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protocols::rna::movers::RNAIdealizeMover Class Reference

Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization. More...

#include <RNAIdealizeMover.hh>

Inheritance diagram for protocols::rna::movers::RNAIdealizeMover:
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Public Member Functions

 RNAIdealizeMover ()
 
 RNAIdealizeMover (core::Size const iterations, bool const noise, bool const final_minimize, core::Real const ang_significance_threshold, bool const handle_suites)
 
 ~RNAIdealizeMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
core::Size get_iterations () const
 
void set_iterations (core::Size const iterations)
 
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 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

void perturb_pose (core::pose::Pose &pose) const
 Add Gaussian noise to the xyz coordinates of each atom. More...
 
void constrain_to_ideal (core::pose::Pose &pose, utility::vector1< core::Size > const &bad_suite_res) const
 
void add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, core::pose::Pose &pose) const
 
void add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::pose::Pose &pose) const
 

Private Attributes

core::pose::Pose ref_pose_
 
core::Size iterations_ = 100
 Number of iterations made (1/n idealization per iteration). More...
 
bool noise_ = false
 
bool final_minimize_ = false
 
core::Real ang_significance_threshold_ = 5
 
bool handle_suites_ = false
 

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

Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization.

Constructor & Destructor Documentation

protocols::rna::movers::RNAIdealizeMover::RNAIdealizeMover ( )
protocols::rna::movers::RNAIdealizeMover::RNAIdealizeMover ( core::Size const  iterations,
bool const  noise,
bool const  final_minimize,
core::Real const  ang_significance_threshold,
bool const  handle_suites 
)
inline
protocols::rna::movers::RNAIdealizeMover::~RNAIdealizeMover ( )
overridedefault

Member Function Documentation

void protocols::rna::movers::RNAIdealizeMover::add_bond_angle_constraint ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
core::id::AtomID const &  atom_id3,
core::pose::Pose pose 
) const
private
void protocols::rna::movers::RNAIdealizeMover::add_bond_constraint ( core::id::AtomID const &  atom_id1,
core::id::AtomID const &  atom_id2,
core::pose::Pose pose 
) const
private
void protocols::rna::movers::RNAIdealizeMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::rna::movers::RNAIdealizeMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::rna::movers::RNAIdealizeMover::constrain_to_ideal ( core::pose::Pose pose,
utility::vector1< core::Size > const &  bad_suite_res 
) const
private
protocols::moves::MoverOP protocols::rna::movers::RNAIdealizeMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::Size protocols::rna::movers::RNAIdealizeMover::get_iterations ( ) const
inline

References iterations_.

std::string protocols::rna::movers::RNAIdealizeMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::rna::movers::RNAIdealizeMover::mover_name ( )
static
void protocols::rna::movers::RNAIdealizeMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References ang_significance_threshold_, final_minimize_, iterations_, and noise_.

void protocols::rna::movers::RNAIdealizeMover::perturb_pose ( core::pose::Pose pose) const
private

Add Gaussian noise to the xyz coordinates of each atom.

Intentionally uses set_xyz because we don't want changes to propagate

References core::pose::Pose::conformation(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::scoring::rg, core::conformation::Conformation::set_xyz(), core::pose::Pose::size(), and core::conformation::Conformation::xyz().

Referenced by apply().

void protocols::rna::movers::RNAIdealizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rna::movers::RNAIdealizeMover::set_iterations ( core::Size const  iterations)
inline

References iterations_.

void protocols::rna::movers::RNAIdealizeMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::rna::movers::operator<<().

Member Data Documentation

core::Real protocols::rna::movers::RNAIdealizeMover::ang_significance_threshold_ = 5
private

Referenced by parse_my_tag().

bool protocols::rna::movers::RNAIdealizeMover::final_minimize_ = false
private

Referenced by apply(), and parse_my_tag().

bool protocols::rna::movers::RNAIdealizeMover::handle_suites_ = false
private
core::Size protocols::rna::movers::RNAIdealizeMover::iterations_ = 100
private

Number of iterations made (1/n idealization per iteration).

Referenced by apply(), get_iterations(), parse_my_tag(), and set_iterations().

bool protocols::rna::movers::RNAIdealizeMover::noise_ = false
private

Referenced by apply(), and parse_my_tag().

core::pose::Pose protocols::rna::movers::RNAIdealizeMover::ref_pose_
private

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