#include <ErraserMinimizerMover.hh>

Inheritance diagram for protocols::rna::movers::ErraserMinimizerMover:

[legend]

Public Member Functions
	ErraserMinimizerMover ()

	~ErraserMinimizerMover () override=default

void	pyrimidine_flip_trial (Pose &pose)

void	setup_fold_tree (Pose &pose)

void	minimize_protein (bool const setting)

void	initialize_from_options (utility::options::OptionCollection const &options, bool const initialize_scorefxn=true)

core::kinematics::MoveMap	movemap_setup (Pose &pose, std::set< core::Size > &cut_upper, std::set< core::Size > &cut_lower, ObjexxFCL::FArray1D< bool > &allow_insert)

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

void	process_entire_pose (Pose &pose)

void	pose_preliminaries (Pose &pose)
	Some pose setup functions that can be separated from apply. More...

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

bool	i_want_this_atom_to_move (core::chemical::ResidueType const &residue_type, core::Size const &atomno)

bool	i_want_this_atom_to_move (Pose const &pose, AtomID const &atom_id)

int	add_virtual_res (Pose &pose)

void	vary_bond_geometry (core::kinematics::MoveMap &mm, Pose &pose, ObjexxFCL::FArray1D< bool > &allow_insert, std::set< core::Size > const &chunk)

void	turn_off_for_chunks (core::kinematics::MoveMap &mm, Pose const &pose, std::set< core::Size > const &chunk)

void	add_fixed_res_constraints (Pose &pose, core::Size const fixed_res_num, core::Size const my_anchor)

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

void	scorefxn (core::scoring::ScoreFunctionOP const &sfxn)

void	edens_scorefxn (core::scoring::ScoreFunctionOP const &sfxn)

void	nstruct (core::Size const nstruct)

core::Size	nstruct ()

void	constrain_phosphate (bool const setting)

void	rank (int const rank)
	Sets the MPI rank of the proc this Mover is running on. More...

int	rank () const
	Returns the MPI rank of the proc this Mover is running on. More...

void	nproc (int const nproc)
	Sets the total MPI nproc. More...

int	nproc () const
	Returns the total MPI nproc. More...

void	work_partition (bool const work_partition)

int	work_partition () const

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

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 Types
typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef utility::tag::Tag	Tag

typedef core::id::AtomID	AtomID

Private Attributes
utility::vector1< std::pair< AtomID, AtomID > >	bonded_atom_list_

utility::vector1< std::pair< AtomID, std::pair< AtomID, AtomID > > >	bond_angle_list_

bool	vary_bond_geometry_

bool	constrain_phosphate_

bool	ready_set_only_

bool	skip_minimize_

bool	attempt_pyrimidine_flip_

bool	minimize_protein_ = true

std::set< core::Size >	fixed_res_list_

utility::vector1< core::Size >	cutpoint_list_

std::string	output_pdb_name_

core::Size	nstruct_ = 1

int	rank_ = 0

int	nproc_ = 1

bool	work_partition_ = true

ScoreFunctionOP	scorefxn_

ScoreFunctionOP	edens_scorefxn_

utility::vector1< std::set< core::Size > >	chunks_

core::Size	virtual_res_pos

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...

Member Typedef Documentation

◆ AtomID

typedef core::id::AtomID protocols::rna::movers::ErraserMinimizerMover::AtomID

private

◆ Pose

typedef core::pose::Pose protocols::rna::movers::ErraserMinimizerMover::Pose

private

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::ScoreFunctionOP

private

◆ Tag

typedef utility::tag::Tag protocols::rna::movers::ErraserMinimizerMover::Tag

private

Constructor & Destructor Documentation

◆ ErraserMinimizerMover()

protocols::rna::movers::ErraserMinimizerMover::ErraserMinimizerMover ( )

References initialize_from_options().

◆ ~ErraserMinimizerMover()

protocols::rna::movers::ErraserMinimizerMover::~ErraserMinimizerMover ( )

overridedefault

Member Function Documentation

◆ add_fixed_res_constraints()

void protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints	(	pose::Pose &	pose,
		core::Size const	fixed_res_num,
		core::Size const	my_anchor
	)

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::chemical::rna::first_base_atom_index(), core::conformation::Residue::has(), core::pose::Pose::residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by process_entire_pose().

◆ add_virtual_res()

int protocols::rna::movers::ErraserMinimizerMover::add_virtual_res ( Pose & pose )

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), protocols::moves::Mover::info(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::full_model_info::set_full_model_info(), core::pose::Pose::size(), protocols::rna::movers::TR(), and core::pose::virtual_type_for_pose().

Referenced by pose_preliminaries().

◆ apply()

void protocols::rna::movers::ErraserMinimizerMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::scoring::ScoreFunctionFactory::create_score_function(), pose_preliminaries(), process_entire_pose(), ready_set_only_, scorefxn_, protocols::rna::movers::TR(), and work_partition_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

◆ constrain_phosphate()

void protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate ( bool const setting )

inline

References constrain_phosphate_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

◆ edens_scorefxn()

void protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn ( core::scoring::ScoreFunctionOP const & sfxn )

inline

References edens_scorefxn_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

◆ get_name()

std::string protocols::rna::movers::ErraserMinimizerMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ i_want_this_atom_to_move() [1/2]

bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move	(	core::chemical::ResidueType const &	residue_type,
		core::Size const &	atomno
	)

References core::scoring::cart_bonded, core::chemical::ResidueType::is_virtual(), and scorefxn_.

Referenced by i_want_this_atom_to_move(), and vary_bond_geometry().

◆ i_want_this_atom_to_move() [2/2]

bool protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move	(	Pose const &	pose,
		AtomID const &	atom_id
	)

inline

References core::id::AtomID::atomno(), i_want_this_atom_to_move(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

◆ initialize_from_options()

void protocols::rna::movers::ErraserMinimizerMover::initialize_from_options	(	utility::options::OptionCollection const &	options,
		bool const	initialize_scorefxn = `true`
	)

References attempt_pyrimidine_flip_, constrain_phosphate_, core::scoring::ScoreFunctionFactory::create_score_function(), cutpoint_list_, ready_set_only_, scorefxn_, skip_minimize_, and protocols::rna::movers::TR().

Referenced by ErraserMinimizerMover().

◆ minimize_protein()

void protocols::rna::movers::ErraserMinimizerMover::minimize_protein ( bool const setting )

inline

References minimize_protein_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

◆ movemap_setup()

kinematics::MoveMap protocols::rna::movers::ErraserMinimizerMover::movemap_setup	(	Pose &	pose,
		std::set< core::Size > &	cut_upper,
		std::set< core::Size > &	cut_lower,
		ObjexxFCL::FArray1D< bool > &	allow_insert
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_h2o, core::chemical::aa_vrt, core::kinematics::FoldTree::downstream_jump_residue(), fixed_res_list_, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::name(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), protocols::rna::movers::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by process_entire_pose().

◆ mover_name()

std::string protocols::rna::movers::ErraserMinimizerMover::mover_name ( )

static

Referenced by get_name(), protocols::rna::movers::ErraserMinimizerMoverCreator::keyname(), and provide_xml_schema().

◆ nproc() [1/2]

int protocols::rna::movers::ErraserMinimizerMover::nproc ( ) const

Returns the total MPI nproc.

References nproc_.

Referenced by nproc().

◆ nproc() [2/2]

void protocols::rna::movers::ErraserMinimizerMover::nproc ( int const nproc )

Sets the total MPI nproc.

References nproc(), and nproc_.

◆ nstruct() [1/2]

core::Size protocols::rna::movers::ErraserMinimizerMover::nstruct ( )

inline

References nstruct_.

◆ nstruct() [2/2]

void protocols::rna::movers::ErraserMinimizerMover::nstruct ( core::Size const nstruct )

inline

References nstruct(), and nstruct_.

Referenced by nstruct().

◆ parse_my_tag()

void protocols::rna::movers::ErraserMinimizerMover::parse_my_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 attempt_pyrimidine_flip_, constrain_phosphate_, core::scoring::ScoreFunctionFactory::create_score_function(), cutpoint_list_, fixed_res_list_, output_pdb_name_, ready_set_only_, scorefxn_, skip_minimize_, protocols::rna::movers::string_to_size_vector(), protocols::rna::movers::TR(), and vary_bond_geometry_.

◆ pose_preliminaries()

void protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries ( Pose & pose )

Some pose setup functions that can be separated from apply.

In erraser2, there are some conventional pose setup operations that are a bit of a distraction from the main body of the apply method; they represent establishing the correct internal representation of the pose more than any actual operation on the pose. So, they all live here.

References add_virtual_res(), attempt_pyrimidine_flip_, chunks_, core::pose::full_model_info::const_full_model_info(), cutpoint_list_, core::pose::rna::figure_out_reasonable_rna_fold_tree(), fixed_res_list_, core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), protocols::rna::movers::identify_chunks(), core::chemical::ResidueTypeBase::is_protein(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), minimize_protein_, nproc_, core::kinematics::FoldTree::num_cutpoint(), pyrimidine_flip_trial(), ready_set_only_, core::pose::Pose::residue_type(), core::pose::Pose::sequence(), setup_fold_tree(), core::pose::Pose::size(), protocols::rna::movers::TR(), and virtual_res_pos.

Referenced by apply().

◆ process_entire_pose()

void protocols::rna::movers::ErraserMinimizerMover::process_entire_pose ( Pose & pose )

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, protocols::viewer::add_conformation_viewer(), add_fixed_res_constraints(), core::conformation::Residue::atom_index(), chunks_, protocols::rna::movers::com_of_true_residues(), core::pose::Pose::conformation(), constrain_phosphate_, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, fixed_res_list_, core::conformation::Residue::has(), protocols::rna::movers::load_checkpoint(), protocols::mean_field::max(), core::optimization::MinimizerOptions::max_iter(), protocols::mean_field::min(), protocols::rna::movers::min_checkpoint_namer(), protocols::rna::movers::min_log_namer(), movemap_setup(), core::optimization::MinimizerOptions::nblist_auto_update(), nstruct_, protocols::stepwise::modeler::output_movemap(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), protocols::hybridization::score, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::Pose::size(), protocols::rna::movers::TR(), turn_off_for_chunks(), vary_bond_geometry(), vary_bond_geometry_, virtual_res_pos, protocols::rna::movers::write_checkpoint(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ provide_xml_schema()

void protocols::rna::movers::ErraserMinimizerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::rna::movers::ErraserMinimizerMoverCreator::provide_xml_schema().

◆ pyrimidine_flip_trial()

void protocols::rna::movers::ErraserMinimizerMover::pyrimidine_flip_trial ( pose::Pose & pose )

References core::chemical::rna::CHI, fixed_res_list_, core::chemical::ResidueType::is_pyrimidine(), core::pose::Pose::residue_type(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::pose::Pose::torsion(), and protocols::rna::movers::TR().

Referenced by pose_preliminaries().

◆ rank() [1/2]

int protocols::rna::movers::ErraserMinimizerMover::rank ( ) const

Returns the MPI rank of the proc this Mover is running on.

References rank_.

Referenced by rank().

◆ rank() [2/2]

void protocols::rna::movers::ErraserMinimizerMover::rank ( int const rank )

Sets the MPI rank of the proc this Mover is running on.

References rank(), and rank_.

◆ scorefxn()

void protocols::rna::movers::ErraserMinimizerMover::scorefxn ( core::scoring::ScoreFunctionOP const & sfxn )

inline

References scorefxn_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

◆ setup_fold_tree()

void protocols::rna::movers::ErraserMinimizerMover::setup_fold_tree ( pose::Pose & pose )

References cutpoint_list_, core::pose::Pose::fold_tree(), core::pose::Pose::size(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by pose_preliminaries().

◆ turn_off_for_chunks()

void protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks	(	core::kinematics::MoveMap &	mm,
		Pose const &	pose,
		std::set< core::Size > const &	chunk
	)

References core::id::D, core::chemical::rings::PHI, core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::chemical::rings::THETA, and core::pose::Pose::total_residue().

Referenced by process_entire_pose().

◆ vary_bond_geometry()

void protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry	(	core::kinematics::MoveMap &	mm,
		pose::Pose &	pose,
		ObjexxFCL::FArray1D< bool > &	allow_insert,
		std::set< core::Size > const &	chunk
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::D, protocols::moves::Mover::get_self_ptr(), i_want_this_atom_to_move(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueType::natoms(), core::chemical::rings::PHI, core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::pose::Pose::size(), core::chemical::rings::THETA, and protocols::rna::movers::TR().

Referenced by process_entire_pose().

◆ work_partition() [1/2]

int protocols::rna::movers::ErraserMinimizerMover::work_partition ( ) const

inline

References work_partition_.

◆ work_partition() [2/2]

void protocols::rna::movers::ErraserMinimizerMover::work_partition ( bool const work_partition )

inline

References work_partition(), and work_partition_.

Referenced by protocols::rna::movers::ERRASER2Protocol::apply(), and work_partition().

Member Data Documentation

◆ attempt_pyrimidine_flip_

bool protocols::rna::movers::ErraserMinimizerMover::attempt_pyrimidine_flip_

private

Referenced by initialize_from_options(), parse_my_tag(), and pose_preliminaries().

◆ bond_angle_list_

utility::vector1< std::pair< AtomID, std::pair< AtomID, AtomID > > > protocols::rna::movers::ErraserMinimizerMover::bond_angle_list_

private

◆ bonded_atom_list_

utility::vector1< std::pair< AtomID, AtomID > > protocols::rna::movers::ErraserMinimizerMover::bonded_atom_list_

private

◆ chunks_

utility::vector1< std::set< core::Size > > protocols::rna::movers::ErraserMinimizerMover::chunks_

private

Referenced by pose_preliminaries(), and process_entire_pose().

◆ constrain_phosphate_

bool protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate_

private

Referenced by constrain_phosphate(), initialize_from_options(), parse_my_tag(), and process_entire_pose().

◆ cutpoint_list_

utility::vector1< core::Size > protocols::rna::movers::ErraserMinimizerMover::cutpoint_list_

private

Referenced by initialize_from_options(), parse_my_tag(), pose_preliminaries(), and setup_fold_tree().

◆ edens_scorefxn_

ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn_

private

Referenced by edens_scorefxn().

◆ fixed_res_list_

std::set< core::Size > protocols::rna::movers::ErraserMinimizerMover::fixed_res_list_

private

Referenced by movemap_setup(), parse_my_tag(), pose_preliminaries(), process_entire_pose(), and pyrimidine_flip_trial().

◆ minimize_protein_

bool protocols::rna::movers::ErraserMinimizerMover::minimize_protein_ = true

private

Referenced by minimize_protein(), and pose_preliminaries().

◆ nproc_

int protocols::rna::movers::ErraserMinimizerMover::nproc_ = 1

private

Referenced by nproc(), and pose_preliminaries().

◆ nstruct_

core::Size protocols::rna::movers::ErraserMinimizerMover::nstruct_ = 1

private

Referenced by nstruct(), and process_entire_pose().

◆ output_pdb_name_

std::string protocols::rna::movers::ErraserMinimizerMover::output_pdb_name_

private

Referenced by parse_my_tag().

◆ rank_

int protocols::rna::movers::ErraserMinimizerMover::rank_ = 0

private

Referenced by rank().

◆ ready_set_only_

bool protocols::rna::movers::ErraserMinimizerMover::ready_set_only_

private

Referenced by apply(), initialize_from_options(), parse_my_tag(), and pose_preliminaries().

◆ scorefxn_

ScoreFunctionOP protocols::rna::movers::ErraserMinimizerMover::scorefxn_

private

Referenced by apply(), i_want_this_atom_to_move(), initialize_from_options(), parse_my_tag(), process_entire_pose(), and scorefxn().

◆ skip_minimize_

bool protocols::rna::movers::ErraserMinimizerMover::skip_minimize_

private

Referenced by initialize_from_options(), and parse_my_tag().

◆ vary_bond_geometry_

bool protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry_

private

Referenced by parse_my_tag(), and process_entire_pose().

◆ virtual_res_pos

core::Size protocols::rna::movers::ErraserMinimizerMover::virtual_res_pos

private

Referenced by pose_preliminaries(), and process_entire_pose().

◆ work_partition_

bool protocols::rna::movers::ErraserMinimizerMover::work_partition_ = true

private

Referenced by apply(), and work_partition().

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

src/protocols/rna/movers/ErraserMinimizerMover.hh
src/protocols/rna/movers/ErraserMinimizerMover.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ AtomID

◆ Pose

◆ ScoreFunctionOP

◆ Tag

Constructor & Destructor Documentation

◆ ErraserMinimizerMover()

◆ ~ErraserMinimizerMover()

Member Function Documentation

◆ add_fixed_res_constraints()

◆ add_virtual_res()

◆ apply()

◆ constrain_phosphate()

◆ edens_scorefxn()

◆ get_name()

◆ i_want_this_atom_to_move() [1/2]

◆ i_want_this_atom_to_move() [2/2]

◆ initialize_from_options()

◆ minimize_protein()

◆ movemap_setup()

◆ mover_name()

◆ nproc() [1/2]

◆ nproc() [2/2]

◆ nstruct() [1/2]

◆ nstruct() [2/2]

◆ parse_my_tag()

◆ pose_preliminaries()

◆ process_entire_pose()

◆ provide_xml_schema()

◆ pyrimidine_flip_trial()

◆ rank() [1/2]

◆ rank() [2/2]

◆ scorefxn()

◆ setup_fold_tree()

◆ turn_off_for_chunks()

◆ vary_bond_geometry()

◆ work_partition() [1/2]

◆ work_partition() [2/2]

Member Data Documentation

◆ attempt_pyrimidine_flip_

◆ bond_angle_list_

◆ bonded_atom_list_

◆ chunks_

◆ constrain_phosphate_

◆ cutpoint_list_

◆ edens_scorefxn_

◆ fixed_res_list_

◆ minimize_protein_

◆ nproc_

◆ nstruct_

◆ output_pdb_name_

◆ rank_

◆ ready_set_only_

◆ scorefxn_

◆ skip_minimize_

◆ vary_bond_geometry_

◆ virtual_res_pos

◆ work_partition_