#include <SeparateDnaFromNonDna.hh>

Inheritance diagram for protocols::dna::SeparateDnaFromNonDna:

Collaboration diagram for protocols::dna::SeparateDnaFromNonDna:

Public Member Functions
	SeparateDnaFromNonDna ()

	SeparateDnaFromNonDna (core::Real x, core::Real y, core::Real z)

	SeparateDnaFromNonDna (numeric::xyzVector< core::Real > const &xyz)

	SeparateDnaFromNonDna (SeparateDnaFromNonDna const &other)

virtual	~SeparateDnaFromNonDna ()

virtual void	apply (core::pose::Pose &pose)
	set up an appropriate fold tree for a non-DNA/DNA interface, and simply pull apart non-DNA and DNA More...

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

numeric::xyzVector< core::Real >	translation () const

virtual void	parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

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

virtual	~Mover ()

virtual MoverSP	create ()

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

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...

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
	this function informs 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
	this function informs 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

Private Attributes
numeric::xyzVector< core::Real >	translation_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 39 of file SeparateDnaFromNonDna.hh.

Constructor & Destructor Documentation

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( )

Definition at line 55 of file SeparateDnaFromNonDna.cc.

Referenced by clone(), and fresh_instance().

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)

Definition at line 60 of file SeparateDnaFromNonDna.cc.

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( numeric::xyzVector< core::Real > const & xyz)

Definition at line 65 of file SeparateDnaFromNonDna.cc.

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( SeparateDnaFromNonDna const & other)

Definition at line 70 of file SeparateDnaFromNonDna.cc.

protocols::dna::SeparateDnaFromNonDna::~SeparateDnaFromNonDna ( )

virtual

Definition at line 76 of file SeparateDnaFromNonDna.cc.

Member Function Documentation

void protocols::dna::SeparateDnaFromNonDna::apply ( core::pose::Pose & pose)

virtual

set up an appropriate fold tree for a non-DNA/DNA interface, and simply pull apart non-DNA and DNA

addition fold-tree considerations will have to be made if there are any 'non-DNA' chains that should stick to the DNA instead of to the non-DNA group

Implements protocols::moves::Mover.

Definition at line 81 of file SeparateDnaFromNonDna.cc.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::pose::Pose::num_jump(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::set_jump(), core::pose::Pose::total_residue(), protocols::dna::TR(), and translation_.

Referenced by protocols::dna::DnaInterfacePacker::unbound_score().

moves::MoverOP protocols::dna::SeparateDnaFromNonDna::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 200 of file SeparateDnaFromNonDna.cc.

References SeparateDnaFromNonDna().

moves::MoverOP protocols::dna::SeparateDnaFromNonDna::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 193 of file SeparateDnaFromNonDna.cc.

References SeparateDnaFromNonDna().

std::string protocols::dna::SeparateDnaFromNonDna::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 177 of file SeparateDnaFromNonDna.cc.

References protocols::dna::SeparateDnaFromNonDnaCreator::mover_name().

void protocols::dna::SeparateDnaFromNonDna::parse_my_tag	(	TagPtr const	,
		moves::DataMap &	,
		protocols::filters::Filters_map const &	,
		moves::Movers_map const &	,
		Pose const &
	)