protocols::stepwise::monte_carlo::mover Namespace Reference

Namespaces
	options

Classes
class	AddMover
class	AddMoverCreator
class	AddOrDeleteMover
class	Attachment
class	DeleteMover
class	DeleteMoverCreator
class	FromScratchMover
class	FromScratchMoverCreator
class	ResampleMover
class	ResampleMoverCreator
class	StepWiseMasterMover
	Central mover of stepwise Monte Carlo protocols, handing work off to special move types. More...
class	StepWiseMove
class	StepWiseMoveSelector
class	TransientCutpointHandler
class	VaryLoopLengthMover
	In stepwise design, vary desired loop lengths by updating FullModelParameters. More...

Typedefs
typedef utility::pointer::shared_ptr < AddMover >	AddMoverOP
typedef utility::pointer::shared_ptr < AddMoverCreator >	AddMoverCreatorOP
typedef utility::pointer::shared_ptr < AddMoverCreator const >	AddMoverCreatorCOP
typedef utility::pointer::shared_ptr < AddOrDeleteMover >	AddOrDeleteMoverOP
typedef utility::pointer::shared_ptr < DeleteMover >	DeleteMoverOP
typedef utility::pointer::shared_ptr < DeleteMoverCreator >	DeleteMoverCreatorOP
typedef utility::pointer::shared_ptr < DeleteMoverCreator const >	DeleteMoverCreatorCOP
typedef utility::pointer::shared_ptr < FromScratchMover >	FromScratchMoverOP
typedef utility::pointer::shared_ptr < FromScratchMover const >	FromScratchMoverCOP
typedef utility::pointer::shared_ptr < FromScratchMoverCreator >	FromScratchMoverCreatorOP
typedef utility::pointer::shared_ptr < FromScratchMoverCreator const >	FromScratchMoverCreatorCOP
typedef utility::pointer::shared_ptr < ResampleMover >	ResampleMoverOP
typedef utility::pointer::shared_ptr < ResampleMover const >	ResampleMoverCOP
typedef utility::pointer::shared_ptr < ResampleMoverCreator >	ResampleMoverCreatorOP
typedef utility::pointer::shared_ptr < ResampleMoverCreator const >	ResampleMoverCreatorCOP
typedef utility::pointer::shared_ptr < StepWiseMasterMover >	StepWiseMasterMoverOP
typedef utility::pointer::shared_ptr < StepWiseMasterMover const >	StepWiseMasterMoverCOP
typedef utility::pointer::shared_ptr < StepWiseMove >	StepWiseMoveOP
typedef utility::pointer::shared_ptr < StepWiseMove const >	StepWiseMoveCOP
typedef utility::pointer::shared_ptr < Attachment >	AttachmentOP
typedef utility::pointer::shared_ptr < Attachment const >	AttachmentCOP
typedef utility::vector1 < core::Size >	MoveElement
typedef utility::vector1 < Attachment >	Attachments
typedef utility::pointer::shared_ptr < StepWiseMoveSelector >	StepWiseMoveSelectorOP
typedef utility::pointer::shared_ptr < StepWiseMoveSelector const >	StepWiseMoveSelectorCOP
typedef utility::pointer::shared_ptr < TransientCutpointHandler >	TransientCutpointHandlerOP
typedef utility::pointer::shared_ptr < TransientCutpointHandler const >	TransientCutpointHandlerCOP
typedef utility::pointer::shared_ptr < VaryLoopLengthMover >	VaryLoopLengthMoverOP
typedef utility::pointer::shared_ptr < VaryLoopLengthMover const >	VaryLoopLengthMoverCOP

Enumerations
enum	AttachmentType {   NO_ATTACHMENT = 0, BOND_TO_PREVIOUS, BOND_TO_NEXT, JUMP_TO_PREV_IN_CHAIN,   JUMP_TO_NEXT_IN_CHAIN, JUMP_DOCK, SUBMOTIF, LAST_ATTACHMENT_TYPE }
enum	MoveType {   NO_MOVE = 0, ADD, DELETE, FROM_SCRATCH,   RESAMPLE, RESAMPLE_INTERNAL_LOCAL, ADD_SUBMOTIF, ADD_LOOP_RES,   DELETE_LOOP_RES, LAST_ADD_OR_DELETE_CHOICE }

Functions
void	filter_for_proximity (pose::Pose const &pose, utility::vector1< core::Size > &partition_res, core::Size const center_res)
std::string	name_from_move (StepWiseMove const &stepwise_move, Pose const &start_pose)
std::string	residue_rebuild_log_namer (core::Size const resample_round, core::Size const nstruct)
std::string	residue_rebuild_checkpoint_namer (core::Size const resample_round, core::Size const nstruct)
void	read_checkpoint_log (utility::vector1< StepWiseMove > &stepwise_moves, core::Size &start_idx, core::Size const resample_round, core::Size const nstruct, Pose const &start_pose)
void	write_checkpoint (utility::vector1< StepWiseMove > const &stepwise_moves, core::Size const start_idx, core::Size const resample_round, core::Size const nstruct, Pose const &output_pose)
void	ensure_appropriate_foldtree_for_move (StepWiseMove const &stepwise_move, Pose &output_pose, core::kinematics::FoldTree &ft_to_restore)
void	set_up_params_for_move (pose::Pose &output_pose, StepWiseMove const &stepwise_move)
modeler::StepWiseModelerOP	setup_unified_stepwise_modeler (protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP mc_options, core::scoring::ScoreFunctionCOP scorefxn)
void	initialize_move_type_name ()
std::string	to_string (MoveType const &move_type)
MoveType	move_type_from_string (std::string const &name)
void	initialize_attachment_type_name ()
std::string	to_string (AttachmentType const &attachment_type)
AttachmentType	attachment_type_from_string (std::string const &name)
std::ostream &	operator<< (std::ostream &os, StepWiseMove const &swa_move)
std::ostream &	operator<< (std::ostream &os, Attachment const &attachment)
bool	operator== (Attachment const &a, Attachment const &b)
bool	operator== (StepWiseMove const &a, StepWiseMove const &b)
bool	check_for_connections_for_all_submotif_residues (MoveElement const &move_element, utility::vector1< StepWiseMove > const &add_moves)
utility::vector1< std::pair < core::Size, core::Size > >	get_design_loops (FullModelParametersCOP parent_full_model_parameters)

Variables
std::map< MoveType, std::string >	move_type_name
std::map< AttachmentType, std::string >	attachment_type_name

Typedef Documentation

typedef utility::pointer::shared_ptr< AddMoverCreator const > protocols::stepwise::monte_carlo::mover::AddMoverCreatorCOP

typedef utility::pointer::shared_ptr< AddMoverCreator > protocols::stepwise::monte_carlo::mover::AddMoverCreatorOP

typedef utility::pointer::shared_ptr< AddMover > protocols::stepwise::monte_carlo::mover::AddMoverOP

typedef utility::pointer::shared_ptr< AddOrDeleteMover > protocols::stepwise::monte_carlo::mover::AddOrDeleteMoverOP

typedef utility::pointer::shared_ptr< Attachment const > protocols::stepwise::monte_carlo::mover::AttachmentCOP

typedef utility::pointer::shared_ptr< Attachment > protocols::stepwise::monte_carlo::mover::AttachmentOP

typedef utility::vector1< Attachment> protocols::stepwise::monte_carlo::mover::Attachments

typedef utility::pointer::shared_ptr< DeleteMoverCreator const > protocols::stepwise::monte_carlo::mover::DeleteMoverCreatorCOP

typedef utility::pointer::shared_ptr< DeleteMoverCreator > protocols::stepwise::monte_carlo::mover::DeleteMoverCreatorOP

typedef utility::pointer::shared_ptr< DeleteMover > protocols::stepwise::monte_carlo::mover::DeleteMoverOP

typedef utility::pointer::shared_ptr< FromScratchMover const > protocols::stepwise::monte_carlo::mover::FromScratchMoverCOP

typedef utility::pointer::shared_ptr< FromScratchMoverCreator const > protocols::stepwise::monte_carlo::mover::FromScratchMoverCreatorCOP

typedef utility::pointer::shared_ptr< FromScratchMoverCreator > protocols::stepwise::monte_carlo::mover::FromScratchMoverCreatorOP

typedef utility::pointer::shared_ptr< FromScratchMover > protocols::stepwise::monte_carlo::mover::FromScratchMoverOP

typedef utility::vector1< core::Size > protocols::stepwise::monte_carlo::mover::MoveElement

typedef utility::pointer::shared_ptr< ResampleMover const > protocols::stepwise::monte_carlo::mover::ResampleMoverCOP

typedef utility::pointer::shared_ptr< ResampleMoverCreator const > protocols::stepwise::monte_carlo::mover::ResampleMoverCreatorCOP

typedef utility::pointer::shared_ptr< ResampleMoverCreator > protocols::stepwise::monte_carlo::mover::ResampleMoverCreatorOP

typedef utility::pointer::shared_ptr< ResampleMover > protocols::stepwise::monte_carlo::mover::ResampleMoverOP

typedef utility::pointer::shared_ptr< StepWiseMasterMover const > protocols::stepwise::monte_carlo::mover::StepWiseMasterMoverCOP

typedef utility::pointer::shared_ptr< StepWiseMasterMover > protocols::stepwise::monte_carlo::mover::StepWiseMasterMoverOP

typedef utility::pointer::shared_ptr< StepWiseMove const > protocols::stepwise::monte_carlo::mover::StepWiseMoveCOP

typedef utility::pointer::shared_ptr< StepWiseMove > protocols::stepwise::monte_carlo::mover::StepWiseMoveOP

typedef utility::pointer::shared_ptr< StepWiseMoveSelector const > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelectorCOP

typedef utility::pointer::shared_ptr< StepWiseMoveSelector > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelectorOP

typedef utility::pointer::shared_ptr< TransientCutpointHandler const > protocols::stepwise::monte_carlo::mover::TransientCutpointHandlerCOP

typedef utility::pointer::shared_ptr< TransientCutpointHandler > protocols::stepwise::monte_carlo::mover::TransientCutpointHandlerOP

typedef utility::pointer::shared_ptr< VaryLoopLengthMover const > protocols::stepwise::monte_carlo::mover::VaryLoopLengthMoverCOP

typedef utility::pointer::shared_ptr< VaryLoopLengthMover > protocols::stepwise::monte_carlo::mover::VaryLoopLengthMoverOP

Enumeration Type Documentation

enum protocols::stepwise::monte_carlo::mover::AttachmentType

Enumerator
NO_ATTACHMENT
BOND_TO_PREVIOUS
BOND_TO_NEXT
JUMP_TO_PREV_IN_CHAIN
JUMP_TO_NEXT_IN_CHAIN
JUMP_DOCK
SUBMOTIF
LAST_ATTACHMENT_TYPE

enum protocols::stepwise::monte_carlo::mover::MoveType

Enumerator
NO_MOVE
ADD
DELETE
FROM_SCRATCH
RESAMPLE
RESAMPLE_INTERNAL_LOCAL
ADD_SUBMOTIF
ADD_LOOP_RES
DELETE_LOOP_RES
LAST_ADD_OR_DELETE_CHOICE

Function Documentation

AttachmentType protocols::stepwise::monte_carlo::mover::attachment_type_from_string

(

std::string const &

name

)

References attachment_type_name, core::sequence::end, initialize_attachment_type_name(), and NO_ATTACHMENT.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMove::StepWiseMove().

bool protocols::stepwise::monte_carlo::mover::check_for_connections_for_all_submotif_residues	(	MoveElement const &	move_element,
		utility::vector1< StepWiseMove > const &	add_moves
	)

References protocols::stepwise::monte_carlo::mover::StepWiseMove::moving_res().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_submotif_add_moves().

void protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move	(	StepWiseMove const &	stepwise_move,
		Pose &	output_pose,
		core::kinematics::FoldTree &	ft_to_restore
	)

References core::kinematics::FoldTree::add_edge(), protocols::stepwise::monte_carlo::mover::StepWiseMove::attachments(), core::pose::Pose::chain_begin(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::Edge::label(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element(), core::scoring::ref, core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::kinematics::FoldTree::slide_jump(), protocols::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model().

void protocols::stepwise::monte_carlo::mover::filter_for_proximity	(	pose::Pose const &	pose,
		utility::vector1< core::Size > &	partition_res,
		core::Size const	center_res
	)

References core::chemical::rna::default_jump_atom(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly().

utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::monte_carlo::mover::get_design_loops

(

FullModelParametersCOP

parent_full_model_parameters

)

References core::pose::full_model_info::CUTPOINT_OPEN.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_vary_loop_length_moves().

void protocols::stepwise::monte_carlo::mover::initialize_attachment_type_name

(

)

References attachment_type_name, BOND_TO_NEXT, BOND_TO_PREVIOUS, core::init::init(), JUMP_DOCK, JUMP_TO_NEXT_IN_CHAIN, JUMP_TO_PREV_IN_CHAIN, NO_ATTACHMENT, and SUBMOTIF.

Referenced by attachment_type_from_string(), and to_string().

void protocols::stepwise::monte_carlo::mover::initialize_move_type_name

(

)

References ADD, ADD_LOOP_RES, ADD_SUBMOTIF, DELETE, DELETE_LOOP_RES, FROM_SCRATCH, core::init::init(), move_type_name, NO_MOVE, RESAMPLE, and RESAMPLE_INTERNAL_LOCAL.

Referenced by move_type_from_string(), and to_string().

MoveType protocols::stepwise::monte_carlo::mover::move_type_from_string

(

std::string const &

name

)

References core::sequence::end, initialize_move_type_name(), move_type_name, and NO_MOVE.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMove::StepWiseMove().

std::string protocols::stepwise::monte_carlo::mover::name_from_move ( StepWiseMove const &  stepwise_move, Pose const &  start_pose  )

inline

References protocols::stepwise::monte_carlo::mover::StepWiseMove::moving_res(), and core::pose::Pose::pdb_info().

std::ostream & protocols::stepwise::monte_carlo::mover::operator<<	(	std::ostream &	os,
		StepWiseMove const &	swa_move
	)

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attachments(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), protocols::stepwise::monte_carlo::mover::StepWiseMove::submotif_tag(), and to_string().

std::ostream & protocols::stepwise::monte_carlo::mover::operator<<	(	std::ostream &	os,
		Attachment const &	attachment
	)

References protocols::stepwise::monte_carlo::mover::Attachment::attached_res(), protocols::stepwise::monte_carlo::mover::Attachment::attachment_type(), and to_string().

bool protocols::stepwise::monte_carlo::mover::operator==	(	Attachment const &	a,
		Attachment const &	b
	)

References protocols::stepwise::monte_carlo::mover::Attachment::attached_res_, and protocols::stepwise::monte_carlo::mover::Attachment::attachment_type_.

bool protocols::stepwise::monte_carlo::mover::operator==	(	StepWiseMove const &	a,
		StepWiseMove const &	b
	)

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attachments_, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element_, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type_, and protocols::stepwise::monte_carlo::mover::StepWiseMove::submotif_tag_.

void protocols::stepwise::monte_carlo::mover::read_checkpoint_log	(	utility::vector1< StepWiseMove > &	stepwise_moves,
		core::Size &	start_idx,
		core::Size const	resample_round,
		core::Size const	nstruct,
		Pose const &	start_pose
	)

References core::pose::full_model_info::const_full_model_info(), and residue_rebuild_log_namer().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model().

std::string protocols::stepwise::monte_carlo::mover::residue_rebuild_checkpoint_namer	(	core::Size const	resample_round,
		core::Size const	nstruct
	)

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), and write_checkpoint().

std::string protocols::stepwise::monte_carlo::mover::residue_rebuild_log_namer	(	core::Size const	resample_round,
		core::Size const	nstruct
	)

Referenced by read_checkpoint_log(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), and write_checkpoint().

void protocols::stepwise::monte_carlo::mover::set_up_params_for_move	(	pose::Pose &	output_pose,
		StepWiseMove const &	stepwise_move
	)

References core::pose::full_model_info::CALC_RMS, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), core::pose::full_model_info::nonconst_full_model_info(), RESAMPLE_INTERNAL_LOCAL, and core::pose::full_model_info::SAMPLE.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model().

modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::setup_unified_stepwise_modeler	(	protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP	mc_options,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize(), protocols::stepwise::monte_carlo::mover::FromScratchMover::parse_my_tag(), and protocols::stepwise::monte_carlo::mover::ResampleMover::parse_my_tag().

std::string protocols::stepwise::monte_carlo::mover::to_string

(

MoveType const &

move_type

)

References initialize_move_type_name(), and move_type_name.

Referenced by protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), and operator<<().

std::string protocols::stepwise::monte_carlo::mover::to_string

(

AttachmentType const &

attachment_type

)

References attachment_type_name, and initialize_attachment_type_name().

void protocols::stepwise::monte_carlo::mover::write_checkpoint	(	utility::vector1< StepWiseMove > const &	stepwise_moves,
		core::Size const	start_idx,
		core::Size const	resample_round,
		core::Size const	nstruct,
		Pose const &	output_pose
	)

References core::pose::Pose::dump_pdb(), residue_rebuild_checkpoint_namer(), and residue_rebuild_log_namer().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model().

Variable Documentation

std::map< AttachmentType, std::string> protocols::stepwise::monte_carlo::mover::attachment_type_name

Referenced by attachment_type_from_string(), initialize_attachment_type_name(), and to_string().

std::map< MoveType, std::string> protocols::stepwise::monte_carlo::mover::move_type_name

Referenced by initialize_move_type_name(), move_type_from_string(), and to_string().