#include <MultiPhosphateSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler:

[legend]

Public Member Functions
	MultiPhosphateSampler (core::pose::Pose const &reference_pose)

	MultiPhosphateSampler (core::pose::Pose &pose_to_prepack, core::Size const moving_res)

	~MultiPhosphateSampler () override

MultiPhosphateSamplerOP	clone_sampler () const

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	sample_phosphates ()

void	sample_phosphates (core::pose::PoseOP &viewer_pose_op)

void	copy_phosphates (core::pose::Pose &mod_pose) const

void	reset_to_original_pose ()

void	set_screen_all (bool const &setting)

bool	screen_all () const

bool	instantiated_some_phosphate () const

void	set_moving_partition_res (utility::vector1< core::Size > const &setting)

void	set_five_prime_phosphate_res (utility::vector1< core::Size > const &setting)

void	set_three_prime_phosphate_res (utility::vector1< core::Size > const &setting)

void	set_force_phosphate_instantiation (bool const &setting)

bool	force_phosphate_instantiation () const

core::pose::Pose &	pose ()

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

core::scoring::ScoreFunctionCOP	get_scorefxn ()

utility::vector1< PhosphateMove >	phosphate_move_list () const

void	set_phosphate_move_list (utility::vector1< PhosphateMove > const &setting)

utility::vector1< core::Size > const &	moving_partition_res ()

void	reset (core::pose::Pose const &pose)

void	initialize_by_prepack (core::pose::Pose &pose, core::Size const moving_res)

void	initialize_by_prepack (core::pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)

void	do_prepack (core::pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)

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 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	initialize_parameters ()

utility::vector1< PhosphateMove >	initialize_phosphate_move_list (core::pose::Pose &pose)

utility::vector1< PhosphateMove >	check_moved (utility::vector1< PhosphateMove > phosphate_move_list, core::pose::Pose const &pose) const

void	find_uninstantiated_phosphates (core::pose::Pose const &pose, utility::vector1< PhosphateMove > const &phosphate_move_list, utility::vector1< PhosphateMove > &actual_phosphate_move_list) const

void	find_phosphate_contacts_other_partition (utility::vector1< core::Size > const &partition_res1, utility::vector1< core::Size > const &partition_res2, core::pose::Pose const &pose, utility::vector1< PhosphateMove > const &phosphate_move_list, utility::vector1< PhosphateMove > &actual_phosphate_move_list) const

bool	check_other_partition_for_contact (core::pose::Pose const &pose, utility::vector1< core::Size > const &other_partition_res, core::Vector const &takeoff_xyz) const

Private Attributes
core::pose::PoseCOP	pose_with_original_phosphates_

core::pose::PoseOP	phosphate_sample_pose_

core::scoring::ScoreFunctionCOP	scorefxn_

core::Real	phosphate_takeoff_donor_distance_cutoff2_

bool	screen_all_

bool	force_phosphate_instantiation_

utility::vector1< core::Size >	moving_partition_res_

utility::vector1< core::Size >	five_prime_phosphate_res_input_

utility::vector1< core::Size >	three_prime_phosphate_res_input_

utility::vector1< PhosphateMove >	phosphate_move_list_

utility::vector1< PhosphateMove >	actual_phosphate_move_list_

bool	instantiated_some_phosphate_

bool	prepacked_

Additional Inherited Members
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::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

◆ MultiPhosphateSampler() [1/2]

protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler ( core::pose::Pose const & reference_pose )

References initialize_parameters(), and reset().

Referenced by clone_sampler().

◆ MultiPhosphateSampler() [2/2]

protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler	(	core::pose::Pose &	pose_to_prepack,
		core::Size const	moving_res
	)

References initialize_by_prepack(), and initialize_parameters().

◆ ~MultiPhosphateSampler()

protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::~MultiPhosphateSampler ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::apply ( core::pose::Pose & )

inlineoverridevirtual

Main Method.

Implements protocols::moves::Mover.

References copy_phosphates(), and pose().

◆ check_moved()

utility::vector1< PhosphateMove > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_moved	(	utility::vector1< PhosphateMove >	phosphate_move_list,
		core::pose::Pose const &	pose
	)		const

private

References find_phosphate_contacts_other_partition(), find_uninstantiated_phosphates(), force_phosphate_instantiation_, core::conformation::Residue::is_RNA(), moving_partition_res_, phosphate_move_list(), phosphate_move_list_, pose(), pose_with_original_phosphates_, prepacked_, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by sample_phosphates().

◆ check_other_partition_for_contact()

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	other_partition_res,
		core::Vector const &	takeoff_xyz
	)		const

private

References core::chemical::ResidueType::Hpos_polar(), phosphate_takeoff_donor_distance_cutoff2_, pose(), core::chemical::rings::q, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by find_phosphate_contacts_other_partition().

◆ clone()

moves::MoverOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

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 clone_sampler().

◆ clone_sampler()

MultiPhosphateSamplerOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::clone_sampler ( ) const

References force_phosphate_instantiation_, MultiPhosphateSampler(), phosphate_move_list_, pose_with_original_phosphates_, and screen_all_.

Referenced by clone().

◆ copy_phosphates()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::copy_phosphates ( core::pose::Pose & mod_pose ) const

References protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), phosphate_move_list_, and phosphate_sample_pose_.

Referenced by apply(), and protocols::stepwise::monte_carlo::mover::DeleteMover::minimize_after_delete().

◆ do_prepack()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	moving_res_list
	)

References core::pose::Pose::clone(), protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), protocols::stepwise::modeler::figure_out_moving_partition_res(), moving_partition_res_, phosphate_move_list_, pose(), pose_with_original_phosphates_, prepacked_, reset(), sample_phosphates(), and protocols::stepwise::modeler::split_pose().

Referenced by initialize_by_prepack().

◆ find_phosphate_contacts_other_partition()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_phosphate_contacts_other_partition	(	utility::vector1< core::Size > const &	partition_res1,
		utility::vector1< core::Size > const &	partition_res2,
		core::pose::Pose const &	pose,
		utility::vector1< PhosphateMove > const &	phosphate_move_list,
		utility::vector1< PhosphateMove > &	actual_phosphate_move_list
	)		const

private

References check_other_partition_for_contact(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, phosphate_move_list(), pose(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by check_moved().

◆ find_uninstantiated_phosphates()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_uninstantiated_phosphates	(	core::pose::Pose const &	pose,
		utility::vector1< PhosphateMove > const &	phosphate_move_list,
		utility::vector1< PhosphateMove > &	actual_phosphate_move_list
	)		const

private

References core::chemical::FIVE_PRIME_PHOSPHATE, protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, core::conformation::Residue::has_variant_type(), phosphate_move_list(), pose(), core::pose::Pose::residue(), core::chemical::THREE_PRIME_PHOSPHATE, and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.

Referenced by check_moved().

◆ force_phosphate_instantiation()

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::force_phosphate_instantiation ( ) const

inline

References force_phosphate_instantiation_.

◆ get_name()

std::string protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ get_scorefxn()

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::get_scorefxn ( )

inline

References scorefxn_.

◆ initialize_by_prepack() [1/2]

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack	(	core::pose::Pose &	pose,
		core::Size const	moving_res
	)

References pose().

Referenced by MultiPhosphateSampler().

◆ initialize_by_prepack() [2/2]

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	moving_res_list
	)

References do_prepack(), protocols::stepwise::modeler::figure_out_moving_partition_res(), moving_partition_res_, and pose().

◆ initialize_parameters()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_parameters ( )

private

References force_phosphate_instantiation_, phosphate_takeoff_donor_distance_cutoff2_, and screen_all_.

Referenced by MultiPhosphateSampler().

◆ initialize_phosphate_move_list()

utility::vector1< PhosphateMove > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list ( core::pose::Pose & pose )

private

References core::pose::full_model_info::const_full_model_info(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, five_prime_phosphate_res_input_, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), phosphate_move_list(), pose(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), screen_all_, core::pose::Pose::size(), protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE, three_prime_phosphate_res_input_, and protocols::TR().

Referenced by sample_phosphates().

◆ instantiated_some_phosphate()

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate ( ) const

inline

References instantiated_some_phosphate_.

◆ moving_partition_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res ( )

inline

References moving_partition_res_.

◆ phosphate_move_list()

utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_move_list ( ) const

inline

References phosphate_move_list_.

Referenced by check_moved(), find_phosphate_contacts_other_partition(), find_uninstantiated_phosphates(), and initialize_phosphate_move_list().

◆ pose()

pose::Pose & protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::pose ( )

References phosphate_sample_pose_.

Referenced by apply(), check_moved(), check_other_partition_for_contact(), do_prepack(), find_phosphate_contacts_other_partition(), find_uninstantiated_phosphates(), initialize_by_prepack(), initialize_phosphate_move_list(), and reset().

◆ reset()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::reset ( core::pose::Pose const & pose )

References core::pose::Pose::clone(), phosphate_sample_pose_, pose(), and pose_with_original_phosphates_.

Referenced by do_prepack(), and MultiPhosphateSampler().

◆ reset_to_original_pose()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::reset_to_original_pose ( )

References phosphate_sample_pose_, and pose_with_original_phosphates_.

◆ sample_phosphates() [1/2]

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates ( )

References actual_phosphate_move_list_, protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply(), check_moved(), protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), force_phosphate_instantiation_, protocols::stepwise::modeler::rna::phosphate::get_phosphate_scorefxn(), initialize_phosphate_move_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::instantiated_phosphate(), instantiated_some_phosphate_, phosphate_move_list_, phosphate_sample_pose_, pose_with_original_phosphates_, scorefxn_, and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::set_force_phosphate_instantiation().

Referenced by do_prepack(), protocols::stepwise::monte_carlo::mover::DeleteMover::minimize_after_delete(), and sample_phosphates().

◆ sample_phosphates() [2/2]

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates ( core::pose::PoseOP & viewer_pose_op )

References phosphate_sample_pose_, and sample_phosphates().

◆ screen_all()

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::screen_all ( ) const

inline

References screen_all_.

◆ set_five_prime_phosphate_res()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_five_prime_phosphate_res ( utility::vector1< core::Size > const & setting )

inline

References five_prime_phosphate_res_input_.

◆ set_force_phosphate_instantiation()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_force_phosphate_instantiation ( bool const & setting )

inline

References force_phosphate_instantiation_.

◆ set_moving_partition_res()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_moving_partition_res ( utility::vector1< core::Size > const & setting )

inline

References moving_partition_res_.

◆ set_phosphate_move_list()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_phosphate_move_list ( utility::vector1< PhosphateMove > const & setting )

inline

References phosphate_move_list_.

◆ set_scorefxn()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_.

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::minimize_after_delete().

◆ set_screen_all()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_screen_all ( bool const & setting )

inline

References screen_all_.

◆ set_three_prime_phosphate_res()

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_three_prime_phosphate_res ( utility::vector1< core::Size > const & setting )

inline

References three_prime_phosphate_res_input_.

Member Data Documentation

◆ actual_phosphate_move_list_

utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::actual_phosphate_move_list_

private

Referenced by sample_phosphates().

◆ five_prime_phosphate_res_input_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::five_prime_phosphate_res_input_

private

Referenced by initialize_phosphate_move_list(), and set_five_prime_phosphate_res().

◆ force_phosphate_instantiation_

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::force_phosphate_instantiation_

private

Referenced by check_moved(), clone_sampler(), force_phosphate_instantiation(), initialize_parameters(), sample_phosphates(), and set_force_phosphate_instantiation().

◆ instantiated_some_phosphate_

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate_

private

Referenced by instantiated_some_phosphate(), and sample_phosphates().

◆ moving_partition_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res_

private

Referenced by check_moved(), do_prepack(), initialize_by_prepack(), moving_partition_res(), and set_moving_partition_res().

◆ phosphate_move_list_

utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_move_list_

private

Referenced by check_moved(), clone_sampler(), copy_phosphates(), do_prepack(), phosphate_move_list(), sample_phosphates(), and set_phosphate_move_list().

◆ phosphate_sample_pose_

core::pose::PoseOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_sample_pose_

private

Referenced by copy_phosphates(), pose(), reset(), reset_to_original_pose(), and sample_phosphates().

◆ phosphate_takeoff_donor_distance_cutoff2_

core::Real protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_takeoff_donor_distance_cutoff2_

private

Referenced by check_other_partition_for_contact(), and initialize_parameters().

◆ pose_with_original_phosphates_

core::pose::PoseCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::pose_with_original_phosphates_

private

Referenced by check_moved(), clone_sampler(), do_prepack(), reset(), reset_to_original_pose(), and sample_phosphates().

◆ prepacked_

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::prepacked_

private

Referenced by check_moved(), and do_prepack().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::scorefxn_

private

Referenced by get_scorefxn(), sample_phosphates(), and set_scorefxn().

◆ screen_all_

bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::screen_all_

private

Referenced by clone_sampler(), initialize_parameters(), initialize_phosphate_move_list(), screen_all(), and set_screen_all().

◆ three_prime_phosphate_res_input_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::three_prime_phosphate_res_input_

private

Referenced by initialize_phosphate_move_list(), and set_three_prime_phosphate_res().

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

src/protocols/stepwise/modeler/rna/phosphate/MultiPhosphateSampler.hh
src/protocols/stepwise/modeler/rna/phosphate/MultiPhosphateSampler.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MultiPhosphateSampler() [1/2]

◆ MultiPhosphateSampler() [2/2]

◆ ~MultiPhosphateSampler()

Member Function Documentation

◆ apply()

◆ check_moved()

◆ check_other_partition_for_contact()

◆ clone()

◆ clone_sampler()

◆ copy_phosphates()

◆ do_prepack()

◆ find_phosphate_contacts_other_partition()

◆ find_uninstantiated_phosphates()

◆ force_phosphate_instantiation()

◆ get_name()

◆ get_scorefxn()

◆ initialize_by_prepack() [1/2]

◆ initialize_by_prepack() [2/2]

◆ initialize_parameters()

◆ initialize_phosphate_move_list()

◆ instantiated_some_phosphate()

◆ moving_partition_res()

◆ phosphate_move_list()

◆ pose()

◆ reset()

◆ reset_to_original_pose()

◆ sample_phosphates() [1/2]

◆ sample_phosphates() [2/2]

◆ screen_all()

◆ set_five_prime_phosphate_res()

◆ set_force_phosphate_instantiation()

◆ set_moving_partition_res()

◆ set_phosphate_move_list()

◆ set_scorefxn()

◆ set_screen_all()

◆ set_three_prime_phosphate_res()

Member Data Documentation

◆ actual_phosphate_move_list_

◆ five_prime_phosphate_res_input_

◆ force_phosphate_instantiation_

◆ instantiated_some_phosphate_

◆ moving_partition_res_

◆ phosphate_move_list_

◆ phosphate_sample_pose_

◆ phosphate_takeoff_donor_distance_cutoff2_

◆ pose_with_original_phosphates_

◆ prepacked_

◆ scorefxn_

◆ screen_all_

◆ three_prime_phosphate_res_input_