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protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives Class Reference

#include <RigidBodyStepWiseSamplerWithResidueAlternatives.hh>

Inheritance diagram for protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives:
Inheritance graph
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Public Member Functions

 RigidBodyStepWiseSamplerWithResidueAlternatives (protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP residue_alternative_rotamer, RigidBodyStepWiseSamplerOP rigid_body_rotamer)
 
 ~RigidBodyStepWiseSamplerWithResidueAlternatives () override
 
void fast_forward ()
 
void fast_forward_to_next_rigid_body ()
 
void fast_forward_to_next_translation ()
 
void fast_forward_to_next_euler_gamma ()
 
ValueList const & get_rigid_body_values ()
 
core::kinematics::Stub get_stub ()
 
core::conformation::Residue const & get_residue_at_origin ()
 
core::conformation::Residue const & get_residue_at_origin (core::Size const seqpos)
 
protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP residue_alternatives_rotamer ()
 
RigidBodyStepWiseSamplerOP rigid_body_rotamer ()
 
std::string get_name () const override
 Name of the class. More...
 
toolbox::SamplerPlusPlusType type () const override
 Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...
 
void apply_rigid_body_only (core::pose::Pose &pose)
 
void fast_forward_to_next_residue_pair (core::Size const i, core::Size const j)
 
void fast_forward_to_next_residue (core::Size const i)
 
core::Vector get_xyz (core::Size const seqpos, std::string const &atom_name)
 
core::conformation::ResidueCOP get_residue (core::Size const seqpos)
 
- Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerComb
 StepWiseSamplerComb ()
 
 ~StepWiseSamplerComb () 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...
 
bool not_end () const override
 Check if reach the end of rotamer list. More...
 
void apply (core::pose::Pose &pose) override
 Apply the current rotamer to pose. More...
 
void set_random (bool const setting) override
 Set the random modeler state. More...
 
virtual void add_external_loop_rotamer (sampler::StepWiseSamplerOP const &rotamer)
 Add one more rotamer sampler to this sampler. More...
 
virtual void clear_rotamer ()
 Clear all rotamer samplers stored in 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...
 
void show (std::ostream &out, core::Size const indent=0) const override
 output summary of class More...
 
- 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Attributes

protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP residue_alternatives_rotamer_
 
RigidBodyStepWiseSamplerOP rigid_body_rotamer_
 
std::map< core::Size,
core::conformation::ResidueOP
transformed_residues
 

Additional Inherited Members

- Public Types inherited from protocols::toolbox::SamplerPlusPlus
typedef utility::vector1
< core::Real
TorsionList
 
- 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::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...
 

Constructor & Destructor Documentation

protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::RigidBodyStepWiseSamplerWithResidueAlternatives ( protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP  residue_alternative_rotamer,
RigidBodyStepWiseSamplerOP  rigid_body_rotamer 
)
protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::~RigidBodyStepWiseSamplerWithResidueAlternatives ( )
overridedefault

Member Function Documentation

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::apply_rigid_body_only ( core::pose::Pose pose)
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward_to_next_euler_gamma ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward_to_next_residue ( core::Size const  i)
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward_to_next_residue_pair ( core::Size const  i,
core::Size const  j 
)
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward_to_next_rigid_body ( )
void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::fast_forward_to_next_translation ( )
std::string protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_name ( ) const
inlineoverridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

conformation::ResidueCOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue ( core::Size const  seqpos)
core::conformation::Residue const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue_at_origin ( )

References rigid_body_rotamer_.

Referenced by get_residue(), and get_xyz().

core::conformation::Residue const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue_at_origin ( core::Size const  seqpos)
ValueList const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_rigid_body_values ( )
core::kinematics::Stub protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_stub ( )
Vector protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_xyz ( core::Size const  seqpos,
std::string const &  atom_name 
)
ResidueAlternativeStepWiseSamplerCombOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::residue_alternatives_rotamer ( )
RigidBodyStepWiseSamplerOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::rigid_body_rotamer ( )
toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::type ( ) const
inlineoverridevirtual

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RIGID_BODY_WITH_RESIDUE_ALTERNATIVES.

Member Data Documentation

protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::residue_alternatives_rotamer_
private
RigidBodyStepWiseSamplerOP protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::rigid_body_rotamer_
private
std::map< core::Size, core::conformation::ResidueOP > protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::transformed_residues
private

Referenced by get_residue().


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