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protocols::relax::AtomCoordinateCstMover Class Reference

#include <AtomCoordinateCstMover.hh>

Inheritance diagram for protocols::relax::AtomCoordinateCstMover:
Inheritance graph
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Public Types

typedef moves::Mover parent
 
- 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

 AtomCoordinateCstMover ()
 
 AtomCoordinateCstMover (AtomCoordinateCstMover const &)
 
 ~AtomCoordinateCstMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual void set_refstruct (core::pose::PoseCOP ref)
 
void cst_sd (core::Real sd)
 
core::Real cst_sd () const
 
void bounded (bool bound)
 
bool bounded () const
 
void cst_width (core::Real width)
 
core::Real cst_width () const
 
void cst_sidechain (bool sidechains)
 
bool cst_sidechain () const
 
void ambiguous_hnq (bool flip_hnq)
 
bool ambiguous_hnq () const
 
void func_groups (bool b)
 
bool func_groups () const
 
void set_loop_segments (protocols::loops::LoopsCOP loops)
 
void set_task_segments (core::pack::task::TaskFactoryCOP taskfactory)
 
- 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::select::residue_selector::ResidueSubset compute_residue_subset (core::pose::Pose const &pose) const
 
core::pose::PoseOP get_constraint_target_pose (core::pose::Pose const &pose) const
 
core::id::SequenceMapping generate_seqmap (core::pose::Pose const &pose, core::pose::Pose const &constraint_target_pose) const
 
core::scoring::constraints::ConstraintCOPs generate_constraints (core::pose::Pose const &pose)
 
core::scoring::constraints::ConstraintCOPs set_constraints_on_func_groups (core::pose::Pose const &pose)
 

Private Attributes

core::pose::PoseCOP refpose_
 If set, the pose to make the constraints to. More...
 
core::Real cst_sd_
 The strenght (standard deviation) of the constraints. More...
 
bool bounded_
 Use bounded constraints instead of harmonic. More...
 
core::Real cst_width_
 The width for bounded constraints. More...
 
bool cst_sidechain_
 Also constrain sidechains? More...
 
bool amb_hnq_
 When making sidechain constraints, should we allow for flipping HNQ residue sidechains? More...
 
protocols::loops::LoopsCOP loop_segments_
 A loop definition of constrained segments. More...
 
core::pack::task::TaskFactoryCOP task_segments_
 A task definition of constrained segments. More...
 
bool func_groups_
 If set to true then coordinate constraints are applied only to the functional groups of the side_chain. More...
 

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::relax::AtomCoordinateCstMover::AtomCoordinateCstMover ( )
protocols::relax::AtomCoordinateCstMover::AtomCoordinateCstMover ( AtomCoordinateCstMover const &  )
default
protocols::relax::AtomCoordinateCstMover::~AtomCoordinateCstMover ( )
overridedefault

Member Function Documentation

void protocols::relax::AtomCoordinateCstMover::ambiguous_hnq ( bool  flip_hnq)
inline
bool protocols::relax::AtomCoordinateCstMover::ambiguous_hnq ( ) const
inline

References amb_hnq_.

Referenced by parse_my_tag().

void protocols::relax::AtomCoordinateCstMover::apply ( core::pose::Pose )
overridevirtual
void protocols::relax::AtomCoordinateCstMover::bounded ( bool  bound)
inline
bool protocols::relax::AtomCoordinateCstMover::bounded ( ) const
inline

References bounded_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::relax::AtomCoordinateCstMover::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.

Referenced by protocols::mpi_refinement::StructAvrgMover::weighted_average().

core::select::residue_selector::ResidueSubset protocols::relax::AtomCoordinateCstMover::compute_residue_subset ( core::pose::Pose const &  pose) const
private
void protocols::relax::AtomCoordinateCstMover::cst_sd ( core::Real  sd)
inline
core::Real protocols::relax::AtomCoordinateCstMover::cst_sd ( ) const
inline

References cst_sd_.

Referenced by parse_my_tag().

void protocols::relax::AtomCoordinateCstMover::cst_sidechain ( bool  sidechains)
inline
bool protocols::relax::AtomCoordinateCstMover::cst_sidechain ( ) const
inline

References cst_sidechain_.

Referenced by parse_my_tag().

void protocols::relax::AtomCoordinateCstMover::cst_width ( core::Real  width)
inline
core::Real protocols::relax::AtomCoordinateCstMover::cst_width ( ) const
inline

References cst_width_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::relax::AtomCoordinateCstMover::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.

void protocols::relax::AtomCoordinateCstMover::func_groups ( bool  b)
inline
bool protocols::relax::AtomCoordinateCstMover::func_groups ( ) const
inline

References func_groups_.

Referenced by parse_my_tag().

core::scoring::constraints::ConstraintCOPs protocols::relax::AtomCoordinateCstMover::generate_constraints ( core::pose::Pose const &  pose)
private
core::id::SequenceMapping protocols::relax::AtomCoordinateCstMover::generate_seqmap ( core::pose::Pose const &  pose,
core::pose::Pose const &  constraint_target_pose 
) const
private
core::pose::PoseOP protocols::relax::AtomCoordinateCstMover::get_constraint_target_pose ( core::pose::Pose const &  pose) const
private
std::string protocols::relax::AtomCoordinateCstMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References protocols::relax::AtomCoordinateCstMoverCreator::mover_name().

std::string protocols::relax::AtomCoordinateCstMover::mover_name ( )
static
void protocols::relax::AtomCoordinateCstMover::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.

References ambiguous_hnq(), bounded(), core::io::pdb::build_pose_from_pdb_as_is(), cst_sd(), cst_sidechain(), cst_width(), func_groups(), core::pack::task::parse_task_operations(), refpose_, and set_task_segments().

void protocols::relax::AtomCoordinateCstMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::scoring::constraints::ConstraintCOPs protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups ( core::pose::Pose const &  pose)
private
void protocols::relax::AtomCoordinateCstMover::set_loop_segments ( protocols::loops::LoopsCOP  loops)
void protocols::relax::AtomCoordinateCstMover::set_refstruct ( core::pose::PoseCOP  ref)
virtual
void protocols::relax::AtomCoordinateCstMover::set_task_segments ( core::pack::task::TaskFactoryCOP  taskfactory)

References task_segments_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::relax::AtomCoordinateCstMover::amb_hnq_
private

When making sidechain constraints, should we allow for flipping HNQ residue sidechains?

Referenced by ambiguous_hnq(), and generate_constraints().

bool protocols::relax::AtomCoordinateCstMover::bounded_
private

Use bounded constraints instead of harmonic.

Referenced by bounded(), generate_constraints(), and set_constraints_on_func_groups().

core::Real protocols::relax::AtomCoordinateCstMover::cst_sd_
private

The strenght (standard deviation) of the constraints.

Referenced by cst_sd(), generate_constraints(), and set_constraints_on_func_groups().

bool protocols::relax::AtomCoordinateCstMover::cst_sidechain_
private

Also constrain sidechains?

Referenced by cst_sidechain(), and generate_constraints().

core::Real protocols::relax::AtomCoordinateCstMover::cst_width_
private

The width for bounded constraints.

Referenced by cst_width(), and generate_constraints().

bool protocols::relax::AtomCoordinateCstMover::func_groups_
private

If set to true then coordinate constraints are applied only to the functional groups of the side_chain.

Referenced by func_groups(), and generate_constraints().

protocols::loops::LoopsCOP protocols::relax::AtomCoordinateCstMover::loop_segments_
private

A loop definition of constrained segments.

Referenced by compute_residue_subset(), and set_loop_segments().

core::pose::PoseCOP protocols::relax::AtomCoordinateCstMover::refpose_
private

If set, the pose to make the constraints to.

Referenced by generate_constraints(), get_constraint_target_pose(), parse_my_tag(), and set_refstruct().

core::pack::task::TaskFactoryCOP protocols::relax::AtomCoordinateCstMover::task_segments_
private

A task definition of constrained segments.

Referenced by compute_residue_subset(), and set_task_segments().


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