protocols::simple_moves::DesignRepackMover Class Reference

a pure virtual base class for movers which redesign and repack the interface More...

#include <DesignRepackMover.hh>

Inheritance diagram for protocols::simple_moves::DesignRepackMover:

Collaboration diagram for protocols::simple_moves::DesignRepackMover:

Public Member Functions
	DesignRepackMover ()
	DesignRepackMover (std::string const name)
void	setup_packer_and_movemap (core::pose::Pose const &pose)
protocols::moves::MoverOP	clone () const =0
	clone has to be overridden only if clone invocation is expected. More...
protocols::moves::MoverOP	fresh_instance () const =0
	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...
virtual void	parse_my_tag (utility::tag::TagPtr const, 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	min_rb (utility::vector1< bool > const min_rb)
void	min_rb (bool const min_rb)
	in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...
utility::vector1< bool > const &	min_rb () const
bool	min_rb_set () const
void	min_sc (utility::vector1< bool > const &min_sc)
utility::vector1< bool > const &	min_sc () const
bool	min_sc_set () const
void	min_bb (utility::vector1< bool > const &min_bb)
utility::vector1< bool > const &	min_bb () const
bool	min_bb_set () const
bool	optimize_foldtree () const
void	optimize_foldtree (bool const opt)
virtual void	apply (core::pose::Pose &)
	a dummy apply so that instantiation of this baseclass would be possible. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	prevent_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size > const &	prevent_repacking () const
void	restrict_to_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size > const &	restrict_to_repacking () const
void	design (bool const des)
bool	design () const
void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionOP	scorefxn_repack () const
core::scoring::ScoreFunctionOP	scorefxn_minimize () const
core::pack::task::PackerTaskCOP	task () const
core::pack::task::PackerTaskOP &	task ()
void	clear_task ()
	after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...
void	clear_task_factory ()
void	use_preset_task (bool const bt)
bool	use_preset_task () const
void	task_factory (core::pack::task::TaskFactoryOP p)
core::pack::task::TaskFactoryOP &	task_factory ()
core::pack::task::TaskFactoryOP	task_factory () const
virtual	~DesignRepackMover ()
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

Protected Attributes
core::scoring::ScoreFunctionOP	scorefxn_repack_
core::scoring::ScoreFunctionOP	scorefxn_minimize_
bool	repack_partner1_
bool	repack_partner2_
bool	design_partner1_
bool	design_partner2_
utility::vector1< bool >	min_sc_
utility::vector1< bool >	curr_min_sc_
utility::vector1< bool >	min_rb_
utility::vector1< bool >	min_bb_
utility::vector1< bool >	curr_min_bb_
utility::vector1< bool >	curr_min_rb_
bool	min_rb_set_
bool	min_sc_set_
bool	min_bb_set_
utility::vector1< core::Size >	target_residues_
core::Real	interface_distance_cutoff_
bool	repack_non_ala_
bool	optimize_foldtree_
bool	automatic_repacking_definition_
core::pack::task::PackerTaskOP	task_
bool	use_preset_task_
utility::vector1< bool >	allowed_aas_
utility::vector1< core::Size >	prevent_repacking_
utility::vector1< core::Size >	restrict_to_repacking_
core::pack::task::TaskFactoryOP	task_factory_
bool	symmetry_

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

a pure virtual base class for movers which redesign and repack the interface

Constructor & Destructor Documentation

protocols::simple_moves::DesignRepackMover::DesignRepackMover

(

)

References allowed_aas_, core::chemical::num_canonical_aas, prevent_repacking_, and restrict_to_repacking_.

protocols::simple_moves::DesignRepackMover::DesignRepackMover

(

std::string const

name)

References allowed_aas_, and core::chemical::num_canonical_aas.

protocols::simple_moves::DesignRepackMover::~DesignRepackMover ( )

virtual

Member Function Documentation

virtual void protocols::simple_moves::DesignRepackMover::apply ( core::pose::Pose &  )

inlinevirtual

a dummy apply so that instantiation of this baseclass would be possible.

Implements protocols::moves::Mover.

Reimplemented in protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::LoopFinder, protocols::simple_moves::ddG, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, and protocols::protein_interface_design::movers::BuildAlaPose.

void protocols::simple_moves::DesignRepackMover::clear_task

(

)

after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered

References task_.

void protocols::simple_moves::DesignRepackMover::clear_task_factory

(

)

References task_factory_.

protocols::moves::MoverOP protocols::simple_moves::DesignRepackMover::clone ( ) const

pure 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.

Implemented in protocols::simple_moves::ddG, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, and protocols::protein_interface_design::movers::BuildAlaPose.

void protocols::simple_moves::DesignRepackMover::design ( bool const  des)

inline

References design_partner1_, and design_partner2_.

bool protocols::simple_moves::DesignRepackMover::design ( ) const

inline

References design_partner1_, and design_partner2_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::LoopMoverFromCommandLine(), parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), and protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags().

protocols::moves::MoverOP protocols::simple_moves::DesignRepackMover::fresh_instance ( ) const

pure 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.

Implemented in protocols::protein_interface_design::movers::LoopRemodel, protocols::simple_moves::ddG, protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, and protocols::protein_interface_design::movers::BuildAlaPose.

std::string protocols::simple_moves::DesignRepackMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::protein_interface_design::movers::PlaceStubMover, protocols::simple_moves::ddG, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, and protocols::protein_interface_design::movers::BuildAlaPose.

void protocols::simple_moves::DesignRepackMover::min_bb ( utility::vector1< bool > const &  min_bb)

inline

References min_bb(), min_bb_, and min_bb_set_.

Referenced by min_bb().

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_bb ( ) const

inline

References min_bb_, and min_bb_set().

Referenced by parse_my_tag().

bool protocols::simple_moves::DesignRepackMover::min_bb_set ( ) const

inline

References min_bb_set_.

Referenced by min_bb(), and setup_packer_and_movemap().

void protocols::simple_moves::DesignRepackMover::min_rb ( utility::vector1< bool > const  min_rb)

inline

References min_rb(), min_rb_, and min_rb_set_.

Referenced by min_rb().

void protocols::simple_moves::DesignRepackMover::min_rb ( bool const  min_rb)

inline

in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code.

References min_rb_, and min_rb_set_.

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_rb ( ) const

inline

References min_rb_, and min_rb_set().

Referenced by parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

bool protocols::simple_moves::DesignRepackMover::min_rb_set ( ) const

inline

References min_rb_set_.

Referenced by min_rb(), and setup_packer_and_movemap().

void protocols::simple_moves::DesignRepackMover::min_sc ( utility::vector1< bool > const &  min_sc)

inline

References min_sc(), min_sc_, and min_sc_set_.

Referenced by min_sc().

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_sc ( ) const

inline

References min_sc_, and min_sc_set().

Referenced by parse_my_tag().

bool protocols::simple_moves::DesignRepackMover::min_sc_set ( ) const

inline

References min_sc_set_.

Referenced by min_sc(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::optimize_foldtree ( ) const

inline

References optimize_foldtree_.

void protocols::simple_moves::DesignRepackMover::optimize_foldtree ( bool const  opt)

inline

References optimize_foldtree_.

void protocols::simple_moves::DesignRepackMover::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.

Reimplemented in protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::simple_moves::ddG, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, and protocols::protein_interface_design::movers::BuildAlaPose.

References automatic_repacking_definition_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), design(), design_partner1_, design_partner2_, protocols::moves::DataMap::get(), core::pose::get_resnum(), interface_distance_cutoff_, min_bb(), min_rb(), min_sc(), optimize_foldtree_, protocols::rosetta_scripts::parse_task_operations(), repack_non_ala_, repack_partner1_, repack_partner2_, scorefxn_minimize(), scorefxn_minimize_, scorefxn_repack(), scorefxn_repack_, symmetry_, target_residues_, task_factory(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), and protocols::protein_interface_design::movers::RepackMinimize::parse_my_tag().

void protocols::simple_moves::DesignRepackMover::prevent_repacking ( utility::vector1< core::Size > const  p)

inline

References prevent_repacking_.

Referenced by protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design().

utility::vector1< core::Size > const& protocols::simple_moves::DesignRepackMover::prevent_repacking ( ) const

inline

References prevent_repacking_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

void protocols::simple_moves::DesignRepackMover::restrict_to_repacking ( utility::vector1< core::Size > const  p)

inline

References restrict_to_repacking_.

utility::vector1< core::Size > const& protocols::simple_moves::DesignRepackMover::restrict_to_repacking ( ) const

inline

References restrict_to_repacking_.

core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_minimize

(

)

const

References scorefxn_minimize_.

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), and protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag().

core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_repack

(

)

const

References scorefxn_repack_.

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), and protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag().

void protocols::simple_moves::DesignRepackMover::set_scorefxn_minimize

(

core::scoring::ScoreFunctionCOP

scorefxn)

References scorefxn_minimize_.

void protocols::simple_moves::DesignRepackMover::set_scorefxn_repack

(

core::scoring::ScoreFunctionCOP

scorefxn)

References scorefxn_repack_.

void protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap

(

core::pose::Pose const &

pose)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, allowed_aas_, protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), automatic_repacking_definition_, protocols::scoring::Interface::calculate(), core::pack::task::TaskFactory::create_packer_task(), curr_min_bb_, curr_min_rb_, curr_min_sc_, protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain1(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain2(), design_partner1_, design_partner2_, protocols::scoring::Interface::distance(), core::kinematics::distance(), core::pose::Pose::fold_tree(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff(), interface_distance_cutoff_, protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), core::pack::make_symmetric_PackerTask_by_truncation(), min_bb_, min_bb_set(), min_rb_, min_rb_set(), min_sc_, min_sc_set(), core::chemical::ResidueType::name(), core::pose::Pose::num_jump(), core::pack::task::parse_resfile(), core::kinematics::FoldTree::partition_by_jump(), prevent_repacking_, protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain1(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain2(), repack_non_ala_, repack_partner1_, repack_partner2_, core::pose::Pose::residue(), restrict_to_repacking_, symmetry_, target_residues_, task_, task_factory_, core::pose::Pose::total_residue(), core::conformation::Residue::type(), core::pose::Pose::update_residue_neighbors(), and use_preset_task_.

Referenced by protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), and protocols::protein_interface_design::movers::RepackMinimize::apply().

core::pack::task::PackerTaskCOP protocols::simple_moves::DesignRepackMover::task

(

)

const

References task_.

Referenced by protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), and protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag().

core::pack::task::PackerTaskOP & protocols::simple_moves::DesignRepackMover::task

(

)

References task_.

void protocols::simple_moves::DesignRepackMover::task_factory

(

core::pack::task::TaskFactoryOP

p)

References task_factory_.

Referenced by protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design().

core::pack::task::TaskFactoryOP & protocols::simple_moves::DesignRepackMover::task_factory

(

)

References task_factory_.

Referenced by protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), and protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag().

core::pack::task::TaskFactoryOP protocols::simple_moves::DesignRepackMover::task_factory

(

)

const

References task_factory_.

void protocols::simple_moves::DesignRepackMover::use_preset_task ( bool const  bt)

inline

References use_preset_task_.

bool protocols::simple_moves::DesignRepackMover::use_preset_task ( ) const

inline

References use_preset_task_.

Member Data Documentation

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::allowed_aas_

protected

Referenced by protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), DesignRepackMover(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::automatic_repacking_definition_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::curr_min_bb_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::curr_min_rb_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::curr_min_sc_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::design_partner1_

protected

Referenced by protocols::protein_interface_design::movers::BuildAlaPose::BuildAlaPose(), protocols::simple_moves::ddG::calculate(), design(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), parse_my_tag(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::design_partner2_

protected

Referenced by protocols::protein_interface_design::movers::BuildAlaPose::BuildAlaPose(), protocols::simple_moves::ddG::calculate(), design(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), parse_my_tag(), and setup_packer_and_movemap().

core::Real protocols::simple_moves::DesignRepackMover::interface_distance_cutoff_

protected

Referenced by parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::min_bb_

protected

Referenced by min_bb(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::min_bb_set_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), min_bb(), min_bb_set(), and protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::min_rb_

protected

Referenced by min_rb(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::min_rb_set_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), min_rb(), min_rb_set(), and protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize().

utility::vector1< bool > protocols::simple_moves::DesignRepackMover::min_sc_

protected

Referenced by min_sc(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::min_sc_set_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), min_sc(), min_sc_set(), and protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize().

bool protocols::simple_moves::DesignRepackMover::optimize_foldtree_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), optimize_foldtree(), parse_my_tag(), and protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize().

utility::vector1< core::Size > protocols::simple_moves::DesignRepackMover::prevent_repacking_

protected

Referenced by protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::cst_cleanup(), DesignRepackMover(), protocols::protein_interface_design::movers::PlaceStubMover::final_cleanup(), prevent_repacking(), setup_packer_and_movemap(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

bool protocols::simple_moves::DesignRepackMover::repack_non_ala_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::repack_partner1_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::BuildAlaPose::BuildAlaPose(), protocols::simple_moves::ddG::calculate(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

bool protocols::simple_moves::DesignRepackMover::repack_partner2_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::BuildAlaPose::BuildAlaPose(), protocols::simple_moves::ddG::calculate(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

utility::vector1< core::Size > protocols::simple_moves::DesignRepackMover::restrict_to_repacking_

protected

Referenced by DesignRepackMover(), protocols::protein_interface_design::movers::PlaceStubMover::final_cleanup(), restrict_to_repacking(), and setup_packer_and_movemap().

core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_minimize_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), scorefxn_minimize(), and set_scorefxn_minimize().

core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_repack_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), parse_my_tag(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), scorefxn_repack(), and set_scorefxn_repack().

bool protocols::simple_moves::DesignRepackMover::symmetry_

protected

Referenced by protocols::protein_interface_design::movers::RepackMinimize::apply(), parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

utility::vector1< core::Size > protocols::simple_moves::DesignRepackMover::target_residues_

protected

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds(), protocols::protein_interface_design::movers::DisulfideMover::DisulfideMover(), parse_my_tag(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::protein_interface_design::movers::RepackMinimize::RepackMinimize(), and setup_packer_and_movemap().

core::pack::task::PackerTaskOP protocols::simple_moves::DesignRepackMover::task_

protected

Referenced by protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::simple_moves::ddG::calculate(), clear_task(), setup_packer_and_movemap(), protocols::simple_moves::ddG::symm_ddG(), and task().

core::pack::task::TaskFactoryOP protocols::simple_moves::DesignRepackMover::task_factory_

protected

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

bool protocols::simple_moves::DesignRepackMover::use_preset_task_

protected

Referenced by setup_packer_and_movemap(), and use_preset_task().

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

• src/protocols/simple_moves/DesignRepackMover.hh
• src/protocols/simple_moves/DesignRepackMover.cc