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protocols::constraint_movers::AddConstraintsToCurrentConformationMover Class Reference

#include <AddConstraintsToCurrentConformationMover.hh>

Inheritance diagram for protocols::constraint_movers::AddConstraintsToCurrentConformationMover:
Inheritance graph
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Public Types

typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
- 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
 

Public Member Functions

 AddConstraintsToCurrentConformationMover ()
 
 ~AddConstraintsToCurrentConformationMover () override
 
void apply (Pose &pose) override
 Main Method. More...
 
virtual
core::scoring::constraints::ConstraintCOPs 
generate_constraints (Pose const &pose)
 
void task_factory (TaskFactoryOP tf)
 
void residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
booluse_distance_cst ()
 
booluse_harmonic_func ()
 
booluse_bounded_func ()
 
boolCA_only ()
 
boolbb_only ()
 
boolinter_chain ()
 
core::Realcst_weight ()
 
core::Realmax_distance ()
 
core::Realcoord_dev ()
 
core::Realbound_width ()
 
core::Sizemin_seq_sep ()
 
bool const & use_distance_cst () const
 
bool const & use_harmonic_func () const
 
bool const & use_bounded_func () const
 
bool const & CA_only () const
 
bool const & bb_only () const
 
bool const & inter_chain () const
 
core::Real const & cst_weight () const
 
core::Real const & max_distance () const
 
core::Real const & coord_dev () const
 
core::Real const & bound_width () const
 
core::Size const & min_seq_sep () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- 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 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...
 
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 std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

core::Size find_best_anchor (core::pose::Pose const &pose) const
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived movers) More...
 
core::scoring::constraints::ConstraintCOPs generate_coordinate_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const
 
core::scoring::constraints::ConstraintCOPs generate_atom_pair_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const
 

Private Attributes

bool use_distance_cst_
 
bool use_harmonic_func_
 
bool CA_only_
 
bool bb_only_
 
bool inter_chain_
 
core::Real cst_weight_
 
core::Real max_distance_
 
core::Real coord_dev_
 
core::Real bound_width_
 
core::Size min_seq_sep_
 
core::select::residue_selector::ResidueSelectorCOP selector_
 
bool use_bounded_func_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::constraint_movers::AddConstraintsToCurrentConformationMover::AddConstraintsToCurrentConformationMover ( )
protocols::constraint_movers::AddConstraintsToCurrentConformationMover::~AddConstraintsToCurrentConformationMover ( )
overridedefault

Member Function Documentation

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::apply ( Pose )
overridevirtual
bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bb_only ( )
inline

References bb_only_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bb_only ( ) const
inline

References bb_only_.

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bound_width ( )
inline

References bound_width_.

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bound_width ( ) const
inline

References bound_width_.

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::CA_only ( )
inline

References CA_only_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::CA_only ( ) const
inline

References CA_only_.

moves::MoverOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

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.

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::coord_dev ( )
inline

References coord_dev_.

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::coord_dev ( ) const
inline

References coord_dev_.

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::cst_weight ( )
inline

References cst_weight_.

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::cst_weight ( ) const
inline

References cst_weight_.

core::Size protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor ( core::pose::Pose const &  pose) const
private
moves::MoverOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

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.

core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  subset 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_constraints ( Pose const &  pose)
virtual
core::scoring::constraints::ConstraintCOPs protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  subset 
) const
private
std::string protocols::constraint_movers::AddConstraintsToCurrentConformationMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::inter_chain ( )
inline

References inter_chain_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::inter_chain ( ) const
inline

References inter_chain_.

core::Real& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::max_distance ( )
inline

References max_distance_.

core::Real const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::max_distance ( ) const
inline

References max_distance_.

core::Size& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::min_seq_sep ( )
inline

References min_seq_sep_.

core::Size const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::min_seq_sep ( ) const
inline

References min_seq_sep_.

std::string protocols::constraint_movers::AddConstraintsToCurrentConformationMover::mover_name ( )
static
void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_task_operations ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
privatevirtual

parse "task_operations" XML option (can be employed virtually by derived movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector_.

Referenced by parse_my_tag(), and task_factory().

void protocols::constraint_movers::AddConstraintsToCurrentConformationMover::task_factory ( TaskFactoryOP  tf)

References residue_selector().

Referenced by parse_task_operations().

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_bounded_func ( )
inline

References use_bounded_func_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_bounded_func ( ) const
inline

References use_bounded_func_.

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_distance_cst ( )
inline

References use_distance_cst_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_distance_cst ( ) const
inline

References use_distance_cst_.

bool& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_harmonic_func ( )
inline

References use_harmonic_func_.

bool const& protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_harmonic_func ( ) const
inline

References use_harmonic_func_.

Member Data Documentation

bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bb_only_
private
core::Real protocols::constraint_movers::AddConstraintsToCurrentConformationMover::bound_width_
private
bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::CA_only_
private
core::Real protocols::constraint_movers::AddConstraintsToCurrentConformationMover::coord_dev_
private
core::Real protocols::constraint_movers::AddConstraintsToCurrentConformationMover::cst_weight_
private
bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::inter_chain_
private
core::Real protocols::constraint_movers::AddConstraintsToCurrentConformationMover::max_distance_
private
core::Size protocols::constraint_movers::AddConstraintsToCurrentConformationMover::min_seq_sep_
private
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_movers::AddConstraintsToCurrentConformationMover::selector_
private
bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_bounded_func_
private
bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_distance_cst_
private
bool protocols::constraint_movers::AddConstraintsToCurrentConformationMover::use_harmonic_func_
private

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