protocols::stepwise::monte_carlo Namespace Reference

Namespaces
	rna

Classes
class	Attachment
class	SWA_Move
class	SWA_MoveSelector

Typedefs
typedef utility::pointer::owning_ptr < SWA_Move >	SWA_MoveOP
typedef utility::pointer::owning_ptr < SWA_Move const >	SWA_MoveCOP
typedef utility::pointer::owning_ptr < Attachment >	AttachmentOP
typedef utility::pointer::owning_ptr < Attachment const >	AttachmentCOP
typedef utility::vector1 < core::Size >	MoveElement
typedef utility::vector1 < Attachment >	Attachments
typedef utility::pointer::owning_ptr < SWA_MoveSelector >	SWA_MoveSelectorOP
typedef utility::pointer::owning_ptr < SWA_MoveSelector const >	SWA_MoveSelectorCOP

Enumerations
enum	AttachmentType {   NO_ATTACHMENT = 0, BOND_TO_PREVIOUS, BOND_TO_NEXT, JUMP_TO_PREV_IN_CHAIN,   JUMP_TO_NEXT_IN_CHAIN, JUMP_INTERCHAIN, LAST_ATTACHMENT_TYPE }
enum	MoveType {   NO_MOVE = 0, ADD, DELETE, FROM_SCRATCH,   RESAMPLE, RESAMPLE_INTERNAL_LOCAL, LAST_ADD_OR_DELETE_CHOICE }

Functions
bool	get_out_tag (std::string &out_tag, Size const &n, std::string const &silent_file)
void	output_to_silent_file (std::string const &out_tag, std::string const &silent_file, pose::Pose &pose, pose::PoseCOP native_pose)
void	output_to_silent_file (std::string const &silent_file, utility::vector1< pose::PoseOP > &pose_list, pose::PoseCOP native_pose)
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, SWA_Move const &swa_move)
std::ostream &	operator<< (std::ostream &os, Attachment const &attachment)

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

Typedef Documentation

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

typedef utility::pointer::owning_ptr< Attachment > protocols::stepwise::monte_carlo::AttachmentOP

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

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

typedef utility::pointer::owning_ptr< SWA_Move const > protocols::stepwise::monte_carlo::SWA_MoveCOP

typedef utility::pointer::owning_ptr< SWA_Move > protocols::stepwise::monte_carlo::SWA_MoveOP

typedef utility::pointer::owning_ptr< SWA_MoveSelector const > protocols::stepwise::monte_carlo::SWA_MoveSelectorCOP

typedef utility::pointer::owning_ptr< SWA_MoveSelector > protocols::stepwise::monte_carlo::SWA_MoveSelectorOP

Enumeration Type Documentation

enum protocols::stepwise::monte_carlo::AttachmentType

Enumerator
NO_ATTACHMENT
BOND_TO_PREVIOUS
BOND_TO_NEXT
JUMP_TO_PREV_IN_CHAIN
JUMP_TO_NEXT_IN_CHAIN
JUMP_INTERCHAIN
LAST_ATTACHMENT_TYPE

enum protocols::stepwise::monte_carlo::MoveType

Enumerator
NO_MOVE
ADD
DELETE
FROM_SCRATCH
RESAMPLE
RESAMPLE_INTERNAL_LOCAL
LAST_ADD_OR_DELETE_CHOICE

Function Documentation

AttachmentType protocols::stepwise::monte_carlo::attachment_type_from_string

(

std::string const

name

)

References attachment_type_name, initialize_attachment_type_name(), NO_ATTACHMENT, and runtime_assert.

Referenced by protocols::stepwise::monte_carlo::SWA_Move::SWA_Move().

bool protocols::stepwise::monte_carlo::get_out_tag	(	std::string &	out_tag,
		Size const &	n,
		std::string const &	silent_file
	)

References protocols::init::init(), initialize_tag_is_done(), and TR.

void protocols::stepwise::monte_carlo::initialize_attachment_type_name

(

)

References attachment_type_name, BOND_TO_NEXT, BOND_TO_PREVIOUS, protocols::init::init(), JUMP_INTERCHAIN, JUMP_TO_NEXT_IN_CHAIN, JUMP_TO_PREV_IN_CHAIN, and NO_ATTACHMENT.

Referenced by attachment_type_from_string(), and to_string().

void protocols::stepwise::monte_carlo::initialize_move_type_name

(

)

References ADD, DELETE, FROM_SCRATCH, protocols::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::move_type_from_string

(

std::string const

name

)

References initialize_move_type_name(), move_type_name, NO_MOVE, and runtime_assert.

Referenced by protocols::stepwise::monte_carlo::SWA_Move::SWA_Move().

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

References protocols::stepwise::monte_carlo::SWA_Move::attachments(), make_tag_with_dashes(), protocols::stepwise::monte_carlo::SWA_Move::move_element(), protocols::stepwise::monte_carlo::SWA_Move::move_type(), and to_string().

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

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

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	out_tag,
		std::string const &	silent_file,
		pose::Pose &	pose,
		pose::PoseCOP	native_pose
	)

References clearPoseExtraScores(), protocols::stepwise::get_number_missing_residue_connections(), rms, s, and protocols::stepwise::superimpose_recursively().

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo::output_movie().

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	silent_file,
		utility::vector1< pose::PoseOP > &	pose_list,
		pose::PoseCOP	native_pose
	)

References tag_from_pose().

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

(

MoveType const &

move_type

)

References initialize_move_type_name(), and move_type_name.

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

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

(

AttachmentType const &

attachment_type

)

References attachment_type_name, and initialize_attachment_type_name().

Variable Documentation

std::map< AttachmentType, std::string> protocols::stepwise::monte_carlo::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::move_type_name

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