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protocols::swa::protein::StepWiseProteinLoopBridger Class Reference

#include <StepWiseProteinLoopBridger.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinLoopBridger:
Inheritance graph
Collaboration diagram for protocols::swa::protein::StepWiseProteinLoopBridger:
Collaboration graph

Public Member Functions

 StepWiseProteinLoopBridger (protocols::swa::StepWisePoseSampleGeneratorOP sample_generator, protocols::swa::StepWiseJobParametersOP job_parameters)
 ~StepWiseProteinLoopBridger ()
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< core::Real >
> const & 
main_chain_torsion_set_lists () const
< core::id::TorsionID > const & 
which_torsions () const
- 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

void setup_torsions (core::pose::Pose const &pose)
void figure_out_loop (core::pose::Pose const &pose)
void output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) const
void fill_chainTORS_info (core::pose::Pose const &pose, utility::vector1< utility::vector1< core::Real > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len, core::Size const &start_res_, core::Size const &end_res_) const
void KIC_loop_close_with_perturbations (core::pose::Pose &pose)
void KIC_loop_close (core::pose::Pose &pose)
void grab_main_chain_torsion_set_list (core::pose::Pose const &pose)
void save_phi_psi_offsets (core::pose::Pose const &pose)
void fix_phi_psi_offsets (core::pose::Pose &pose) const
void sample_omega_recursively (core::pose::Pose &pose, int const offset, utility::vector1< utility::vector1< core::Real > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len, utility::vector1< core::Size > const &pivots, utility::vector1< core::Size > const &order)
void initialize_is_fixed_res (utility::vector1< core::Size > const &fixed_res, std::string const &working_sequence)

Private Attributes

protocols::swa::StepWisePoseSampleGeneratorOP sample_generator_
utility::vector1< Sizeworking_bridge_res_
utility::vector1< boolis_pre_proline_
utility::vector1< boolis_fixed_res_
loops::Loop loop_
< core::id::TorsionID
< utility::vector1< core::Real > > 
core::scoring::Ramachandran ramachandran_
int const num_perturb_steps_
core::Real const perturb_torsion_
core::Real const idl_CA_C_N_
core::Real const idl_C_N_CA_
core::Real const idl_C_N_
core::Real const OMEGA_MEAN_
bool const use_icoor_geometry_
bool const verbose_
utility::vector1< core::Realphi_offsets_
utility::vector1< core::Realpsi_offsets_
Size start_res_
Size middle_res_
Size end_res_
Size middle_offset_
Size seg_len_
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 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::StepWiseProteinLoopBridger::StepWiseProteinLoopBridger ( protocols::swa::StepWisePoseSampleGeneratorOP  sample_generator,
protocols::swa::StepWiseJobParametersOP  job_parameters 
protocols::swa::protein::StepWiseProteinLoopBridger::~StepWiseProteinLoopBridger ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinLoopBridger::apply ( core::pose::Pose pose_to_visualize)
void protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop ( core::pose::Pose const &  pose)
void protocols::swa::protein::StepWiseProteinLoopBridger::fill_chainTORS_info ( core::pose::Pose const &  pose,
utility::vector1< utility::vector1< core::Real > > &  atoms,
utility::vector1< core::Real > &  dt_ang,
utility::vector1< core::Real > &  db_ang,
utility::vector1< core::Real > &  db_len,
core::Size const &  start_res_,
core::Size const &  end_res_ 
) const
void protocols::swa::protein::StepWiseProteinLoopBridger::fix_phi_psi_offsets ( core::pose::Pose pose) const
std::string protocols::swa::protein::StepWiseProteinLoopBridger::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinLoopBridger::grab_main_chain_torsion_set_list ( core::pose::Pose const &  pose)
void protocols::swa::protein::StepWiseProteinLoopBridger::initialize_is_fixed_res ( utility::vector1< core::Size > const &  fixed_res,
std::string const &  working_sequence 

References is_fixed_res_.

Referenced by StepWiseProteinLoopBridger().

void protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close ( core::pose::Pose pose)
void protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close_with_perturbations ( core::pose::Pose pose)
utility::vector1< utility::vector1< core::Real > > const & protocols::swa::protein::StepWiseProteinLoopBridger::main_chain_torsion_set_lists ( ) const
void protocols::swa::protein::StepWiseProteinLoopBridger::output_chainTORS ( utility::vector1< core::Real > const &  dt_ang,
utility::vector1< core::Real > const &  db_ang,
utility::vector1< core::Real > const &  db_len 
) const
void protocols::swa::protein::StepWiseProteinLoopBridger::sample_omega_recursively ( core::pose::Pose pose,
int const  offset,
utility::vector1< utility::vector1< core::Real > > &  atoms,
utility::vector1< core::Real > &  dt_ang,
utility::vector1< core::Real > &  db_ang,
utility::vector1< core::Real > &  db_len,
utility::vector1< core::Size > const &  pivots,
utility::vector1< core::Size > const &  order 
void protocols::swa::protein::StepWiseProteinLoopBridger::save_phi_psi_offsets ( core::pose::Pose const &  pose)
void protocols::swa::protein::StepWiseProteinLoopBridger::setup_torsions ( core::pose::Pose const &  pose)
utility::vector1< core::id::TorsionID > const & protocols::swa::protein::StepWiseProteinLoopBridger::which_torsions ( ) const

References which_torsions_.

Member Data Documentation

Size protocols::swa::protein::StepWiseProteinLoopBridger::end_res_
core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_C_N_

Referenced by KIC_loop_close().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_C_N_CA_

Referenced by KIC_loop_close().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_CA_C_N_

Referenced by KIC_loop_close().

utility::vector1< bool > protocols::swa::protein::StepWiseProteinLoopBridger::is_fixed_res_
utility::vector1< bool > protocols::swa::protein::StepWiseProteinLoopBridger::is_pre_proline_
loops::Loop protocols::swa::protein::StepWiseProteinLoopBridger::loop_

Referenced by figure_out_loop(), and KIC_loop_close().

utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinLoopBridger::main_chain_torsion_sets_for_moving_residues_
Size protocols::swa::protein::StepWiseProteinLoopBridger::middle_offset_

Referenced by KIC_loop_close().

Size protocols::swa::protein::StepWiseProteinLoopBridger::middle_res_

Referenced by KIC_loop_close().

int const protocols::swa::protein::StepWiseProteinLoopBridger::num_perturb_steps_
core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::OMEGA_MEAN_
core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::perturb_torsion_
utility::vector1< core::Real > protocols::swa::protein::StepWiseProteinLoopBridger::phi_offsets_
Size protocols::swa::protein::StepWiseProteinLoopBridger::pose_count_
utility::vector1< core::Real > protocols::swa::protein::StepWiseProteinLoopBridger::psi_offsets_
core::scoring::Ramachandran protocols::swa::protein::StepWiseProteinLoopBridger::ramachandran_
protocols::swa::StepWisePoseSampleGeneratorOP protocols::swa::protein::StepWiseProteinLoopBridger::sample_generator_

Referenced by apply().

Size protocols::swa::protein::StepWiseProteinLoopBridger::seg_len_
Size protocols::swa::protein::StepWiseProteinLoopBridger::start_res_
bool const protocols::swa::protein::StepWiseProteinLoopBridger::use_icoor_geometry_

Referenced by KIC_loop_close().

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

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