#include <AddMover.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::mover::AddMover:

[legend]

Public Member Functions
	AddMover (core::scoring::ScoreFunctionCOP scorefxn=nullptr)

	~AddMover () override

void	apply (core::pose::Pose &pose, core::Size const res_to_add_in_full_model_numbering, core::Size const res_to_build_off_in_full_model_numbering)

void	apply (core::pose::Pose &pose, StepWiseMove const &swa_move)

void	apply (core::pose::Pose &pose_to_visualize) override
	Apply the minimizer to one pose. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	set_kT (core::Real const &setting)

void	set_sample_range_small (core::Real const setting)

void	set_sample_range_large (core::Real const setting)

void	set_internal_cycles (core::Size const setting)

void	set_sample_pH (bool const setting)

void	set_presample_added_residue (core::Size const setting)

void	set_presample_by_swa (core::Size const setting)

void	set_designing_with_noncanonicals (bool const setting)

void	set_start_added_residue_in_aform (core::Size const setting)

void	set_minimize_single_res (core::Size const setting)

void	set_stepwise_modeler (protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler)

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...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
void	sample_by_swa (core::pose::Pose &pose, core::Size const res_to_add) const

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

void	do_append (core::pose::Pose &pose)

void	do_prepend (core::pose::Pose &pose)

void	append_other_pose (core::pose::Pose &pose, core::Size const offset, core::Size const other_pose_idx)

void	prepend_other_pose (core::pose::Pose &pose, core::Size const offset, core::Size const other_pose_idx)

void	append_residue (core::pose::Pose &pose, core::Size const offset)

void	prepend_residue (core::pose::Pose &pose, core::Size const offset)

bool	check_same_chain (core::pose::Pose const &pose, core::Size const res_to_add_in_full_model_numbering, core::Size const res_to_build_off_in_full_model_numbering)

bool	check_same_chain (core::pose::Pose const &pose)

void	setup_initial_torsions (core::pose::Pose &pose)

core::Size	get_add_res (StepWiseMove const &swa_move, core::pose::Pose const &pose) const

void	setup_initial_jump (core::pose::Pose &pose)

core::conformation::ResidueOP	create_residue_to_add (core::pose::Pose const &pose)
	: figure out the res type of the residue to add and create it More...

Private Attributes
core::chemical::ResidueTypeSetCAP	rsd_set_

core::scoring::ScoreFunctionCOP	scorefxn_

bool	presample_added_residue_ = true

bool	presample_by_swa_ = false

bool	minimize_single_res_ = false

bool	start_added_residue_in_aform_ = false

bool	designing_with_noncanonicals_ = false

core::Size	internal_cycles_ = 50

bool	sample_pH_ = false

rna::RNA_TorsionMoverOP	rna_torsion_mover_

core::Real	sample_range_small_ = 5.0

core::Real	sample_range_large_ = 40.0

core::Real	kT_ = 0.5

protocols::stepwise::modeler::StepWiseModelerOP	stepwise_modeler_

core::Size	suite_num_ = 0

core::Size	nucleoside_num_ = 0

core::Size	res_to_add_in_full_model_numbering_ = 0

core::Size	res_to_build_off_in_full_model_numbering_ = 0

StepWiseMove	swa_move_

std::string	move_str_

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

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

◆ AddMover()

protocols::stepwise::monte_carlo::mover::AddMover::AddMover ( core::scoring::ScoreFunctionCOP scorefxn = nullptr )

◆ ~AddMover()

protocols::stepwise::monte_carlo::mover::AddMover::~AddMover ( )

overridedefault

Member Function Documentation

◆ append_other_pose()

void protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose	(	core::pose::Pose &	pose,
		core::Size const	offset,
		core::Size const	other_pose_idx
	)

private

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, core::pose::full_model_info::get_res_list_from_full_model_info(), protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), protocols::stepwise::modeler::merge_in_other_pose_by_bond(), protocols::stepwise::modeler::merge_in_other_pose_by_jump(), core::pose::full_model_info::nonconst_full_model_info(), nucleoside_num_, core::scoring::other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), core::pose::full_model_info::FullModelInfo::remove_other_pose_at_idx(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, suite_num_, and swa_move_.

Referenced by do_append().

◆ append_residue()

void protocols::stepwise::monte_carlo::mover::AddMover::append_residue	(	core::pose::Pose &	pose,
		core::Size const	offset
	)

private

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_polymer_residue_after_seqpos(), core::chemical::ResidueType::atom_name(), protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, core::chemical::C_METHYLAMIDATION, create_residue_to_add(), core::chemical::rna::default_jump_atom(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::pose::Pose::insert_residue_by_atoms(), core::pose::Pose::insert_residue_by_jump(), protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_RNA(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, core::kinematics::FoldTree::jump_nr(), nucleoside_num_, core::pose::remove_variant_type_from_pose_residue(), core::pose::full_model_info::reorder_full_model_info_after_append(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::slide_jump(), suite_num_, swa_move_, core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::ResidueType::upper_connect_atom(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by do_append().

◆ apply() [1/3]

void protocols::stepwise::monte_carlo::mover::AddMover::apply	(	core::pose::Pose &	pose,
		core::Size const	res_to_add_in_full_model_numbering,
		core::Size const	res_to_build_off_in_full_model_numbering
	)

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, check_same_chain(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN, and viewer_pose.

Referenced by apply().

◆ apply() [2/3]

void protocols::stepwise::monte_carlo::mover::AddMover::apply	(	core::pose::Pose &	pose,
		StepWiseMove const &	swa_move
	)

References check_same_chain(), do_append(), do_prepend(), protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants(), get_add_res(), core::pose::full_model_info::get_res_list_from_full_model_info(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, nucleoside_num_, presample_added_residue_, presample_by_swa_, res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, sample_by_monte_carlo_internal(), sample_by_swa(), setup_initial_torsions(), suite_num_, swa_move_, and viewer_pose.

◆ apply() [3/3]

void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose & pose_to_visualize )

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References apply(), core::pose::full_model_info::const_full_model_info(), and move_str_.

◆ check_same_chain() [1/2]

bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( core::pose::Pose const & pose )

private

References check_same_chain(), res_to_add_in_full_model_numbering_, and res_to_build_off_in_full_model_numbering_.

◆ check_same_chain() [2/2]

bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain	(	core::pose::Pose const &	pose,
		core::Size const	res_to_add_in_full_model_numbering,
		core::Size const	res_to_build_off_in_full_model_numbering
	)

private

References core::pose::full_model_info::get_chain_for_full_model_resnum().

Referenced by apply(), and check_same_chain().

◆ clone()

protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::AddMover::clone ( ) const

overridevirtual

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.

◆ create_residue_to_add()

core::conformation::ResidueOP protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add ( core::pose::Pose const & pose )

private

: figure out the res type of the residue to add and create it

: also handles the question of 'what if I have chemical modifications' and 'what if I have protonation sampling turned on'. Probably should factor out these concerns.

References core::chemical::aa_from_oneletter_code(), protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide(), protocols::stepwise::modeler::rna::choose_randomly_from_allowed_at_position(), core::pose::full_model_info::const_full_model_info(), designing_with_noncanonicals_, core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::chemical::name_from_aa(), res_to_add_in_full_model_numbering_, core::pose::Pose::residue_type_set_for_pose(), core::scoring::rg, sample_pH_, and protocols::TR().

Referenced by append_residue(), and prepend_residue().

◆ do_append()

void protocols::stepwise::monte_carlo::mover::AddMover::do_append ( core::pose::Pose & pose )

private

References append_other_pose(), append_residue(), protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), core::pose::full_model_info::get_res_list_from_full_model_info(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, core::pose::full_model_info::nonconst_full_model_info(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, core::pose::Pose::size(), and swa_move_.

Referenced by apply().

◆ do_prepend()

void protocols::stepwise::monte_carlo::mover::AddMover::do_prepend ( core::pose::Pose & pose )

private

References core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), core::pose::full_model_info::nonconst_full_model_info(), prepend_other_pose(), prepend_residue(), res_to_add_in_full_model_numbering_, and res_to_build_off_in_full_model_numbering_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::AddMover::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_add_res()

Size protocols::stepwise::monte_carlo::mover::AddMover::get_add_res	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose
	)		const

private

Referenced by apply().

◆ get_name()

std::string protocols::stepwise::monte_carlo::mover::AddMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::stepwise::monte_carlo::mover::AddMover::mover_name ( )

static

Referenced by get_name(), protocols::stepwise::monte_carlo::mover::AddMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::stepwise::monte_carlo::mover::AddMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References internal_cycles_, kT_, minimize_single_res_, move_str_, core::scoring::parse_score_function(), presample_added_residue_, presample_by_swa_, sample_range_large_, sample_range_small_, scorefxn_, and start_added_residue_in_aform_.

◆ prepend_other_pose()

void protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose	(	core::pose::Pose &	pose,
		core::Size const	offset,
		core::Size const	other_pose_idx
	)

private

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, core::pose::full_model_info::get_res_list_from_full_model_info(), protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), protocols::stepwise::modeler::merge_in_other_pose_by_bond(), protocols::stepwise::modeler::merge_in_other_pose_by_jump(), core::pose::full_model_info::nonconst_full_model_info(), nucleoside_num_, core::scoring::other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), core::pose::full_model_info::FullModelInfo::remove_other_pose_at_idx(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, suite_num_, and swa_move_.

Referenced by do_prepend().

◆ prepend_residue()

void protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue	(	core::pose::Pose &	pose,
		core::Size const	offset
	)

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueType::atom_name(), protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, core::chemical::C_METHYLAMIDATION, create_residue_to_add(), core::chemical::rna::default_jump_atom(), core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::insert_residue_by_atoms(), core::pose::Pose::insert_residue_by_jump(), protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::FoldTree::jump_nr(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, nucleoside_num_, core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::remove_variant_type_from_pose_residue(), core::pose::full_model_info::reorder_full_model_info_after_prepend(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::slide_jump(), suite_num_, swa_move_, core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::ResidueType::upper_connect_atom(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by do_prepend().

◆ provide_xml_schema()

void protocols::stepwise::monte_carlo::mover::AddMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::stepwise::monte_carlo::mover::AddMoverCreator::provide_xml_schema().

◆ sample_by_monte_carlo_internal()

void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_monte_carlo_internal ( core::pose::Pose & pose ) const

private

References internal_cycles_, kT_, nucleoside_num_, rna_torsion_mover_, sample_range_large_, sample_range_small_, scorefxn_, suite_num_, and protocols::TR().

Referenced by apply().

◆ sample_by_swa()

void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_swa	(	core::pose::Pose &	pose,
		core::Size const	res_to_add
	)		const

private

References core::pose::full_model_info::get_moving_res_from_full_model_info(), minimize_single_res_, and stepwise_modeler_.

Referenced by apply().

◆ set_designing_with_noncanonicals()

void protocols::stepwise::monte_carlo::mover::AddMover::set_designing_with_noncanonicals ( bool const setting )

inline

References designing_with_noncanonicals_.

◆ set_internal_cycles()

void protocols::stepwise::monte_carlo::mover::AddMover::set_internal_cycles ( core::Size const setting )

inline

References internal_cycles_.

◆ set_kT()

void protocols::stepwise::monte_carlo::mover::AddMover::set_kT ( core::Real const & setting )

inline

References kT_.

◆ set_minimize_single_res()

void protocols::stepwise::monte_carlo::mover::AddMover::set_minimize_single_res ( core::Size const setting )

inline

References minimize_single_res_.

◆ set_presample_added_residue()

void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_added_residue ( core::Size const setting )

inline

References presample_added_residue_.

◆ set_presample_by_swa()

void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_by_swa ( core::Size const setting )

inline

References presample_by_swa_.

◆ set_sample_pH()

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_pH ( bool const setting )

inline

References sample_pH_.

◆ set_sample_range_large()

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_large ( core::Real const setting )

inline

References sample_range_large_.

◆ set_sample_range_small()

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_small ( core::Real const setting )

inline

References sample_range_small_.

◆ set_start_added_residue_in_aform()

void protocols::stepwise::monte_carlo::mover::AddMover::set_start_added_residue_in_aform ( core::Size const setting )

inline

References start_added_residue_in_aform_.

◆ set_stepwise_modeler()

void protocols::stepwise::monte_carlo::mover::AddMover::set_stepwise_modeler ( protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler )

References stepwise_modeler_.

◆ setup_initial_jump()

void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump ( core::pose::Pose & pose )

private

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attachment_type(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::full_to_sub(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::kinematics::FoldTree::get_parent_residue(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, core::pose::full_model_info::nonconst_full_model_info(), res_to_add_in_full_model_numbering_, core::pose::Pose::set_jump(), core::kinematics::Jump::set_translation(), swa_move_, and protocols::hybridization::t.

Referenced by setup_initial_torsions().

◆ setup_initial_torsions()

void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions ( core::pose::Pose & pose )

private

References protocols::stepwise::monte_carlo::mover::StepWiseMove::is_jump(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_RNA(), nucleoside_num_, core::pose::Pose::residue_type(), rna_torsion_mover_, setup_initial_jump(), start_added_residue_in_aform_, suite_num_, and swa_move_.

Referenced by apply().

Member Data Documentation

◆ designing_with_noncanonicals_

bool protocols::stepwise::monte_carlo::mover::AddMover::designing_with_noncanonicals_ = false

private

Referenced by create_residue_to_add(), and set_designing_with_noncanonicals().

◆ internal_cycles_

core::Size protocols::stepwise::monte_carlo::mover::AddMover::internal_cycles_ = 50

private

Referenced by parse_my_tag(), sample_by_monte_carlo_internal(), and set_internal_cycles().

◆ kT_

core::Real protocols::stepwise::monte_carlo::mover::AddMover::kT_ = 0.5

private

Referenced by parse_my_tag(), sample_by_monte_carlo_internal(), and set_kT().

◆ minimize_single_res_

bool protocols::stepwise::monte_carlo::mover::AddMover::minimize_single_res_ = false

private

Referenced by parse_my_tag(), sample_by_swa(), and set_minimize_single_res().

◆ move_str_

std::string protocols::stepwise::monte_carlo::mover::AddMover::move_str_

private

Referenced by apply(), and parse_my_tag().

◆ nucleoside_num_

core::Size protocols::stepwise::monte_carlo::mover::AddMover::nucleoside_num_ = 0

private

Referenced by append_other_pose(), append_residue(), apply(), prepend_other_pose(), prepend_residue(), sample_by_monte_carlo_internal(), and setup_initial_torsions().

◆ presample_added_residue_

bool protocols::stepwise::monte_carlo::mover::AddMover::presample_added_residue_ = true

private

Referenced by apply(), parse_my_tag(), and set_presample_added_residue().

◆ presample_by_swa_

bool protocols::stepwise::monte_carlo::mover::AddMover::presample_by_swa_ = false

private

Referenced by apply(), parse_my_tag(), and set_presample_by_swa().

◆ res_to_add_in_full_model_numbering_

core::Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_add_in_full_model_numbering_ = 0

private

Referenced by append_other_pose(), append_residue(), apply(), check_same_chain(), create_residue_to_add(), do_append(), do_prepend(), prepend_other_pose(), prepend_residue(), and setup_initial_jump().

◆ res_to_build_off_in_full_model_numbering_

core::Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_build_off_in_full_model_numbering_ = 0

private

Referenced by append_other_pose(), append_residue(), apply(), check_same_chain(), do_append(), do_prepend(), prepend_other_pose(), and prepend_residue().

◆ rna_torsion_mover_

rna::RNA_TorsionMoverOP protocols::stepwise::monte_carlo::mover::AddMover::rna_torsion_mover_

private

Referenced by sample_by_monte_carlo_internal(), and setup_initial_torsions().

◆ rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::monte_carlo::mover::AddMover::rsd_set_

private

◆ sample_pH_

bool protocols::stepwise::monte_carlo::mover::AddMover::sample_pH_ = false

private

Referenced by create_residue_to_add(), and set_sample_pH().

◆ sample_range_large_

core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_large_ = 40.0

private

Referenced by parse_my_tag(), sample_by_monte_carlo_internal(), and set_sample_range_large().

◆ sample_range_small_

core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_small_ = 5.0

private

Referenced by parse_my_tag(), sample_by_monte_carlo_internal(), and set_sample_range_small().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::mover::AddMover::scorefxn_

private

Referenced by parse_my_tag(), and sample_by_monte_carlo_internal().

◆ start_added_residue_in_aform_

bool protocols::stepwise::monte_carlo::mover::AddMover::start_added_residue_in_aform_ = false

private

Referenced by parse_my_tag(), set_start_added_residue_in_aform(), and setup_initial_torsions().

◆ stepwise_modeler_

protocols::stepwise::modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::AddMover::stepwise_modeler_

private

Referenced by sample_by_swa(), and set_stepwise_modeler().

◆ suite_num_

core::Size protocols::stepwise::monte_carlo::mover::AddMover::suite_num_ = 0

private

Referenced by append_other_pose(), append_residue(), apply(), prepend_other_pose(), prepend_residue(), sample_by_monte_carlo_internal(), and setup_initial_torsions().

◆ swa_move_

StepWiseMove protocols::stepwise::monte_carlo::mover::AddMover::swa_move_

private

Referenced by append_other_pose(), append_residue(), apply(), do_append(), prepend_other_pose(), prepend_residue(), setup_initial_jump(), and setup_initial_torsions().

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

src/protocols/stepwise/monte_carlo/mover/AddMover.hh
src/protocols/stepwise/monte_carlo/mover/AddMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ AddMover()

◆ ~AddMover()

Member Function Documentation

◆ append_other_pose()

◆ append_residue()

◆ apply() [1/3]

◆ apply() [2/3]

◆ apply() [3/3]

◆ check_same_chain() [1/2]

◆ check_same_chain() [2/2]

◆ clone()

◆ create_residue_to_add()

◆ do_append()

◆ do_prepend()

◆ fresh_instance()

◆ get_add_res()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ prepend_other_pose()

◆ prepend_residue()

◆ provide_xml_schema()

◆ sample_by_monte_carlo_internal()

◆ sample_by_swa()

◆ set_designing_with_noncanonicals()

◆ set_internal_cycles()

◆ set_kT()

◆ set_minimize_single_res()

◆ set_presample_added_residue()

◆ set_presample_by_swa()

◆ set_sample_pH()

◆ set_sample_range_large()

◆ set_sample_range_small()

◆ set_start_added_residue_in_aform()

◆ set_stepwise_modeler()

◆ setup_initial_jump()

◆ setup_initial_torsions()

Member Data Documentation

◆ designing_with_noncanonicals_

◆ internal_cycles_

◆ kT_

◆ minimize_single_res_

◆ move_str_

◆ nucleoside_num_

◆ presample_added_residue_

◆ presample_by_swa_

◆ res_to_add_in_full_model_numbering_

◆ res_to_build_off_in_full_model_numbering_

◆ rna_torsion_mover_

◆ rsd_set_

◆ sample_pH_

◆ sample_range_large_

◆ sample_range_small_

◆ scorefxn_

◆ start_added_residue_in_aform_

◆ stepwise_modeler_

◆ suite_num_

◆ swa_move_