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protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer Class Reference

#include <StepWiseProteinCCD_Closer.hh>

Inheritance diagram for protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer:
Inheritance graph
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Public Member Functions

 StepWiseProteinCCD_Closer (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
 ~StepWiseProteinCCD_Closer () override
 
void init (core::pose::Pose &pose)
 
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
 
void get_closure_solution (core::pose::Pose &pose_to_visualize)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
utility::vector1
< core::id::TorsionID > const & 
which_torsions () const
 
void set_ccd_close_res (core::Size const value)
 
void set_working_moving_res_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Realgrab_main_chain_torsion_set_list (core::pose::Pose const &pose)
 
utility::vector1< core::Real >
const & 
main_chain_torsion_set () const
 
utility::vector1< core::Real >
const & 
main_chain_torsion_set_save () const
 
core::Size ntries () const
 
bool closed_loop () 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
 
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

bool CCD_loop_close (core::pose::Pose &pose)
 
void CCD_loop_close_sample_omega_recursively (core::pose::Pose &pose, int const offset)
 
void setup_torsions (core::pose::Pose const &pose)
 
void figure_out_loop (core::pose::Pose const &pose)
 
void figure_out_movemap (core::pose::Pose const &pose)
 
void save_phi_psi_omega_over_loop_residues (core::pose::Pose const &pose)
 
void restore_phi_psi_omega_over_loop_residues (core::pose::Pose &pose)
 
void restore_phi_psi_over_loop_residues (core::pose::Pose &pose)
 
void fix_jump_atoms_at_loop_boundaries (core::pose::Pose &pose)
 
core::Size check_for_unique_cutpoint_flanked_by_bridge_res (core::pose::Pose const &pose)
 
core::Size check_for_unique_cutpoint (core::pose::Pose const &pose)
 

Private Attributes

loops::loop_closure::ccd::CCDLoopClosureMoverOP ccd_loop_closure_mover_
 
utility::vector1< core::Sizeworking_bridge_res_
 
utility::vector1< core::Sizemoving_residues_
 
utility::vector1< boolis_pre_proline_
 
core::Size ccd_close_res_
 
loops::Loop loop_
 
core::kinematics::MoveMapOP mm_
 
utility::vector1
< core::id::TorsionID
which_torsions_
 
utility::vector1< core::Realmain_chain_torsion_set_
 
utility::vector1< core::Realmain_chain_torsion_set_save_
 
bool closed_loop_
 
core::Size ntries_
 

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...
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::StepWiseProteinCCD_Closer ( protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP  working_parameters)
protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::~StepWiseProteinCCD_Closer ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::apply ( core::pose::Pose pose_to_visualize)
overridevirtual
bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively ( core::pose::Pose pose,
int const  offset 
)
private
Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint ( core::pose::Pose const &  pose)
private
Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint_flanked_by_bridge_res ( core::pose::Pose const &  pose)
private
bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::closed_loop ( ) const
inline

References closed_loop_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_loop ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::get_closure_solution ( core::pose::Pose pose_to_visualize)
std::string protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::grab_main_chain_torsion_set_list ( core::pose::Pose const &  pose)
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::init ( core::pose::Pose pose)
utility::vector1< core::Real > const & protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set ( ) const

References main_chain_torsion_set_.

Referenced by apply().

utility::vector1< core::Real > const & protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set_save ( ) const
core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ntries ( ) const
inline

References ntries_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::restore_phi_psi_omega_over_loop_residues ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::restore_phi_psi_over_loop_residues ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::save_phi_psi_omega_over_loop_residues ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::set_ccd_close_res ( core::Size const  value)
inline

References ccd_close_res_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::set_working_moving_res_list ( utility::vector1< core::Size > const &  setting)
inline

References moving_residues_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::setup_torsions ( core::pose::Pose const &  pose)
private
utility::vector1< core::id::TorsionID > const & protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::which_torsions ( ) const

References which_torsions_.

Referenced by apply().

Member Data Documentation

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ccd_close_res_
private
loops::loop_closure::ccd::CCDLoopClosureMoverOP protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ccd_loop_closure_mover_
private

Referenced by CCD_loop_close().

bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::closed_loop_
private
utility::vector1< bool > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::is_pre_proline_
private
loops::Loop protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::loop_
private
utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set_
private
utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set_save_
private
core::kinematics::MoveMapOP protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::mm_
private
utility::vector1< core::Size > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::moving_residues_
private
core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ntries_
private

Referenced by CCD_loop_close(), init(), and ntries().

utility::vector1< core::id::TorsionID > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::which_torsions_
private
utility::vector1< core::Size > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::working_bridge_res_
private

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