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protocols::calc_taskop_movers::DesignRepackMover Class Reference

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

#include <DesignRepackMover.hh>

Inheritance diagram for protocols::calc_taskop_movers::DesignRepackMover:
Inheritance graph
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Public Member Functions

 DesignRepackMover ()
 
 DesignRepackMover (std::string const &name)
 
void setup_packer_and_movemap (core::pose::Pose const &pose)
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 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 (core::select::residue_selector::ResidueSelectorOP min_sc)
 
utility::vector1< boolmin_sc (core::pose::Pose const &pose) const
 
bool min_sc_set () const
 
void min_bb (core::select::residue_selector::ResidueSelectorOP min_bb)
 
utility::vector1< boolmin_bb (core::pose::Pose const &pose) const
 
bool min_bb_set () const
 
bool optimize_foldtree () const
 
void optimize_foldtree (bool const opt)
 
void apply (core::pose::Pose &) override
 a dummy apply so that instantiation of this baseclass would be possible. More...
 
std::string get_name () const override
 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::PackerTaskOPtask ()
 
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::TaskFactoryOPtask_factory ()
 
core::pack::task::TaskFactoryOP task_factory () const
 
 ~DesignRepackMover () override
 
void target_residues (core::select::residue_selector::ResidueSelectorCOP setting)
 Replace the current target_residue setting with the passed residue selector. More...
 
core::select::residue_selector::ResidueSelectorCOP target_residues () const
 
utility::vector1< core::Sizetarget_residues (core::pose::Pose const &pose) const
 
- Public Member Functions inherited from protocols::moves::Mover
 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...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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 show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
get_xsd_complex_type ()
 
- 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 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< boolmin_rb_
 
utility::vector1< boolcurr_min_sc_
 
utility::vector1< boolcurr_min_bb_
 
utility::vector1< boolcurr_min_rb_
 
bool min_rb_set_
 
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< boolallowed_aas_
 
utility::vector1< core::Sizeprevent_repacking_
 
utility::vector1< core::Sizerestrict_to_repacking_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool symmetry_
 

Private Attributes

core::select::residue_selector::ResidueSelectorOP min_sc_
 
core::select::residue_selector::ResidueSelectorOP min_bb_
 
core::select::residue_selector::ResidueSelectorCOP target_residues_
 

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 std::list< std::string > Strings
 
- 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::calc_taskop_movers::DesignRepackMover::DesignRepackMover ( )
protocols::calc_taskop_movers::DesignRepackMover::DesignRepackMover ( std::string const &  name)
protocols::calc_taskop_movers::DesignRepackMover::~DesignRepackMover ( )
overridedefault

Member Function Documentation

void protocols::calc_taskop_movers::DesignRepackMover::apply ( core::pose::Pose )
inlineoverridevirtual
void protocols::calc_taskop_movers::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::calc_taskop_movers::DesignRepackMover::clear_task_factory ( )

References task_factory_.

void protocols::calc_taskop_movers::DesignRepackMover::design ( bool const  des)
inline
bool protocols::calc_taskop_movers::DesignRepackMover::design ( ) const
inline
std::string protocols::calc_taskop_movers::DesignRepackMover::get_name ( ) const
overridevirtual
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type ( )
static
void protocols::calc_taskop_movers::DesignRepackMover::min_bb ( core::select::residue_selector::ResidueSelectorOP  min_bb)

References min_bb_.

Referenced by parse_my_tag(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::min_bb ( core::pose::Pose const &  pose) const

References min_bb_.

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

References min_bb_.

Referenced by setup_packer_and_movemap().

void protocols::calc_taskop_movers::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::calc_taskop_movers::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::calc_taskop_movers::DesignRepackMover::min_rb ( ) const
inline
bool protocols::calc_taskop_movers::DesignRepackMover::min_rb_set ( ) const
inline

References min_rb_set_.

Referenced by min_rb(), and setup_packer_and_movemap().

void protocols::calc_taskop_movers::DesignRepackMover::min_sc ( core::select::residue_selector::ResidueSelectorOP  min_sc)

References min_sc_.

Referenced by parse_my_tag(), and setup_packer_and_movemap().

utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::min_sc ( core::pose::Pose const &  pose) const

References min_sc_.

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

References min_sc_.

Referenced by setup_packer_and_movemap().

bool protocols::calc_taskop_movers::DesignRepackMover::optimize_foldtree ( ) const
inline

References optimize_foldtree_.

void protocols::calc_taskop_movers::DesignRepackMover::optimize_foldtree ( bool const  opt)
inline

References optimize_foldtree_.

void protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

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

References automatic_repacking_definition_, design(), design_partner1_, design_partner2_, core::pose::get_resnum_string(), core::scoring::get_score_function_name(), interface_distance_cutoff_, min_bb(), min_rb(), min_sc(), optimize_foldtree_, core::select::residue_selector::OR_combine(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), protocols::antibody::design::repack, repack_non_ala_, repack_partner1_, repack_partner2_, scorefxn_minimize(), scorefxn_minimize_, scorefxn_repack(), scorefxn_repack_, symmetry_, target_residues(), task_factory(), and protocols::calc_taskop_movers::TR().

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

void protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking ( utility::vector1< core::Size > const &  p)
inline
utility::vector1< core::Size > const& protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking ( ) const
inline
void protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking ( utility::vector1< core::Size > const &  p)
inline
utility::vector1< core::Size > const& protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking ( ) const
inline
core::scoring::ScoreFunctionOP protocols::calc_taskop_movers::DesignRepackMover::scorefxn_minimize ( ) const
core::scoring::ScoreFunctionOP protocols::calc_taskop_movers::DesignRepackMover::scorefxn_repack ( ) const
void protocols::calc_taskop_movers::DesignRepackMover::set_scorefxn_minimize ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_minimize_.

void protocols::calc_taskop_movers::DesignRepackMover::set_scorefxn_repack ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_repack_.

void protocols::calc_taskop_movers::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::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::task_operations::ProteinInterfaceDesignOperation::design_chain1(), protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2(), design_partner1_, design_partner2_, protocols::scoring::Interface::distance(), core::kinematics::distance(), core::pose::Pose::fold_tree(), protocols::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff(), interface_distance_cutoff_, core::chemical::ResidueType::is_disulfide_bonded(), 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::pose::Pose::num_jump(), core::pack::task::parse_resfile(), core::kinematics::FoldTree::partition_by_jump(), prevent_repacking_, protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1(), protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain2(), repack_non_ala_, repack_partner1_, repack_partner2_, core::pose::Pose::residue(), restrict_to_repacking_, core::pose::Pose::size(), symmetry_, target_residues(), task_, task_factory_, 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().

void protocols::calc_taskop_movers::DesignRepackMover::target_residues ( core::select::residue_selector::ResidueSelectorCOP  setting)

Replace the current target_residue setting with the passed residue selector.

References target_residues_.

core::select::residue_selector::ResidueSelectorCOP protocols::calc_taskop_movers::DesignRepackMover::target_residues ( ) const
utility::vector1< core::Size > protocols::calc_taskop_movers::DesignRepackMover::target_residues ( core::pose::Pose const &  pose) const
core::pack::task::PackerTaskCOP protocols::calc_taskop_movers::DesignRepackMover::task ( ) const
core::pack::task::PackerTaskOP & protocols::calc_taskop_movers::DesignRepackMover::task ( )

References task_.

void protocols::calc_taskop_movers::DesignRepackMover::task_factory ( core::pack::task::TaskFactoryOP  p)
core::pack::task::TaskFactoryOP & protocols::calc_taskop_movers::DesignRepackMover::task_factory ( )
core::pack::task::TaskFactoryOP protocols::calc_taskop_movers::DesignRepackMover::task_factory ( ) const

References task_factory_.

void protocols::calc_taskop_movers::DesignRepackMover::use_preset_task ( bool const  bt)
inline

References use_preset_task_.

bool protocols::calc_taskop_movers::DesignRepackMover::use_preset_task ( ) const
inline

References use_preset_task_.

Member Data Documentation

utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::allowed_aas_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::automatic_repacking_definition_
protected
utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::curr_min_bb_
protected
utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::curr_min_rb_
protected
utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::curr_min_sc_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::design_partner1_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::design_partner2_
protected
core::Real protocols::calc_taskop_movers::DesignRepackMover::interface_distance_cutoff_
protected
core::select::residue_selector::ResidueSelectorOP protocols::calc_taskop_movers::DesignRepackMover::min_bb_
private

Referenced by min_bb(), and min_bb_set().

utility::vector1< bool > protocols::calc_taskop_movers::DesignRepackMover::min_rb_
protected

Referenced by min_rb(), and setup_packer_and_movemap().

bool protocols::calc_taskop_movers::DesignRepackMover::min_rb_set_
protected

Referenced by min_rb(), and min_rb_set().

core::select::residue_selector::ResidueSelectorOP protocols::calc_taskop_movers::DesignRepackMover::min_sc_
private

Referenced by min_sc(), and min_sc_set().

bool protocols::calc_taskop_movers::DesignRepackMover::optimize_foldtree_
protected
utility::vector1< core::Size > protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::repack_non_ala_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::repack_partner1_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::repack_partner2_
protected
utility::vector1< core::Size > protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking_
protected
core::scoring::ScoreFunctionOP protocols::calc_taskop_movers::DesignRepackMover::scorefxn_minimize_
protected
core::scoring::ScoreFunctionOP protocols::calc_taskop_movers::DesignRepackMover::scorefxn_repack_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::symmetry_
protected
core::select::residue_selector::ResidueSelectorCOP protocols::calc_taskop_movers::DesignRepackMover::target_residues_
private

Referenced by target_residues().

core::pack::task::PackerTaskOP protocols::calc_taskop_movers::DesignRepackMover::task_
protected
core::pack::task::TaskFactoryOP protocols::calc_taskop_movers::DesignRepackMover::task_factory_
protected
bool protocols::calc_taskop_movers::DesignRepackMover::use_preset_task_
protected

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