euler_gamma_max, Real const centroid_euler_gamma_bin)
virtual std::string get_name () const
 Name of the class. More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerOneValueComb
 StepWiseSamplerOneValueComb ()
virtual ~StepWiseSamplerOneValueComb ()
ValueList const & get_value_list (Size const id)
ValueList const & get_value_list (utility::vector1< Size > const &id_list)
virtual void add_external_loop_rotamer (StepWiseSamplerOneValueOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSizedComb
 StepWiseSamplerSizedComb ()
 StepWiseSamplerSizedComb (StepWiseSamplerSizedOP outer_loop_rotamer, StepWiseSamplerSizedOP inner_loop_rotamer)
virtual ~StepWiseSamplerSizedComb ()
virtual void reset ()
 Reset to the first (or random if random()) rotamer. More...
virtual void operator++ ()
 Move to next rotamer. More...
virtual core::Size size () const
 Get the total number of rotamers in sampler. More...
virtual void add_external_loop_rotamer (StepWiseSamplerSizedOP const &rotamer)
 Add one more rotamer sampler to this sampler. This one is 'external' to any previously existing rotamers, i.e., this new only gets incremented when all previous existing rotamers complete their cycle. More...
virtual void add_internal_loop_rotamer (StepWiseSamplerSizedOP const &rotamer)
 Add one more rotamer sampler to this sampler. This one is 'internal' to existing rotamers, i.e., when this one completes its cycle, the existing. More...
virtual void clear_rotamer ()
 Clear all rotamer samplers stored in this sampler. More...
void fast_forward (Size const sampler_number)
 Move sampler to end. More...
virtual void set_random (bool const setting)
 Set the random modeler state. More...
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
virtual ~StepWiseSamplerSized ()
virtual bool not_end () const
 Check if reach the end of rotamer list. More...
Size const & id () const
virtual void fast_forward ()
virtual void set_id (Size const setting)
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
 StepWiseSamplerBase ()
virtual ~StepWiseSamplerBase ()
virtual bool random () const
 Check if is random modeler. 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
void set_type (std::string const &setting)
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
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Member Functions

void calculate_jump (pose::Pose &pose, Size const seq_num, kinematics::Stub const &moving_res_stub)
void transform_single_residue (pose::Pose &pose, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_stub)
void apply_by_jump (pose::Pose &pose, Size const &seq_num, core::kinematics::Stub const &moving_res_stub)

Private Attributes

Size const moving_res_
conformation::ResidueCOP moving_residue_at_origin_
kinematics::Stub reference_stub_
kinematics::Stub moving_res_stub_
RigidBodyStepWiseSamplerValueRange value_range_
kinematics::Jump jump_
id::AtomID jump_atom_id_
Size const reference_res_
utility::vector1< Sizemoving_partition_res_
pose::PoseCOP pose_at_origin_

Additional Inherited Members

- Public Types inherited from protocols::stepwise::sampler::StepWiseSamplerBase
typedef utility::vector1
< core::Real
- 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::stringStrings
- 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::stepwise::sampler::StepWiseSamplerSizedComb
utility::vector1< core::Sizeid2list (core::Size const id) const
 Convert input id number to the individual id_list for each stored rotamer sampler. More...
core::Size list2id (utility::vector1< core::Size > const &id_list) const
 Convert id_list for each stored rotamer sampler stored to the global id number. More...
- Protected Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerBase
bool is_init () const
 Check if the sampler has been initialized. More...
void set_init (bool const setting)
 Set the initialization state. More...
template<class T >
void set_and_reinit (T &params, T const &setting)
 Set value of a parameter, return to pre-init state. 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::stepwise::sampler::StepWiseSamplerSizedComb
utility::vector1< core::Sizeid_list_
< StepWiseSamplerSizedOP
- Protected Attributes inherited from protocols::stepwise::sampler::StepWiseSamplerSized
core::Size id_

Constructor & Destructor Documentation

protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler ( pose::Pose const &  pose,
Size const  moving_res 
protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler ( Size const  moving_res,
core::conformation::Residue const &  moving_residue_at_origin,
core::kinematics::Stub const &  reference_stub 
protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::~RigidBodyStepWiseSampler ( )

Member Function Documentation

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose)

Apply the current rotamer to pose.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSizedComb.

References protocols::stepwise::sampler::StepWiseSamplerSized::id_.

Referenced by apply().

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose,
Size const  id 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose,
core::conformation::Residue const &  moving_residue_at_origin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose,
core::conformation::Residue const &  moving_residue_at_origin,
Size const  id 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::conformation::Residue residue_initially_at_origin)
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( Vector xyz_initially_at_origin,
Size const  seqpos 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply_by_jump ( pose::Pose pose,
Size const &  seq_num,
core::kinematics::Stub const &  moving_res_stub 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump ( pose::Pose pose,
Size const  seq_num,
kinematics::Stub const &  moving_res_stub 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_end ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_next_euler_gamma ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_next_translation ( )
std::string protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_name ( ) const

Name of the class.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerOneValueComb.

References moving_res_, and utility::to_string().

core::conformation::Residue const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_residue_at_origin ( Size const  seqpos)

References pose_at_origin_.

core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( )
core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( utility::vector1< Size > const &  id_list)
core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( Size const  id)
utility::vector1< Real > const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_values ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::init ( void  )
utility::vector1< Size > const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_partition_res ( ) const
Size const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res ( ) const
core::conformation::Residue const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_residue_at_origin ( ) const

Referenced by calculate_jump().

core::pose::PoseCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::pose_at_origin ( )

References pose_at_origin_.

Size const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_res ( ) const
core::kinematics::Stub const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_stub ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_alpha_values ( Real const  centroid_euler_alpha_min,
Real const  centroid_euler_alpha_max,
Real const  centroid_euler_alpha_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_gamma_values ( Real const  centroid_euler_gamma_min,
Real const  centroid_euler_gamma_max,
Real const  centroid_euler_gamma_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_z_values ( Real const  centroid_euler_z_min,
Real const  centroid_euler_z_max,
Real const  centroid_euler_z_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_x_values ( Real const  centroid_x_min,
Real const  centroid_x_max,
Real const  centroid_x_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_y_values ( Real const  centroid_y_min,
Real const  centroid_y_max,
Real const  centroid_y_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_z_values ( Real const  centroid_z_min,
Real const  centroid_z_max,
Real const  centroid_z_bin 
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::transform_single_residue ( pose::Pose pose,
Size const &  seq_num,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_stub 
virtual StepWiseSamplerType protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::type ( ) const

Type of class (see enum in StepWiseSamplerTypes.hh)

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerOneValueComb.

References protocols::stepwise::sampler::RIGID_BODY.

RigidBodyStepWiseSamplerValueRange& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::value_range ( )

Member Data Documentation

kinematics::Jump protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::jump_

Referenced by apply_by_jump(), and calculate_jump().

id::AtomID protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::jump_atom_id_

Referenced by apply_by_jump(), and calculate_jump().

utility::vector1< Size > protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_partition_res_

Referenced by apply(), and RigidBodyStepWiseSampler().

Size const protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res_
kinematics::Stub protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res_stub_

Referenced by apply_by_jump(), and get_stub().

conformation::ResidueCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_residue_at_origin_
pose::PoseCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::pose_at_origin_
Size const protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_res_
kinematics::Stub protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_stub_
RigidBodyStepWiseSamplerValueRange protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::value_range_

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