protocols::stepwise::monte_carlo::rna::AddMover Class Reference

#include <AddMover.hh>

Public Member Functions
	AddMover (core::scoring::ScoreFunctionOP scorefxn)
	~AddMover ()
void	apply (core::pose::Pose &pose, Size const res_to_add_in_full_model_numbering, Size const res_to_build_off_in_full_model_numbering)
void	apply (core::pose::Pose &pose, SWA_Move const &swa_move)
virtual void	apply (core::pose::Pose &pose_to_visualize)
	Apply the minimizer to one pose. More...
virtual std::string	get_name () const
	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 (Size const setting)
void	set_presample_added_residue (Size const setting)
void	set_presample_by_swa (Size const setting)
void	set_start_added_residue_in_aform (Size const setting)
void	set_minimize_single_res (Size const setting)
void	set_stepwise_modeler (protocols::stepwise::sampling::StepWiseModelerOP stepwise_modeler)
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~Mover ()
virtual MoverSP	create ()
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	parse_state (SerializableState const &state)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void	save_state (SerializableState &state)
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
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...
void	set_current_tag (std::string const &new_tag)
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	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...
void	type (const std::string &type_in)
virtual MoverOP	clone () const
	Return a clone of the Mover object. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string	get_type () const
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...
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 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...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	sample_by_swa (core::pose::Pose &pose, 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 (pose::Pose &pose, Size const offset, Size const other_pose_idx)
void	prepend_other_pose (pose::Pose &pose, Size const offset, Size const other_pose_idx)
void	append_residue (pose::Pose &pose, Size const offset)
void	prepend_residue (pose::Pose &pose, Size const offset)
bool	check_same_chain (pose::Pose const &pose, Size const res_to_add_in_full_model_numbering, Size const res_to_build_off_in_full_model_numbering)
bool	check_same_chain (pose::Pose const &pose)
void	setup_initial_torsions (pose::Pose &pose)

Private Attributes
core::chemical::ResidueTypeSetCAP	rsd_set_
core::scoring::ScoreFunctionOP	scorefxn_
bool	presample_added_residue_
bool	presample_by_swa_
bool	minimize_single_res_
bool	start_added_residue_in_aform_
Size	internal_cycles_
RNA_TorsionMoverOP	rna_torsion_mover_
core::Real	sample_range_small_
core::Real	sample_range_large_
core::Real	kT_
protocols::stepwise::sampling::StepWiseModelerOP	stepwise_modeler_
Size	suite_num_
Size	nucleoside_num_
Size	res_to_add_in_full_model_numbering_
Size	res_to_build_off_in_full_model_numbering_
SWA_Move	swa_move_

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 protocols::filters::Filters_map	Filters_map
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

protocols::stepwise::monte_carlo::rna::AddMover::AddMover

(

core::scoring::ScoreFunctionOP

scorefxn

)

protocols::stepwise::monte_carlo::rna::AddMover::~AddMover

(

)

Member Function Documentation

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

private

References protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, get_res_list_from_full_model_info(), utility::vector1< T, class >::index(), protocols::stepwise::monte_carlo::SWA_Move::is_jump(), protocols::stepwise::merge_in_other_pose_by_bond(), protocols::stepwise::merge_in_other_pose_by_jump(), nonconst_full_model_info(), nucleoside_num_, 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_, runtime_assert, suite_num_, and swa_move_.

Referenced by do_append().

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

private

References add_variant_type_to_pose_residue(), core::pose::Pose::append_polymer_residue_after_seqpos(), protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, protocols::stepwise::sampling::rna::choose_random_if_unspecified_nucleotide(), default_jump_atom(), core::pose::Pose::fold_tree(), get_res_list_from_full_model_info(), core::pose::Pose::insert_residue_by_jump(), protocols::stepwise::monte_carlo::SWA_Move::is_jump(), jump_nr, core::kinematics::FoldTree::jump_nr(), nonconst_full_model_info(), nucleoside_num_, remove_variant_type_from_pose_residue(), 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(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), runtime_assert, core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::slide_jump(), suite_num_, and swa_move_.

Referenced by do_append().

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

References protocols::stepwise::monte_carlo::ADD, protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, check_same_chain(), protocols::stepwise::monte_carlo::JUMP_INTERCHAIN, protocols::stepwise::monte_carlo::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::JUMP_TO_PREV_IN_CHAIN, and runtime_assert.

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

References protocols::stepwise::monte_carlo::SWA_Move::attached_res(), protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), check_same_chain(), do_append(), do_prepend(), protocols::stepwise::fix_up_jump_atoms_and_residue_type_variants(), get_res_list_from_full_model_info(), protocols::stepwise::monte_carlo::JUMP_INTERCHAIN, protocols::stepwise::monte_carlo::SWA_Move::moving_res(), nucleoside_num_, presample_added_residue_, presample_by_swa_, res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, runtime_assert, sample_by_monte_carlo_internal(), sample_by_swa(), setup_initial_torsions(), suite_num_, and swa_move_.

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

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

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

private

References get_chain_for_full_model_resnum().

Referenced by apply(), and check_same_chain().

bool protocols::stepwise::monte_carlo::rna::AddMover::check_same_chain ( 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_.

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

private

References append_other_pose(), append_residue(), protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), get_res_list_from_full_model_info(), utility::vector1< T, class >::index(), protocols::stepwise::monte_carlo::JUMP_INTERCHAIN, nonconst_full_model_info(), res_to_add_in_full_model_numbering_, res_to_build_off_in_full_model_numbering_, runtime_assert, swa_move_, and core::pose::Pose::total_residue().

Referenced by apply().

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

private

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

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

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

private

References protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), protocols::stepwise::monte_carlo::BOND_TO_NEXT, get_res_list_from_full_model_info(), utility::vector1< T, class >::index(), protocols::stepwise::monte_carlo::SWA_Move::is_jump(), protocols::stepwise::merge_in_other_pose_by_bond(), protocols::stepwise::merge_in_other_pose_by_jump(), nonconst_full_model_info(), nucleoside_num_, 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_, runtime_assert, suite_num_, and swa_move_.

Referenced by do_prepend().

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

private

References add_variant_type_to_pose_residue(), protocols::stepwise::monte_carlo::SWA_Move::attachment_type(), protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::sampling::rna::choose_random_if_unspecified_nucleotide(), default_jump_atom(), core::pose::Pose::fold_tree(), get_res_list_from_full_model_info(), core::pose::Pose::insert_residue_by_jump(), protocols::stepwise::monte_carlo::SWA_Move::is_jump(), jump_nr, core::kinematics::FoldTree::jump_nr(), nonconst_full_model_info(), nucleoside_num_, core::pose::Pose::prepend_polymer_residue_before_seqpos(), remove_variant_type_from_pose_residue(), 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(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), runtime_assert, core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::slide_jump(), suite_num_, swa_move_, and protocols::TR.

Referenced by do_prepend().

void protocols::stepwise::monte_carlo::rna::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().

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

private

References get_moving_res_from_full_model_info(), minimize_single_res_, runtime_assert, and stepwise_modeler_.

Referenced by apply().

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

inline

References internal_cycles_.

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

inline

References kT_.

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

inline

References minimize_single_res_.

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

inline

References presample_added_residue_.

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

inline

References presample_by_swa_.

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

inline

References sample_range_large_.

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

inline

References sample_range_small_.

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

inline

References start_added_residue_in_aform_.

void protocols::stepwise::monte_carlo::rna::AddMover::set_stepwise_modeler

(

protocols::stepwise::sampling::StepWiseModelerOP

stepwise_modeler

)

References stepwise_modeler_.

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

private

References core::chemical::ResidueType::is_RNA(), nucleoside_num_, core::pose::Pose::residue_type(), rna_torsion_mover_, sample_range_large_, start_added_residue_in_aform_, and suite_num_.

Referenced by apply().

Member Data Documentation

Size protocols::stepwise::monte_carlo::rna::AddMover::internal_cycles_

private

Referenced by sample_by_monte_carlo_internal(), and set_internal_cycles().

core::Real protocols::stepwise::monte_carlo::rna::AddMover::kT_

private

Referenced by sample_by_monte_carlo_internal(), and set_kT().

bool protocols::stepwise::monte_carlo::rna::AddMover::minimize_single_res_

private

Referenced by sample_by_swa(), and set_minimize_single_res().

Size protocols::stepwise::monte_carlo::rna::AddMover::nucleoside_num_

private

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

bool protocols::stepwise::monte_carlo::rna::AddMover::presample_added_residue_

private

Referenced by apply(), and set_presample_added_residue().

bool protocols::stepwise::monte_carlo::rna::AddMover::presample_by_swa_

private

Referenced by apply(), and set_presample_by_swa().

Size protocols::stepwise::monte_carlo::rna::AddMover::res_to_add_in_full_model_numbering_

private

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

Size protocols::stepwise::monte_carlo::rna::AddMover::res_to_build_off_in_full_model_numbering_

private

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

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

private

Referenced by sample_by_monte_carlo_internal(), and setup_initial_torsions().

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

private

core::Real protocols::stepwise::monte_carlo::rna::AddMover::sample_range_large_

private

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

core::Real protocols::stepwise::monte_carlo::rna::AddMover::sample_range_small_

private

Referenced by sample_by_monte_carlo_internal(), and set_sample_range_small().

core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::rna::AddMover::scorefxn_

private

Referenced by sample_by_monte_carlo_internal().

bool protocols::stepwise::monte_carlo::rna::AddMover::start_added_residue_in_aform_

private

Referenced by set_start_added_residue_in_aform(), and setup_initial_torsions().

protocols::stepwise::sampling::StepWiseModelerOP protocols::stepwise::monte_carlo::rna::AddMover::stepwise_modeler_

private

Referenced by sample_by_swa(), and set_stepwise_modeler().

Size protocols::stepwise::monte_carlo::rna::AddMover::suite_num_

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 protocols::stepwise::monte_carlo::rna::AddMover::swa_move_

private

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

---

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

• symlinks/rosetta/src/protocols/stepwise/monte_carlo/mover/AddMover.hh
• symlinks/rosetta/src/protocols/stepwise/monte_carlo/mover/AddMover.cc