Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler Class Reference

#include <StepWiseRNA_ConnectionSampler.hh>

Public Member Functions

 StepWiseRNA_ConnectionSampler (stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters_)
 
 ~StepWiseRNA_ConnectionSampler ()
 
virtual void apply (pose::Pose &pose_to_visualize)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_silent_file (std::string const &setting)
 
void set_scorefxn (scoring::ScoreFunctionCOP const &scorefxn)
 
void set_pose_list (utility::vector1< pose::PoseOP > &pose_list)
 
utility::vector1< pose::PoseOP > & get_pose_list ()
 
void set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
 
void add_residue_alternative_set (sampler::copy_dofs::ResidueAlternativeSet const &residue_alternative_set)
 
void set_options (options::StepWiseModelerOptionsCOP options)
 
- Public Member Functions inherited from protocols::moves::MoverForPoseList
 MoverForPoseList ()
 
 ~MoverForPoseList ()
 
virtual void apply (utility::vector1< core::pose::PoseOP > &pose_list)
 
virtual void apply (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)
 
- 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
 
void set_type (std::string const &setting)
 
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
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

 StepWiseRNA_ConnectionSampler ()
 
void figure_out_reference_res (pose::Pose const &pose)
 
void figure_out_reference_res_with_rigid_body_rotamer (pose::Pose const &pose)
 
bool initialize_poses_and_checkers (pose::Pose &pose)
 
Size get_max_ntries ()
 
Size get_num_pose_kept ()
 
void reinstantiate_backbone_and_add_constraint_at_moving_res (pose::Pose &pose, Size const &five_prime_chain_break_res)
 
void initialize_euler_angle_grid_parameters ()
 
void initialize_xyz_grid_parameters ()
 
void initialize_sampler ()
 
void initialize_full_rigid_body_sampler ()
 
sampler::StepWiseSamplerBaseOP get_full_bond_sampler ()
 
sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP get_rsd_alternatives_rotamer ()
 
void initialize_rigid_body_rotamer ()
 
void initialize_screeners (pose::Pose &pose)
 
void initialize_residue_level_screeners (pose::Pose &pose)
 
void initialize_pose_level_screeners (pose::Pose &pose)
 
void update_base_bin_map (rigid_body::BaseBin const &base_bin)
 
void initialize_moving_residue_pose_list (pose::Pose const &pose)
 
Size which_residue_alternative_set_is_moving_residue () const
 
utility::vector1
< core::conformation::ResidueOP
get_moving_rsd_list () const
 
Size truly_floating_base ()
 
void check_working_parameters (pose::Pose const &pose)
 
bool presample_virtual_sugars (pose::Pose &pose)
 

Private Attributes

Size const moving_res_
 
Size reference_res_
 
utility::vector1< Sizemoving_partition_res_
 
utility::vector1< pose::PoseOPpose_list_
 
scoring::ScoreFunctionCOP scorefxn_
 
sampler::rigid_body::RigidBodyStepWiseSamplerOP rigid_body_rotamer_
 
protocols::stepwise::sampler::StepWiseSamplerBaseOP sampler_
 
utility::vector1
< screener::StepWiseScreenerOP
screeners_
 
screener::TagDefinitionOP tag_definition_
 
StepWiseRNA_CountStruct count_data_
 
std::string silent_file_
 
bool kic_modeler_
 
bool rebuild_bulge_mode_
 
options::StepWiseModelerOptionsCOP options_
 
utility::vector1
< sampler::copy_dofs::ResidueAlternativeSet
residue_alternative_sets_
 
checker::RNA_AtrRepCheckerOP atr_rep_checker_
 
checker::RNA_AtrRepCheckerOP virt_sugar_atr_rep_checker_
 
checker::RNA_VDW_BinCheckerOP VDW_bin_checker_
 
checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
 
utility::vector1< Sizefive_prime_chain_breaks_
 
utility::vector1< Sizethree_prime_chain_breaks_
 
utility::vector1< Sizechain_break_gap_sizes_
 
utility::vector1
< checker::RNA_ChainClosableGeometryCheckerOP > 
chain_closable_geometry_checkers_
 
utility::vector1< Sizecutpoints_closed_
 
utility::vector1
< checker::RNA_ChainClosureCheckerOP > 
chain_closure_checkers_
 
checker::RNA_BaseCentroidCheckerOP base_centroid_checker_
 
pose::PoseOP screening_pose_
 
pose::PoseOP virt_sugar_screening_pose_
 
StepWiseRNA_PoseSelectionOP pose_selection_
 
o2prime::O2PrimePackerOP o2prime_packer_
 
phosphate::MultiPhosphateSamplerOP phosphate_sampler_
 
kinematics::Stub moving_res_base_stub_
 
rigid_body::BaseBinMap base_bin_map_
 
Real max_distance_squared_
 
bool rigid_body_modeler_
 
bool try_sugar_instantiation_
 
Distance o2prime_instantiation_distance_cutoff_
 
std::string const extra_tag_
 
bool const virt_sugar_atr_rep_screen_
 
bool const build_pose_from_scratch_
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::StepWiseRNA_ConnectionSampler ( )
private
protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::StepWiseRNA_ConnectionSampler ( stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_)
protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::~StepWiseRNA_ConnectionSampler ( )

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::add_residue_alternative_set ( sampler::copy_dofs::ResidueAlternativeSet const &  residue_alternative_set)
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::apply ( pose::Pose pose_to_visualize)
virtual
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::check_working_parameters ( pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::figure_out_reference_res ( pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::figure_out_reference_res_with_rigid_body_rotamer ( pose::Pose const &  pose)
private
sampler::StepWiseSamplerBaseOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_full_bond_sampler ( )
private
Size protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_max_ntries ( )
private
utility::vector1< core::conformation::ResidueOP > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_moving_rsd_list ( ) const
private
std::string protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Size protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_num_pose_kept ( )
private
utility::vector1< PoseOP > & protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_pose_list ( )

References pose_list_.

sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::get_rsd_alternatives_rotamer ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_euler_angle_grid_parameters ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_full_rigid_body_sampler ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_moving_residue_pose_list ( pose::Pose const &  pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_pose_level_screeners ( pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_residue_level_screeners ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_rigid_body_rotamer ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_sampler ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_screeners ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_xyz_grid_parameters ( )
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::presample_virtual_sugars ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::reinstantiate_backbone_and_add_constraint_at_moving_res ( pose::Pose pose,
Size const &  five_prime_chain_break_res 
)
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::set_options ( options::StepWiseModelerOptionsCOP  options)

References options_.

void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::set_pose_list ( utility::vector1< pose::PoseOP > &  pose_list)

References pose_list_.

void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::set_scorefxn ( scoring::ScoreFunctionCOP const &  scorefxn)

References scorefxn_.

void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::set_silent_file ( std::string const &  setting)
inline
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker)
Size protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::truly_floating_base ( )
private
void protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::update_base_bin_map ( rigid_body::BaseBin const &  base_bin)
private
Size protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::which_residue_alternative_set_is_moving_residue ( ) const
private

Member Data Documentation

checker::RNA_AtrRepCheckerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::atr_rep_checker_
private
rigid_body::BaseBinMap protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::base_bin_map_
private
checker::RNA_BaseCentroidCheckerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::base_centroid_checker_
private
bool const protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::build_pose_from_scratch_
private

Referenced by apply(), and get_full_bond_sampler().

utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::chain_break_gap_sizes_
private
utility::vector1< checker::RNA_ChainClosableGeometryCheckerOP > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::chain_closable_geometry_checkers_
private
utility::vector1< checker::RNA_ChainClosureCheckerOP > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::chain_closure_checkers_
private
StepWiseRNA_CountStruct protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::count_data_
private
utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::cutpoints_closed_
private
std::string const protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::extra_tag_
private
utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::five_prime_chain_breaks_
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::kic_modeler_
private
Real protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::max_distance_squared_
private
utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::moving_partition_res_
private
Size const protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::moving_res_
private
kinematics::Stub protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::moving_res_base_stub_
private
Distance protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::o2prime_instantiation_distance_cutoff_
private
o2prime::O2PrimePackerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::o2prime_packer_
private
options::StepWiseModelerOptionsCOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::options_
private
phosphate::MultiPhosphateSamplerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::phosphate_sampler_
private
utility::vector1< pose::PoseOP > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::pose_list_
private
StepWiseRNA_PoseSelectionOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::pose_selection_
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::rebuild_bulge_mode_
private
Size protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::reference_res_
private
utility::vector1< sampler::copy_dofs::ResidueAlternativeSet > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::residue_alternative_sets_
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::rigid_body_modeler_
private
sampler::rigid_body::RigidBodyStepWiseSamplerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::rigid_body_rotamer_
private
protocols::stepwise::sampler::StepWiseSamplerBaseOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::sampler_
private
scoring::ScoreFunctionCOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::scorefxn_
private
utility::vector1< screener::StepWiseScreenerOP > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::screeners_
private
pose::PoseOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::screening_pose_
private
std::string protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::silent_file_
private
screener::TagDefinitionOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::tag_definition_
private
utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::three_prime_chain_breaks_
private
bool protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::try_sugar_instantiation_
private
checker::RNA_VDW_BinCheckerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::user_input_VDW_bin_checker_
private
checker::RNA_VDW_BinCheckerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::VDW_bin_checker_
private
checker::RNA_AtrRepCheckerOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::virt_sugar_atr_rep_checker_
private
bool const protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::virt_sugar_atr_rep_screen_
private
pose::PoseOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::virt_sugar_screening_pose_
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::working_parameters_
private

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