protocols::fldsgn::CircularPermutation Class Reference

#include <CircularPermutation.hh>

Inheritance diagram for protocols::fldsgn::CircularPermutation:

Public Types
typedef core::Size	Size
typedef core::pose::Pose	Pose
typedef core::kinematics::MoveMap	MoveMap
typedef core::kinematics::MoveMapOP	MoveMapOP
typedef protocols::moves::MoverOP	MoverOP
typedef utility::tag::TagCOP	TagCOP
typedef protocols::filters::Filters_map	Filters_map
typedef basic::datacache::DataMap	DataMap
typedef protocols::moves::Movers_map	Movers_map
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

Public Member Functions
	CircularPermutation ()
	default constructor More...
	CircularPermutation (CircularPermutation const &rval)
	copy constructor More...
virtual	~CircularPermutation ()
	default destructor More...
virtual MoverOP	clone () const
	clone this object More...
virtual MoverOP	fresh_instance () const
	create this type of object More...
Size	new_terminal_pos () const
	total number of cycles More...
void	new_terminal_pos (Size const s)
	new N- & C- terminal position More...
Size	which_chain (Size const s, Pose const pose) const
	total number of cycles More...
void	split_chains (Pose &pose, utility::vector1< Size > const &pos)
virtual void	apply (Pose &pose)
	apply defined moves to given Pose More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &)
	parse xml file More...
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~Mover ()
virtual MoverSP	create ()
MoverCOP	get_self_ptr () const
MoverOP	get_self_ptr ()
MoverCAP	get_self_weak_ptr () const
MoverAP	get_self_weak_ptr ()
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
void	set_type (std::string const &setting)
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	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)
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...
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 Types
typedef protocols::moves::Mover	Super

Private Member Functions
CircularPermutation &	operator= (CircularPermutation const &rval)
	copy assignment More...

Private Attributes
Size	new_terminal_pos_
	new N- & C- terminal position More...
bool	ignore_chain_
Size	split_

Additional Inherited Members
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...

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::fldsgn::CircularPermutation::DataMap

typedef protocols::filters::Filters_map protocols::fldsgn::CircularPermutation::Filters_map

typedef core::kinematics::MoveMap protocols::fldsgn::CircularPermutation::MoveMap

typedef core::kinematics::MoveMapOP protocols::fldsgn::CircularPermutation::MoveMapOP

typedef protocols::moves::MoverOP protocols::fldsgn::CircularPermutation::MoverOP

typedef protocols::moves::Movers_map protocols::fldsgn::CircularPermutation::Movers_map

typedef core::pose::Pose protocols::fldsgn::CircularPermutation::Pose

typedef core::Size protocols::fldsgn::CircularPermutation::Size

typedef protocols::moves::Mover protocols::fldsgn::CircularPermutation::Super

private

typedef utility::tag::TagCOP protocols::fldsgn::CircularPermutation::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::CircularPermutation::CircularPermutation

(

)

default constructor

Referenced by clone(), and fresh_instance().

protocols::fldsgn::CircularPermutation::CircularPermutation

(

CircularPermutation const &

rval

)

copy constructor

copy constructor

protocols::fldsgn::CircularPermutation::~CircularPermutation ( )

virtual

default destructor

Member Function Documentation

void protocols::fldsgn::CircularPermutation::apply ( Pose &  pose )

virtual

apply defined moves to given Pose

main apply

Implements protocols::moves::Mover.

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::Pose::chain(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), core::pose::Pose::fold_tree(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), ignore_chain_, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::pose::symmetry::make_asymmetric_pose(), new_terminal_pos_, core::conformation::Conformation::reset_chain_endings(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), split_, split_chains(), core::pose::Pose::total_residue(), protocols::fldsgn::TR(), and which_chain().

CircularPermutation::MoverOP protocols::fldsgn::CircularPermutation::clone ( ) const

virtual

clone this object

Reimplemented from protocols::moves::Mover.

References CircularPermutation().

CircularPermutation::MoverOP protocols::fldsgn::CircularPermutation::fresh_instance ( ) const

virtual

create this type of object

Reimplemented from protocols::moves::Mover.

References CircularPermutation().

std::string protocols::fldsgn::CircularPermutation::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::fldsgn::CircularPermutationCreator::mover_name().

CircularPermutation::Size protocols::fldsgn::CircularPermutation::new_terminal_pos

(

)

const

total number of cycles

References new_terminal_pos_.

void protocols::fldsgn::CircularPermutation::new_terminal_pos

(

Size const

s

)

new N- & C- terminal position

References new_terminal_pos_.

CircularPermutation& protocols::fldsgn::CircularPermutation::operator= ( CircularPermutation const &  rval )

private

copy assignment

Remarks

Mover base class prevents this from working properly...

void protocols::fldsgn::CircularPermutation::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  , Filters_map const &  , Movers_map const &  , Pose const &    )

virtual

parse xml file

parse xml

Reimplemented from protocols::moves::Mover.

References ignore_chain_, new_terminal_pos_, and split_.

void protocols::fldsgn::CircularPermutation::split_chains	(	Pose &	pose,
		utility::vector1< Size > const &	pos
	)

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::Conformation::insert_chain_ending(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().

Referenced by apply().

CircularPermutation::Size protocols::fldsgn::CircularPermutation::which_chain	(	Size const	s,
		Pose const	pose
	)		const

total number of cycles

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), and core::conformation::Conformation::num_chains().

Referenced by apply().

Member Data Documentation

bool protocols::fldsgn::CircularPermutation::ignore_chain_

private

Referenced by apply(), and parse_my_tag().

Size protocols::fldsgn::CircularPermutation::new_terminal_pos_

private

new N- & C- terminal position

Referenced by apply(), new_terminal_pos(), and parse_my_tag().

Size protocols::fldsgn::CircularPermutation::split_

private

Referenced by apply(), and parse_my_tag().

---

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

• src/protocols/fldsgn/CircularPermutation.hh
• src/protocols/fldsgn/CircularPermutation.cc