#include <SeedSetupMover.hh>

Inheritance diagram for protocols::seeded_abinitio::SeedSetupMover:

Collaboration diagram for protocols::seeded_abinitio::SeedSetupMover:

Public Member Functions
	SeedSetupMover ()

virtual	~SeedSetupMover ()

void	apply (core::pose::Pose &pose)

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	clear_task_factory ()

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::pack::task::TaskFactoryOP &	task_factory ()
	getters 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 Member Functions
void	set_packerTasks_target_and_seeds (core::pose::Pose &pose, protocols::loops::Loops &seeds, utility::vector1< core::Size > &designable_residues, utility::vector1< core::Size > &norepack_res, core::pack::task::TaskFactoryOP &tf)

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::pack::task::PackerTaskOP	task_

core::kinematics::MoveMapOP	movemap_
	movemap More...

bool	repack_target_
	switches for folding and desing behavior: More...

bool	repack_foldpose_

bool	allow_all_aas_

bool	design_target_

bool	design_foldpose_

utility::vector1< std::pair < std::string, std::string > >	seed_vector_

std::string	design_res_
	designable residues More...

std::string	norepack_res_
	dont repack residues More...

protocols::loops::Loops	all_seeds_

core::scoring::ScoreFunctionOP	scorefxn_repack_
	in case someone wanted to instantly design, but really this is only for debugging purposes in there More...

core::scoring::ScoreFunctionOP	scorefxn_minimize_

bool	design_

bool	chi_chain1_
	let chi angles of chain 1 move More...

bool	chi_chain2_
	let chi angles of chain 2 move More...

bool	interface_chi1_
	interface chi angles be movable More...

bool	interface_chi2_

core::Real	interface_distance_cutoff_

bool	packtask_
	set helper taskfactory More...

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 34 of file SeedSetupMover.hh.

Constructor & Destructor Documentation

protocols::seeded_abinitio::SeedSetupMover::SeedSetupMover ( )

Definition at line 84 of file SeedSetupMover.cc.

References allow_all_aas_, chi_chain1_, chi_chain2_, design_foldpose_, design_res_, design_target_, norepack_res_, packtask_, repack_foldpose_, and repack_target_.

Referenced by clone().

protocols::seeded_abinitio::SeedSetupMover::~SeedSetupMover ( )

virtual

Definition at line 82 of file SeedSetupMover.cc.

Member Function Documentation

void protocols::seeded_abinitio::SeedSetupMover::apply ( core::pose::Pose & pose)

virtual

void protocols::seeded_abinitio::SeedSetupMover::clear_task_factory ( )

Definition at line 119 of file SeedSetupMover.cc.

References task_factory_.

Referenced by apply().

protocols::moves::MoverOP protocols::seeded_abinitio::SeedSetupMover::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Definition at line 104 of file SeedSetupMover.cc.

References SeedSetupMover().

protocols::moves::MoverOP protocols::seeded_abinitio::SeedSetupMover::fresh_instance ( ) const

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Definition at line 109 of file SeedSetupMover.cc.

std::string protocols::seeded_abinitio::SeedSetupMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 371 of file SeedSetupMover.cc.

References protocols::seeded_abinitio::SeedSetupMoverCreator::mover_name().

void protocols::seeded_abinitio::SeedSetupMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Definition at line 376 of file SeedSetupMover.cc.

References allow_all_aas_, chi_chain1_, chi_chain2_, design_, design_foldpose_, design_res_, design_target_, protocols::moves::DataMap::get(), interface_chi1_, interface_chi2_, interface_distance_cutoff_, movemap_, norepack_res_, packtask_, protocols::rosetta_scripts::parse_movemap(), repack_foldpose_, repack_target_, scorefxn_minimize_, scorefxn_repack_, and seed_vector_.

void protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds	(	core::pose::Pose &	pose,
		protocols::loops::Loops &	seeds,
		utility::vector1< core::Size > &	designable_residues,
		utility::vector1< core::Size > &	norepack_res,
		core::pack::task::TaskFactoryOP &	tf
	)

private

Definition at line 147 of file SeedSetupMover.cc.

References core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), design_foldpose_, design_target_, protocols::loops::Loops::is_loop_residue(), protocols::seeded_abinitio::is_part(), core::conformation::Conformation::num_chains(), repack_foldpose_, repack_target_, protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation::set_residues(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::seeded_abinitio::SeedSetupMover::task_factory ( core::pack::task::TaskFactoryOP tf)

Definition at line 114 of file SeedSetupMover.cc.

References task_factory_.

core::pack::task::TaskFactoryOP & protocols::seeded_abinitio::SeedSetupMover::task_factory ( )

getters

Definition at line 133 of file SeedSetupMover.cc.

References task_factory_.

Member Data Documentation

protocols::loops::Loops protocols::seeded_abinitio::SeedSetupMover::all_seeds_

private

Definition at line 88 of file SeedSetupMover.hh.

Referenced by apply().

bool protocols::seeded_abinitio::SeedSetupMover::allow_all_aas_

private

Definition at line 74 of file SeedSetupMover.hh.

Referenced by parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::chi_chain1_

private

let chi angles of chain 1 move

Definition at line 96 of file SeedSetupMover.hh.

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

bool protocols::seeded_abinitio::SeedSetupMover::chi_chain2_

private

let chi angles of chain 2 move

Definition at line 98 of file SeedSetupMover.hh.

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

bool protocols::seeded_abinitio::SeedSetupMover::design_

private

Definition at line 93 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::seeded_abinitio::SeedSetupMover::design_foldpose_

private

Definition at line 76 of file SeedSetupMover.hh.

Referenced by parse_my_tag(), SeedSetupMover(), and set_packerTasks_target_and_seeds().

std::string protocols::seeded_abinitio::SeedSetupMover::design_res_

private

designable residues

Definition at line 82 of file SeedSetupMover.hh.

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

bool protocols::seeded_abinitio::SeedSetupMover::design_target_

private

Definition at line 75 of file SeedSetupMover.hh.

Referenced by parse_my_tag(), SeedSetupMover(), and set_packerTasks_target_and_seeds().

bool protocols::seeded_abinitio::SeedSetupMover::interface_chi1_

private

interface chi angles be movable

Definition at line 101 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

bool protocols::seeded_abinitio::SeedSetupMover::interface_chi2_

private

Definition at line 102 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

core::Real protocols::seeded_abinitio::SeedSetupMover::interface_distance_cutoff_

private

Definition at line 103 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

core::kinematics::MoveMapOP protocols::seeded_abinitio::SeedSetupMover::movemap_

private

movemap

Definition at line 69 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

std::string protocols::seeded_abinitio::SeedSetupMover::norepack_res_

private

dont repack residues

Definition at line 85 of file SeedSetupMover.hh.

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

bool protocols::seeded_abinitio::SeedSetupMover::packtask_

private

set helper taskfactory

Definition at line 105 of file SeedSetupMover.hh.

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

bool protocols::seeded_abinitio::SeedSetupMover::repack_foldpose_

private

Definition at line 73 of file SeedSetupMover.hh.

Referenced by parse_my_tag(), SeedSetupMover(), and set_packerTasks_target_and_seeds().

bool protocols::seeded_abinitio::SeedSetupMover::repack_target_

private

switches for folding and desing behavior:

Definition at line 72 of file SeedSetupMover.hh.

Referenced by parse_my_tag(), SeedSetupMover(), and set_packerTasks_target_and_seeds().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedSetupMover::scorefxn_minimize_

private

Definition at line 92 of file SeedSetupMover.hh.

Referenced by parse_my_tag().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedSetupMover::scorefxn_repack_

private

in case someone wanted to instantly design, but really this is only for debugging purposes in there

Definition at line 91 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

utility::vector1< std::pair < std::string,std::string > > protocols::seeded_abinitio::SeedSetupMover::seed_vector_

private

Definition at line 79 of file SeedSetupMover.hh.

Referenced by apply(), and parse_my_tag().

core::pack::task::PackerTaskOP protocols::seeded_abinitio::SeedSetupMover::task_

private

Definition at line 66 of file SeedSetupMover.hh.

core::pack::task::TaskFactoryOP protocols::seeded_abinitio::SeedSetupMover::task_factory_

private

this taskfactory contains all the information about which residues should be repacked and designed it assumes the fold pose is the last chain. Seeds are parse at runtime and incorporated into this taskfactory

Definition at line 65 of file SeedSetupMover.hh.

Referenced by apply(), clear_task_factory(), and task_factory().

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

src/protocols/seeded_abinitio/SeedSetupMover.hh
src/protocols/seeded_abinitio/SeedSetupMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation