protocols::swa::monte_carlo Namespace Reference

Classes
class	RNA_AddMover
class	RNA_AddOrDeleteMover
class	RNA_DeleteMover
class	RNA_O2StarMover
class	RNA_SWA_MonteCarloMover
class	RNA_TorsionMover
class	SubToFullInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...

Typedefs
typedef utility::pointer::owning_ptr < RNA_AddMover >	RNA_AddMoverOP
typedef utility::pointer::owning_ptr < RNA_AddOrDeleteMover >	RNA_AddOrDeleteMoverOP
typedef utility::pointer::owning_ptr < RNA_DeleteMover >	RNA_DeleteMoverOP
typedef utility::pointer::owning_ptr < RNA_O2StarMover >	RNA_O2StarMoverOP
typedef utility::pointer::owning_ptr < RNA_SWA_MonteCarloMover >	RNA_SWA_MonteCarloMoverOP
typedef utility::pointer::owning_ptr < RNA_TorsionMover >	RNA_TorsionMoverOP
typedef utility::pointer::owning_ptr < SubToFullInfo >	SubToFullInfoOP

Enumerations
enum	MovingResidueCase {   NO_CASE =0, CHAIN_TERMINUS_5PRIME, CHAIN_TERMINUS_3PRIME, INTERNAL,   FLOATING_BASE }
enum	AddOrDeleteChoice { NO_ADD_OR_DELETE =0, ADD, DELETE }

Functions
MovingResidueCase	get_moving_residue_case (pose::Pose const &pose, Size const i)
void	get_potential_delete_residues (pose::Pose &pose, utility::vector1< Size > &possible_res, utility::vector1< MovingResidueCase > &moving_residue_cases, utility::vector1< AddOrDeleteChoice > &add_or_delete_choices)
void	get_potential_add_residues (pose::Pose &pose, utility::vector1< Size > &possible_res, utility::vector1< MovingResidueCase > &moving_residue_cases, utility::vector1< AddOrDeleteChoice > &add_or_delete_choices)
void	get_random_residue_at_chain_terminus (pose::Pose &pose, Size &residue_at_chain_terminus, MovingResidueCase &moving_residue_case, AddOrDeleteChoice &add_or_delete_choice, bool const disallow_delete)
SubToFullInfo const &	const_sub_to_full_info_from_pose (pose::Pose &pose)
SubToFullInfo &	nonconst_sub_to_full_info_from_pose (pose::Pose &pose)
utility::vector1< Size >	reorder_after_delete (utility::vector1< Size > moving_res_list, Size const &res_to_delete)
std::map< Size, Size >	reorder_after_delete (std::map< Size, Size > sub_to_full, Size const &res_to_delete)
utility::vector1< Size >	reorder_after_insert (utility::vector1< Size > moving_res_list, Size const &res_to_add)
std::map< Size, Size >	reorder_after_prepend (std::map< Size, Size > sub_to_full, Size const &res_to_add)
std::map< Size, Size >	reorder_after_append (std::map< Size, Size > sub_to_full, Size const &res_to_add)
void	reorder_sub_to_full_info_after_delete (pose::Pose &pose, Size const res_to_delete)
void	reorder_sub_to_full_info_after_append (pose::Pose &pose, Size const res_to_add)
void	reorder_sub_to_full_info_after_prepend (pose::Pose &pose, Size const res_to_add)

Typedef Documentation

typedef utility::pointer::owning_ptr< RNA_AddMover > protocols::swa::monte_carlo::RNA_AddMoverOP

Definition at line 28 of file RNA_AddMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_AddOrDeleteMover > protocols::swa::monte_carlo::RNA_AddOrDeleteMoverOP

Definition at line 28 of file RNA_AddOrDeleteMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_DeleteMover > protocols::swa::monte_carlo::RNA_DeleteMoverOP

Definition at line 28 of file RNA_DeleteMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_O2StarMover > protocols::swa::monte_carlo::RNA_O2StarMoverOP

Definition at line 28 of file RNA_O2StarMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_SWA_MonteCarloMover > protocols::swa::monte_carlo::RNA_SWA_MonteCarloMoverOP

Definition at line 28 of file RNA_SWA_MonteCarloMover.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_TorsionMover > protocols::swa::monte_carlo::RNA_TorsionMoverOP

Definition at line 28 of file RNA_TorsionMover.fwd.hh.

typedef utility::pointer::owning_ptr< SubToFullInfo > protocols::swa::monte_carlo::SubToFullInfoOP

Definition at line 28 of file SubToFullInfo.fwd.hh.

Enumeration Type Documentation

enum protocols::swa::monte_carlo::AddOrDeleteChoice

Enumerator
NO_ADD_OR_DELETE
ADD
DELETE

Definition at line 26 of file types.hh.

enum protocols::swa::monte_carlo::MovingResidueCase

Enumerator
NO_CASE
CHAIN_TERMINUS_5PRIME
CHAIN_TERMINUS_3PRIME
INTERNAL
FLOATING_BASE

Definition at line 24 of file types.hh.

Function Documentation

SubToFullInfo const& protocols::swa::monte_carlo::const_sub_to_full_info_from_pose

(

pose::Pose &

pose)

Pose must already contain a sub_to_full_info object or this method will fail.

Definition at line 81 of file SubToFullInfo.cc.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SUB_TO_FULL_INFO.

MovingResidueCase protocols::swa::monte_carlo::get_moving_residue_case	(	pose::Pose const &	pose,
		Size const	i
	)

Definition at line 44 of file RNA_SWA_MonteCarloUtil.cc.

References CHAIN_TERMINUS_3PRIME, CHAIN_TERMINUS_5PRIME, FLOATING_BASE, core::pose::Pose::fold_tree(), INTERNAL, NO_CASE, and core::pose::Pose::total_residue().

Referenced by protocols::swa::monte_carlo::RNA_TorsionMover::random_torsion_move().

void protocols::swa::monte_carlo::get_potential_add_residues	(	pose::Pose &	pose,
		utility::vector1< Size > &	possible_res,
		utility::vector1< MovingResidueCase > &	moving_residue_cases,
		utility::vector1< AddOrDeleteChoice > &	add_or_delete_choices
	)

Definition at line 106 of file RNA_SWA_MonteCarloUtil.cc.

References ADD, CHAIN_TERMINUS_3PRIME, CHAIN_TERMINUS_5PRIME, core::pose::Pose::fold_tree(), nonconst_sub_to_full_info_from_pose(), and core::pose::Pose::total_residue().

Referenced by get_random_residue_at_chain_terminus().

void protocols::swa::monte_carlo::get_potential_delete_residues	(	pose::Pose &	pose,
		utility::vector1< Size > &	possible_res,
		utility::vector1< MovingResidueCase > &	moving_residue_cases,
		utility::vector1< AddOrDeleteChoice > &	add_or_delete_choices
	)

Definition at line 69 of file RNA_SWA_MonteCarloUtil.cc.

References CHAIN_TERMINUS_3PRIME, CHAIN_TERMINUS_5PRIME, DELETE, core::pose::Pose::fold_tree(), nonconst_sub_to_full_info_from_pose(), and core::pose::Pose::total_residue().

Referenced by get_random_residue_at_chain_terminus(), and protocols::swa::monte_carlo::RNA_DeleteMover::wipe_out_moving_residues().

void protocols::swa::monte_carlo::get_random_residue_at_chain_terminus	(	pose::Pose &	pose,
		Size &	residue_at_chain_terminus,
		MovingResidueCase &	moving_residue_case,
		AddOrDeleteChoice &	add_or_delete_choice,
		bool const	disallow_delete
	)

Definition at line 158 of file RNA_SWA_MonteCarloUtil.cc.

References get_potential_add_residues(), get_potential_delete_residues(), and core::conformation::symmetry::RG().

Referenced by protocols::swa::monte_carlo::RNA_AddOrDeleteMover::apply().

SubToFullInfo & protocols::swa::monte_carlo::nonconst_sub_to_full_info_from_pose

(

pose::Pose &

pose)

Either returns a non-const reference to the rna_scoring object already stored in the pose, or creates a new rna scoring info object, places it in the pose, and returns a non-const reference to it.

Definition at line 92 of file SubToFullInfo.cc.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SUB_TO_FULL_INFO.

Referenced by protocols::swa::monte_carlo::RNA_AddOrDeleteMover::apply(), protocols::swa::monte_carlo::RNA_AddMover::apply(), protocols::swa::monte_carlo::RNA_TorsionMover::apply(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::apply(), protocols::swa::monte_carlo::RNA_O2StarMover::apply(), get_potential_add_residues(), get_potential_delete_residues(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), reorder_sub_to_full_info_after_append(), reorder_sub_to_full_info_after_delete(), and reorder_sub_to_full_info_after_prepend().

std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_append	(	std::map< Size, Size >	sub_to_full,
		Size const &	res_to_add
	)

Definition at line 181 of file SubToFullInfo.cc.

Referenced by reorder_sub_to_full_info_after_append().

utility::vector1<Size> protocols::swa::monte_carlo::reorder_after_delete	(	utility::vector1< Size >	moving_res_list,
		Size const &	res_to_delete
	)

Definition at line 106 of file SubToFullInfo.cc.

Referenced by reorder_sub_to_full_info_after_delete().

std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_delete	(	std::map< Size, Size >	sub_to_full,
		Size const &	res_to_delete
	)

Definition at line 123 of file SubToFullInfo.cc.

utility::vector1<Size> protocols::swa::monte_carlo::reorder_after_insert	(	utility::vector1< Size >	moving_res_list,
		Size const &	res_to_add
	)

Definition at line 141 of file SubToFullInfo.cc.

Referenced by reorder_sub_to_full_info_after_append(), and reorder_sub_to_full_info_after_prepend().

std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_prepend	(	std::map< Size, Size >	sub_to_full,
		Size const &	res_to_add
	)

Definition at line 163 of file SubToFullInfo.cc.

Referenced by reorder_sub_to_full_info_after_prepend().

void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_append	(	pose::Pose &	pose,
		Size const	res_to_add
	)

Definition at line 216 of file SubToFullInfo.cc.

References nonconst_sub_to_full_info_from_pose(), reorder_after_append(), and reorder_after_insert().

Referenced by protocols::swa::monte_carlo::RNA_AddMover::apply().

void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_delete	(	pose::Pose &	pose,
		Size const	res_to_delete
	)

Definition at line 202 of file SubToFullInfo.cc.

References nonconst_sub_to_full_info_from_pose(), and reorder_after_delete().

Referenced by protocols::swa::monte_carlo::RNA_DeleteMover::apply().

void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_prepend	(	pose::Pose &	pose,
		Size const	res_to_add
	)

Definition at line 230 of file SubToFullInfo.cc.

References nonconst_sub_to_full_info_from_pose(), reorder_after_insert(), and reorder_after_prepend().

Referenced by protocols::swa::monte_carlo::RNA_AddMover::apply().