Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::denovo::movers::RNA_HelixMover Class Reference

rotations and translations of helix along helical axis More...

#include <RNA_HelixMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_HelixMover:
Inheritance graph
[legend]

Public Member Functions

 RNA_HelixMover (utility::vector1< utility::vector1< core::Size > > const &helix_regions, core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler, bool const &move_first_rigid_body)
 Construct the mover object. More...
 
 ~RNA_HelixMover () override
 
void apply (core::pose::Pose &pose) override
 
void set_pose (core::pose::Pose const &pose)
 
void get_helix_ends ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_rot_magnitude (core::Real const &rot_mag)
 
void set_trans_magnitude (core::Real const &trans_mag)
 
- 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Member Functions

std::pair< core::Vector,
core::Vector
get_helical_axis_and_center (core::pose::Pose const &pose, core::Size const &region) const
 
core::Vector get_bp_center (core::pose::Pose const &pose, std::pair< core::Size, core::Size > const &bp_res) const
 
core::Vector get_bb_pos (core::pose::Pose const &pose, core::Size const &res) const
 
core::Vector get_backbone_centroid (core::pose::Pose const &pose, core::Size const &res) const
 

Private Attributes

utility::vector1
< utility::vector1< core::Size > > 
helix_regions_
 
utility::vector1
< utility::vector1< core::Size > > 
helix_regions_with_jumps_and_ends_
 
utility::vector1< core::Sizehelix_regions_jumps_
 
utility::vector1< core::Sizehelix_regions_jumps_final_
 
core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler_
 
utility::vector1< std::pair
< std::pair< core::Size,
core::Size >, std::pair
< core::Size, core::Size > > > 
helix_ends_
 
utility::vector1< std::pair
< std::pair< core::Size,
core::Size >, std::pair
< core::Size, core::Size > > > 
helix_ends_final_
 
core::kinematics::FoldTree pose_fold_tree_
 
bool pose_is_set_
 
bool move_first_rigid_body_
 
utility::vector1
< protocols::rigid::RigidBodySpinMoverOP
spin_movers_
 
utility::vector1
< protocols::rigid::RigidBodyTransMoverOP
trans_movers_
 
core::Real rot_mag_
 
core::Real trans_mag_
 

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
 
- 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 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

rotations and translations of helix along helical axis

Constructor & Destructor Documentation

protocols::rna::denovo::movers::RNA_HelixMover::RNA_HelixMover ( utility::vector1< utility::vector1< core::Size > > const &  helix_regions,
core::import_pose::RNA_BasePairHandlerCOP  rna_base_pair_handler,
bool const &  move_first_rigid_body 
)

Construct the mover object.

References get_helix_ends().

protocols::rna::denovo::movers::RNA_HelixMover::~RNA_HelixMover ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::movers::RNA_HelixMover::apply ( core::pose::Pose pose)
overridevirtual
core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid ( core::pose::Pose const &  pose,
core::Size const &  res 
) const
private
core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos ( core::pose::Pose const &  pose,
core::Size const &  res 
) const
private
core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_bp_center ( core::pose::Pose const &  pose,
std::pair< core::Size, core::Size > const &  bp_res 
) const
private

References get_bb_pos().

Referenced by get_helical_axis_and_center().

std::pair< core::Vector, core::Vector > protocols::rna::denovo::movers::RNA_HelixMover::get_helical_axis_and_center ( core::pose::Pose const &  pose,
core::Size const &  region 
) const
private

References get_bp_center(), and helix_ends_final_.

Referenced by apply().

void protocols::rna::denovo::movers::RNA_HelixMover::get_helix_ends ( )
std::string protocols::rna::denovo::movers::RNA_HelixMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::movers::RNA_HelixMover::set_pose ( core::pose::Pose const &  pose)
void protocols::rna::denovo::movers::RNA_HelixMover::set_rot_magnitude ( core::Real const &  rot_mag)
inline

References rot_mag_.

void protocols::rna::denovo::movers::RNA_HelixMover::set_trans_magnitude ( core::Real const &  trans_mag)
inline

References trans_mag_.

Member Data Documentation

utility::vector1< std::pair< std::pair< core::Size, core::Size>, std::pair< core::Size, core::Size > > > protocols::rna::denovo::movers::RNA_HelixMover::helix_ends_
private

Referenced by get_helix_ends(), and set_pose().

utility::vector1< std::pair< std::pair< core::Size, core::Size>, std::pair< core::Size, core::Size > > > protocols::rna::denovo::movers::RNA_HelixMover::helix_ends_final_
private
utility::vector1< utility::vector1< core::Size > > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_
private

Referenced by get_helix_ends(), and set_pose().

utility::vector1< core::Size > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_jumps_
private

Referenced by set_pose().

utility::vector1< core::Size > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_jumps_final_
private

Referenced by set_pose().

utility::vector1< utility::vector1< core::Size > > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_with_jumps_and_ends_
private

Referenced by apply(), and set_pose().

bool protocols::rna::denovo::movers::RNA_HelixMover::move_first_rigid_body_
private

Referenced by set_pose().

core::kinematics::FoldTree protocols::rna::denovo::movers::RNA_HelixMover::pose_fold_tree_
private

Referenced by apply(), and set_pose().

bool protocols::rna::denovo::movers::RNA_HelixMover::pose_is_set_
private

Referenced by apply(), and set_pose().

core::import_pose::RNA_BasePairHandlerCOP protocols::rna::denovo::movers::RNA_HelixMover::rna_base_pair_handler_
private

Referenced by get_helix_ends().

core::Real protocols::rna::denovo::movers::RNA_HelixMover::rot_mag_
private

Referenced by apply(), and set_rot_magnitude().

utility::vector1< protocols::rigid::RigidBodySpinMoverOP > protocols::rna::denovo::movers::RNA_HelixMover::spin_movers_
private

Referenced by apply(), and set_pose().

core::Real protocols::rna::denovo::movers::RNA_HelixMover::trans_mag_
private

Referenced by apply(), and set_trans_magnitude().

utility::vector1< protocols::rigid::RigidBodyTransMoverOP > protocols::rna::denovo::movers::RNA_HelixMover::trans_movers_
private

Referenced by apply(), and set_pose().


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