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protocols::swa::protein::StepWiseProteinCCD_Closer Class Reference

#include <StepWiseProteinCCD_Closer.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinCCD_Closer:
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Collaboration diagram for protocols::swa::protein::StepWiseProteinCCD_Closer:
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Public Member Functions

 StepWiseProteinCCD_Closer (protocols::swa::StepWisePoseSampleGeneratorOP sample_generator, protocols::swa::StepWiseJobParametersOP job_parameters)
 
 ~StepWiseProteinCCD_Closer ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
utility::vector1
< utility::vector1< core::Real >
> const & 
main_chain_torsion_set_lists () const
 
utility::vector1
< core::id::TorsionID > const & 
which_torsions () const
 
void set_ccd_close_res (Size const value)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

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 grab_main_chain_torsion_set_list (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)
 

Private Attributes

protocols::swa::StepWisePoseSampleGeneratorOP sample_generator_
 
utility::vector1< Sizeworking_bridge_res_
 
utility::vector1< Sizemoving_residues_
 
utility::vector1< boolis_pre_proline_
 
Size ccd_close_res_
 
loops::Loop loop_
 
core::kinematics::MoveMap mm_
 
utility::vector1
< core::id::TorsionID
which_torsions_
 
utility::vector1
< utility::vector1< core::Real > > 
main_chain_torsion_sets_for_moving_residues_
 
utility::vector1< core::Realmain_chain_torsion_set_for_moving_residues_save_
 
bool const verbose_
 
Size pose_count_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::swa::protein::StepWiseProteinCCD_Closer::StepWiseProteinCCD_Closer ( protocols::swa::StepWisePoseSampleGeneratorOP  sample_generator,
protocols::swa::StepWiseJobParametersOP  job_parameters 
)

References working_bridge_res_.

protocols::swa::protein::StepWiseProteinCCD_Closer::~StepWiseProteinCCD_Closer ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinCCD_Closer::apply ( core::pose::Pose pose_to_visualize)
virtual
bool protocols::swa::protein::StepWiseProteinCCD_Closer::CCD_loop_close ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively ( core::pose::Pose pose,
int const  offset 
)
private
void protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop ( core::pose::Pose const &  pose)
private
std::string protocols::swa::protein::StepWiseProteinCCD_Closer::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinCCD_Closer::grab_main_chain_torsion_set_list ( core::pose::Pose const &  pose)
private
utility::vector1< utility::vector1< core::Real > > const & protocols::swa::protein::StepWiseProteinCCD_Closer::main_chain_torsion_set_lists ( ) const
void protocols::swa::protein::StepWiseProteinCCD_Closer::restore_phi_psi_omega_over_loop_residues ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinCCD_Closer::restore_phi_psi_over_loop_residues ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinCCD_Closer::save_phi_psi_omega_over_loop_residues ( core::pose::Pose const &  pose)
private
void protocols::swa::protein::StepWiseProteinCCD_Closer::set_ccd_close_res ( Size const  value)
inline

References ccd_close_res_.

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

References which_torsions_.

Member Data Documentation

Size protocols::swa::protein::StepWiseProteinCCD_Closer::ccd_close_res_
private
utility::vector1< bool > protocols::swa::protein::StepWiseProteinCCD_Closer::is_pre_proline_
private
loops::Loop protocols::swa::protein::StepWiseProteinCCD_Closer::loop_
private
utility::vector1< core::Real > protocols::swa::protein::StepWiseProteinCCD_Closer::main_chain_torsion_set_for_moving_residues_save_
private
utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinCCD_Closer::main_chain_torsion_sets_for_moving_residues_
private
core::kinematics::MoveMap protocols::swa::protein::StepWiseProteinCCD_Closer::mm_
private

Referenced by CCD_loop_close(), and figure_out_loop().

utility::vector1< Size > protocols::swa::protein::StepWiseProteinCCD_Closer::moving_residues_
private

Referenced by setup_torsions().

Size protocols::swa::protein::StepWiseProteinCCD_Closer::pose_count_
private

Referenced by apply(), and CCD_loop_close().

protocols::swa::StepWisePoseSampleGeneratorOP protocols::swa::protein::StepWiseProteinCCD_Closer::sample_generator_
private

Referenced by apply().

bool const protocols::swa::protein::StepWiseProteinCCD_Closer::verbose_
private
utility::vector1< core::id::TorsionID > protocols::swa::protein::StepWiseProteinCCD_Closer::which_torsions_
private
utility::vector1< Size > protocols::swa::protein::StepWiseProteinCCD_Closer::working_bridge_res_
private

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