protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler Class Reference

#include <RigidBodyStepWiseSampler.hh>

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

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
RigidBodyStepWiseSamplerValueRange &	value_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...
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	fast_forward ()
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 Strings &	info ()
	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::Size >	moving_partition_res_
core::pose::PoseCOP	pose_at_origin_

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::stepwise::sampler::StepWiseSamplerSizedComb
utility::vector1< core::Size >	id2list (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::Size >	id_list_
utility::vector1 < StepWiseSamplerSizedOP >	rotamer_list_
Protected Attributes inherited from protocols::stepwise::sampler::StepWiseSamplerSized
core::Size	id_

Constructor & Destructor Documentation

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

References protocols::stepwise::modeler::figure_out_moving_partition_res(), protocols::toolbox::rigid_body::initialize_stub(), moving_partition_res_, moving_res_, moving_residue_at_origin_, pose_at_origin_, reference_res_, reference_stub_, and protocols::toolbox::rigid_body::transform_moving_partition_to_origin().

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
	)

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

overridedefault

Member Function Documentation

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

overridevirtual

Apply the current rotamer to pose.

Implements protocols::toolbox::SamplerPlusPlus.

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

Referenced by apply().

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

overridevirtual

Apply the i-th rotamer to pose.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

References apply_by_jump(), get_stub(), protocols::toolbox::SamplerPlusPlus::is_init(), and moving_res_.

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

References apply(), and protocols::stepwise::sampler::StepWiseSamplerSized::id_.

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

References get_stub(), protocols::toolbox::SamplerPlusPlus::is_init(), moving_res_, and transform_single_residue().

void protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply

(

core::conformation::Residue &

residue_initially_at_origin

)

References protocols::toolbox::rigid_body::get_atom_coordinates(), get_stub(), moving_partition_res_, core::conformation::Residue::seqpos(), and core::conformation::Residue::set_xyz().

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

References protocols::toolbox::rigid_body::get_specific_atom_coordinate(), get_stub(), and moving_partition_res_.

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  )

private

References calculate_jump(), jump_, jump_atom_id_, moving_res_stub_, and core::pose::Pose::set_jump().

Referenced by apply().

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  )

private

References core::kinematics::AtomTree::atom_dont_do_update(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::pose::Pose::atom_tree(), core::kinematics::FoldTree::downstream_atom(), core::pose::Pose::fold_tree(), core::kinematics::tree::Atom::get_self_ptr(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), core::chemical::ResidueTypeBase::is_polymer(), jump_, jump_atom_id_, protocols::stepwise::modeler::look_for_unique_jump_to_moving_res(), moving_residue_at_origin(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by apply_by_jump().

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

(

)

References protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward().

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

(

)

References protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward().

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

(

)

References protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward().

Referenced by protocols::stepwise::screener::StubDistanceScreener::fast_forward(), and protocols::stepwise::screener::CentroidDistanceScreener::fast_forward().

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

overridevirtual

Name of the class.

Implements protocols::toolbox::SamplerPlusPlus.

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

core::conformation::Residue const & protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_residue_at_origin

(

core::Size const

seqpos

)

References pose_at_origin_.

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

(

)

References protocols::stepwise::sampler::StepWiseSamplerSizedComb::id_list_.

Referenced by apply(), and get_stub().

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

(

utility::vector1< core::Size > const &

id_list

)

References protocols::stepwise::sampler::StepWiseSamplerOneValueComb::get_value_list(), core::kinematics::Stub::M, moving_res_stub_, reference_stub_, protocols::stepwise::sampler::rigid_body::EulerAngles::set_alpha(), and core::kinematics::Stub::v.

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

(

core::Size const

id

)

References get_stub(), and protocols::stepwise::sampler::StepWiseSamplerSizedComb::id2list().

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

(

)

References protocols::stepwise::sampler::StepWiseSamplerOneValueComb::get_value_list(), and protocols::stepwise::sampler::StepWiseSamplerSizedComb::id_list_.

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

overridevirtual

Initialization.

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::stepwise::sampler::StepWiseSamplerOneValueComb::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::clear_rotamer(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::euler_alpha_values(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::euler_gamma_values(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::euler_z_values(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::init(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::init(), value_range_, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::x_values(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::y_values(), and protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::z_values().

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

inline

References moving_partition_res_.

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

inline

References moving_res_.

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

inline

References moving_residue_at_origin_.

Referenced by calculate_jump().

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

(

)

References pose_at_origin_.

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

inline

References reference_res_.

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

inline

References reference_stub_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_euler_alpha_values(), and value_range_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_euler_gamma_values(), and value_range_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_euler_z_values(), and value_range_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_x_values(), and value_range_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_y_values(), and value_range_.

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
	)

References protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_z_values(), and value_range_.

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  )

private

References protocols::toolbox::rigid_body::get_atom_coordinates(), and core::pose::Pose::set_xyz().

Referenced by apply().

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

inlineoverridevirtual

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

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RIGID_BODY.

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

inline

References value_range_.

Member Data Documentation

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

private

Referenced by apply_by_jump(), and calculate_jump().

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

private

Referenced by apply_by_jump(), and calculate_jump().

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

private

Referenced by apply(), moving_partition_res(), and RigidBodyStepWiseSampler().

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

private

Referenced by apply(), get_name(), moving_res(), and RigidBodyStepWiseSampler().

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

private

Referenced by apply_by_jump(), and get_stub().

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

private

Referenced by moving_residue_at_origin(), and RigidBodyStepWiseSampler().

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

private

Referenced by get_residue_at_origin(), pose_at_origin(), and RigidBodyStepWiseSampler().

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

private

Referenced by reference_res(), and RigidBodyStepWiseSampler().

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

private

Referenced by get_stub(), reference_stub(), and RigidBodyStepWiseSampler().

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

private

Referenced by init(), set_euler_alpha_values(), set_euler_gamma_values(), set_euler_z_values(), set_x_values(), set_y_values(), set_z_values(), and value_range().

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

• src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSampler.hh
• src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSampler.cc