manages information about segments of residues More...

#include <NamedMover.hh>

Inheritance diagram for protocols::denovo_design::components::NamedMover:

Public Member Functions
	NamedMover ()

	NamedMover (std::string const &id, std::string const &parent_id)

virtual	~NamedMover ()

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
	setup the parameters via an xml tag More...

virtual void	apply (core::pose::Pose &pose)
	performs setup and applies loop building More...

virtual void	apply_permutation (StructureData &perm) const =0
	uses the StructureData to set up, builds structure, and updates permutation More...

virtual void	setup_permutation (StructureData &perm) const =0
	Choose and store build options in the StructureData object. More...

virtual core::pose::PoseOP	build_pose (StructureData const &perm) const =0
	Creates a pose based on the information saved to the provided StructureData object. More...

virtual void	process_permutation (StructureData &perm) const =0
	Performs processing of the StructureData object. More...

virtual void	check_permutation (StructureData const &perm) const =0
	checks an unbuilt permutation modified by setup_permutation to see if it is acceptable for building More...

virtual bool	check (StructureData const &perm) const =0
	checks the built StructureData vs. the desired params. More...

std::string const &	id () const
	returns an identifier for this mover More...

std::string const &	parent_id () const
	returns the name of the parent mover More...

virtual void	set_id (std::string const &idval)
	sets an identifier for this mover More...

void	set_parent_id (std::string const &parent)
	sets an identifier for the parent of this mover, for nested moves More...

StringList const &	segment_names () const
	names of segment pieces built by this mover More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	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)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. 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...

Protected Member Functions
std::string	add_parent_prefix (std::string const &s) const
	adds prefix if necessary, returns result More...

void	add_segment_name (std::string const &sname)
	adds a segment name More...

void	set_segment_names (StringList const &snames)
	sets segment names More...

void	clear_segment_names ()
	clears segment names 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...

Private Attributes
std::string	id_

std::string	parent_id_

StringList	segment_names_

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...

Detailed Description

manages information about segments of residues

Constructor & Destructor Documentation

protocols::denovo_design::components::NamedMover::NamedMover ( )

References segment_names_.

protocols::denovo_design::components::NamedMover::NamedMover	(	std::string const &	id,
		std::string const &	parent_id
	)

References segment_names_.

virtual protocols::denovo_design::components::NamedMover::~NamedMover ( )

inlinevirtual

Member Function Documentation

std::string protocols::denovo_design::components::NamedMover::add_parent_prefix ( std::string const & s ) const

protected

adds prefix if necessary, returns result

References protocols::denovo_design::PARENT_DELIMETER, and parent_id().

Referenced by protocols::denovo_design::connection::Connection::disallow_pair(), protocols::denovo_design::connection::Connection::find_available_lower_termini(), protocols::denovo_design::connection::Connection::find_available_upper_termini(), protocols::denovo_design::connection::Connection::pair_allowed(), and set_id().

void protocols::denovo_design::components::NamedMover::add_segment_name ( std::string const & sname )

inlineprotected

adds a segment name

References segment_names_.

Referenced by parse_my_tag().

void protocols::denovo_design::components::NamedMover::apply ( core::pose::Pose & pose )

virtual

performs setup and applies loop building

Default steps to apply():

Pulls StructureData from the pose
setup_permutation() stores data about this connection which is not static for every apply() call
apply_permutation() uses the StructureData object to build the loop
check() checks the built structure

Steps to apply():

Pulls StructureData from the pose
setup_permutation() stores data about this connection which is not static for every apply() call
apply_permutation() uses the StructureData object to build the loop
check() checks the built loop

Implements protocols::moves::Mover.

Reimplemented in protocols::denovo_design::connection::Connection, and protocols::denovo_design::connection::BridgeChains.

References apply_permutation(), check(), check_permutation(), core::pose::Pose::clear(), protocols::moves::FAIL_RETRY, protocols::moves::Mover::get_last_move_status(), protocols::moves::Mover::get_name(), id(), protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), setup_permutation(), protocols::denovo_design::components::EXCN_Setup::show(), and protocols::TR().

virtual void protocols::denovo_design::components::NamedMover::apply_permutation ( StructureData & perm ) const

pure virtual

uses the StructureData to set up, builds structure, and updates permutation

Steps should be:

Use StructureData to collect information about the structure to be built
Build the pose as instructed by the StructureData object
Store the pose in the StructureData object

Implemented in protocols::denovo_design::connection::Connection.

Referenced by apply().

virtual core::pose::PoseOP protocols::denovo_design::components::NamedMover::build_pose ( StructureData const & perm ) const

pure virtual

Creates a pose based on the information saved to the provided StructureData object.

Use setup_permutation to insert information into the StructureData, then build_pose() to create a pose

Implemented in protocols::denovo_design::connection::Connection.

virtual bool protocols::denovo_design::components::NamedMover::check ( StructureData const & perm ) const

pure virtual

checks the built StructureData vs. the desired params.

should return true if it matches, false otherwise

Implemented in protocols::denovo_design::connection::Connection.

Referenced by apply().

virtual void protocols::denovo_design::components::NamedMover::check_permutation ( StructureData const & perm ) const

pure virtual

checks an unbuilt permutation modified by setup_permutation to see if it is acceptable for building

Exceptions

EXCN_PreFilterFailed on failure

Implemented in protocols::denovo_design::connection::Connection.

Referenced by apply().

void protocols::denovo_design::components::NamedMover::clear_segment_names ( )

inlineprotected

clears segment names

References segment_names_.

std::string const & protocols::denovo_design::components::NamedMover::id ( ) const

returns an identifier for this mover

References id_.

std::string const & protocols::denovo_design::components::NamedMover::parent_id ( ) const

returns the name of the parent mover

References parent_id_.

Referenced by add_parent_prefix().

void protocols::denovo_design::components::NamedMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

setup the parameters via an xml tag

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::denovo_design::connection::ConnectTerminiWithDisulfide, protocols::denovo_design::connection::BridgeTomponents, protocols::denovo_design::connection::StapleChains, protocols::denovo_design::connection::Connection, protocols::denovo_design::connection::BridgeChains, protocols::denovo_design::connection::BridgeChains, and protocols::denovo_design::connection::ExtendChain.

References add_segment_name(), segment_names(), set_id(), and set_parent_id().

Referenced by protocols::denovo_design::connection::Connection::parse_my_tag().

virtual void protocols::denovo_design::components::NamedMover::process_permutation ( StructureData & perm ) const

pure virtual

Performs processing of the StructureData object.

Exceptions

EXCN_Process on failure

Assumed that the StructureData contains a pose which is consistent with the StructureData

Implemented in protocols::denovo_design::connection::Connection, and protocols::denovo_design::connection::ExtendChain.

StringList const& protocols::denovo_design::components::NamedMover::segment_names ( ) const

inline

names of segment pieces built by this mover

References segment_names_.

Referenced by protocols::denovo_design::connection::Connection::build_pose(), protocols::denovo_design::connection::Connection::clear_segments_and_compute_valid_segment_values(), and parse_my_tag().

void protocols::denovo_design::components::NamedMover::set_id ( std::string const & idval )

virtual

sets an identifier for this mover

Reimplemented in protocols::denovo_design::connection::Connection.

References add_parent_prefix(), and id_.

Referenced by parse_my_tag(), and set_parent_id().

void protocols::denovo_design::components::NamedMover::set_parent_id ( std::string const & parent )

sets an identifier for the parent of this mover, for nested moves

References id_, protocols::denovo_design::PARENT_DELIMETER, parent_id_, segment_names_, and set_id().

Referenced by parse_my_tag().

void protocols::denovo_design::components::NamedMover::set_segment_names ( StringList const & snames )

inlineprotected

sets segment names

References segment_names_.

Referenced by protocols::denovo_design::connection::Connection::set_id().

virtual void protocols::denovo_design::components::NamedMover::setup_permutation ( StructureData & perm ) const

pure virtual

Choose and store build options in the StructureData object.

Exceptions

EXCN_Setup on setup failure

You can store build-specified information (loop length, desired abego, etc.) in the StructureData object which will be used later when apply_permutation() is called. This function SHOULD NOT engage in any pose modification

Implemented in protocols::denovo_design::connection::StapleChains, protocols::denovo_design::connection::Connection, protocols::denovo_design::connection::BridgeChains, and protocols::denovo_design::connection::ExtendChain.

Referenced by apply().