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

#include <RigidBodyStepWiseSampler.hh>

Inheritance diagram for protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler:
Inheritance graph

Public Member Functions

 RigidBodyStepWiseSampler (core::pose::Pose const &pose, core::Size const moving_res)
 RigidBodyStepWiseSampler (core::Size const moving_res, core::conformation::Residue const &moving_residue_at_origin, core::kinematics::Stub const &reference_stub)
 ~RigidBodyStepWiseSampler () override
void init () override
 Initialization. More...
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
void apply (core::pose::Pose &pose, core::Size const id) override
 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, core::Size const id)
void apply (core::conformation::Residue &residue_initially_at_origin)
void apply (core::Vector &xyz_initially_at_origin, core::Size const seqpos)
core::kinematics::Stub const & get_stub ()
core::kinematics::Stub const & get_stub (utility::vector1< core::Size > const &id_list)
core::kinematics::Stub const & get_stub (core::Size const id)
core::kinematics::Stub const & reference_stub ()
core::conformation::Residue const & get_residue_at_origin (core::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 ()
core::Size const & moving_res () const
core::conformation::Residue const & moving_residue_at_origin () const
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...
core::Size const & reference_res () const
utility::vector1< core::Size > const & moving_partition_res () const
RigidBodyStepWiseSamplerValueRangevalue_range ()
void set_x_values (core::Real const centroid_x_min, core::Real const centroid_x_max, core::Real const centroid_x_bin)
void set_y_values (core::Real const centroid_y_min, core::Real const centroid_y_max, core::Real const centroid_y_bin)
void set_z_values (core::Real const centroid_z_min, core::Real const centroid_z_max, core::Real const centroid_z_bin)
void set_euler_alpha_values (core::Real const centroid_euler_alpha_min, core::Real const centroid_euler_alpha_max, core::Real const centroid_euler_alpha_bin)
void set_euler_z_values (core::Real const centroid_euler_z_min, core::Real const centroid_euler_z_max, core::Real const centroid_euler_z_bin)
void set_euler_gamma_values (core::Real const centroid_euler_gamma_min, core::Real const centroid_euler_gamma_max, core::Real const centroid_euler_gamma_bin)
std::string get_name () const override
 Name of the class. More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerOneValueComb
 StepWiseSamplerOneValueComb ()
 ~StepWiseSamplerOneValueComb () override
ValueList const & get_value_list (core::Size const id)
ValueList const & get_value_list (utility::vector1< core::Size > const &id_list)
virtual void add_external_loop_rotamer (StepWiseSamplerOneValueOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
std::string get_name () const override
 Name of the class. More...
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in SamplerPlusPlusTypes.hh) More...
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSizedComb
 StepWiseSamplerSizedComb ()
 StepWiseSamplerSizedComb (StepWiseSamplerSizedOP outer_loop_rotamer, StepWiseSamplerSizedOP inner_loop_rotamer)
 ~StepWiseSamplerSizedComb () override
void init () override
 Initialization. More...
void reset () override
 Reset to the first (or random if random()) rotamer. More...
void operator++ () override
 Move to next rotamer. More...
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
void apply (core::pose::Pose &pose, core::Size const id) override
 Apply the i-th rotamer to pose. More...
core::Size size () const override
 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 (core::Size const sampler_number)
 Move sampler to end. More...
std::string get_name () const override
 Name of the class. More...
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in SamplerPlusPlusTypes.hh) More...
void set_random (bool const setting) override
 Set the random modeler state. More...
void show (std::ostream &out, core::Size const indent=0) const override
 output summary of class More...
virtual void fast_forward ()
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
 StepWiseSamplerSized ()
 ~StepWiseSamplerSized () override
bool not_end () const override
 Check if reach the end of rotamer list. More...
core::Size const & id () const
virtual void set_id (core::Size const setting)
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSampler
 StepWiseSampler ()
 ~StepWiseSampler () override
virtual bool random () const
 Check if is random modeler. More...
- Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
 SamplerPlusPlus ()
 ~SamplerPlusPlus () override
- 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 Member Functions

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

Private Attributes

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

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
typedef utility::vector1< core::RealTorsionList
- 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::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::toolbox::SamplerPlusPlus
bool is_init () const
 return OP to the subsampler that controls exactly this torsion_id (assume only one). This is worked out in recces/sampler/MC_Sampler & derived classes – wouldn't be too hard to generalize to stepwise/sampler/ classes, too. 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_
utility::vector1< StepWiseSamplerSizedOProtamer_list_
- Protected Attributes inherited from protocols::stepwise::sampler::StepWiseSamplerSized
core::Size id_

Constructor & Destructor Documentation

◆ RigidBodyStepWiseSampler() [1/2]

protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler ( core::pose::Pose const &  pose,
core::Size const  moving_res 

◆ RigidBodyStepWiseSampler() [2/2]

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

◆ ~RigidBodyStepWiseSampler()

protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::~RigidBodyStepWiseSampler ( )

Member Function Documentation

◆ apply() [1/6]

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::conformation::Residue residue_initially_at_origin)

◆ apply() [2/6]

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

Apply the current rotamer to pose.

Implements protocols::toolbox::SamplerPlusPlus.

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

Referenced by apply().

◆ apply() [3/6]

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose,
core::conformation::Residue const &  moving_residue_at_origin 

◆ apply() [4/6]

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose pose,
core::conformation::Residue const &  moving_residue_at_origin,
core::Size const  id 

◆ apply() [5/6]

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::pose::Pose ,
core::Size const   

◆ apply() [6/6]

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply ( core::Vector xyz_initially_at_origin,
core::Size const  seqpos 

◆ apply_by_jump()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply_by_jump ( core::pose::Pose pose,
core::Size const &  seq_num,
core::kinematics::Stub const &  moving_res_stub 

◆ calculate_jump()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump ( core::pose::Pose pose,
core::Size const  seq_num,
core::kinematics::Stub const &  moving_res_stub 

◆ fast_forward_to_end()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_end ( )

◆ fast_forward_to_next_euler_gamma()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_next_euler_gamma ( )

◆ fast_forward_to_next_translation()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::fast_forward_to_next_translation ( )

◆ get_name()

std::string protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_name ( ) const

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

References moving_res_, and core::id::to_string().

◆ get_residue_at_origin()

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

References pose_at_origin_.

◆ get_stub() [1/3]

core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( )

◆ get_stub() [2/3]

core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( core::Size const  id)

◆ get_stub() [3/3]

core::kinematics::Stub const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub ( utility::vector1< core::Size > const &  id_list)

◆ get_values()

utility::vector1< Real > const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_values ( )

◆ init()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::init ( )

◆ moving_partition_res()

utility::vector1< core::Size > const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_partition_res ( ) const

References moving_partition_res_.

◆ moving_res()

core::Size const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res ( ) const

References moving_res_.

Referenced by RigidBodyStepWiseSampler().

◆ moving_residue_at_origin()

core::conformation::Residue const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_residue_at_origin ( ) const

References moving_residue_at_origin_.

Referenced by calculate_jump().

◆ pose_at_origin()

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

References pose_at_origin_.

◆ reference_res()

core::Size const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_res ( ) const

References reference_res_.

◆ reference_stub()

core::kinematics::Stub const& protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_stub ( )

References reference_stub_.

◆ set_euler_alpha_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_alpha_values ( core::Real const  centroid_euler_alpha_min,
core::Real const  centroid_euler_alpha_max,
core::Real const  centroid_euler_alpha_bin 

◆ set_euler_gamma_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_gamma_values ( core::Real const  centroid_euler_gamma_min,
core::Real const  centroid_euler_gamma_max,
core::Real const  centroid_euler_gamma_bin 

◆ set_euler_z_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_euler_z_values ( core::Real const  centroid_euler_z_min,
core::Real const  centroid_euler_z_max,
core::Real const  centroid_euler_z_bin 

◆ set_x_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_x_values ( core::Real const  centroid_x_min,
core::Real const  centroid_x_max,
core::Real const  centroid_x_bin 

◆ set_y_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_y_values ( core::Real const  centroid_y_min,
core::Real const  centroid_y_max,
core::Real const  centroid_y_bin 

◆ set_z_values()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::set_z_values ( core::Real const  centroid_z_min,
core::Real const  centroid_z_max,
core::Real const  centroid_z_bin 

◆ transform_single_residue()

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::transform_single_residue ( core::pose::Pose pose,
core::Size const &  seq_num,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_stub 

◆ type()

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::type ( ) const

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RIGID_BODY.

◆ value_range()

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

References value_range_.

Member Data Documentation

◆ jump_

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

Referenced by apply_by_jump(), and calculate_jump().

◆ jump_atom_id_

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

Referenced by apply_by_jump(), and calculate_jump().

◆ moving_partition_res_

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

◆ moving_res_

core::Size const protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res_

◆ moving_res_stub_

core::kinematics::Stub protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_res_stub_

Referenced by apply_by_jump(), and get_stub().

◆ moving_residue_at_origin_

core::conformation::ResidueCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::moving_residue_at_origin_

◆ pose_at_origin_

core::pose::PoseCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::pose_at_origin_

◆ reference_res_

core::Size const protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_res_

◆ reference_stub_

core::kinematics::Stub protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::reference_stub_

◆ value_range_

RigidBodyStepWiseSamplerValueRange protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::value_range_

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