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protocols::stepwise::modeler::StepWiseConnectionSampler Class Reference

#include <StepWiseConnectionSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::StepWiseConnectionSampler:
Inheritance graph
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Public Member Functions

 StepWiseConnectionSampler (working_parameters::StepWiseWorkingParametersCOP &working_parameters_)
 
 ~StepWiseConnectionSampler () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP const &scorefxn)
 
void set_pose_list (utility::vector1< core::pose::PoseOP > &pose_list)
 
utility::vector1
< core::pose::PoseOP > & 
get_pose_list ()
 
void set_user_input_VDW_bin_checker (rna::checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
 
void set_master_packer (packer::StepWiseMasterPackerOP master_packer)
 
void add_residue_alternative_set (sampler::copy_dofs::ResidueAlternativeSet const &residue_alternative_set)
 
void set_options (options::StepWiseModelerOptionsCOP options)
 
void set_input_streams (utility::vector1< protein::InputStreamWithResidueInfoOP > const &input_streams)
 
- Public Member Functions inherited from protocols::moves::MoverForPoseList
 MoverForPoseList ()
 
 ~MoverForPoseList () override
 
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 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

 StepWiseConnectionSampler ()
 
void figure_out_reference_res (core::pose::Pose const &pose)
 
void figure_out_reference_res_with_rigid_body_rotamer (core::pose::Pose const &pose)
 
void initialize_useful_info (core::pose::Pose const &pose)
 
bool initialize_pose (core::pose::Pose &pose)
 
void initialize_checkers (core::pose::Pose const &pose)
 
core::Size get_max_ntries ()
 
core::Size get_num_pose_kept ()
 
void initialize_euler_angle_grid_parameters ()
 
void initialize_xyz_grid_parameters ()
 
bool initialize_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerSizedOP initialize_protein_bond_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerOP initialize_rna_bond_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerOP initialize_tna_bond_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerOP initialize_ligand_bond_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerOP initialize_generic_polymer_bond_sampler (core::pose::Pose const &pose)
 
sampler::StepWiseSamplerOP initialize_carbohydrate_bond_sampler (core::pose::Pose const &pose)
 
void initialize_full_rigid_body_sampler ()
 
sampler::StepWiseSamplerOP get_full_bond_sampler ()
 
sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP get_rsd_alternatives_rotamer ()
 
void initialize_rigid_body_rotamer ()
 
void initialize_screeners (core::pose::Pose &pose)
 
void initialize_residue_level_screeners (core::pose::Pose &pose)
 
void initialize_pose_level_screeners (core::pose::Pose &pose)
 
void initialize_moving_residue_pose_list (core::pose::Pose const &pose)
 
void initialize_protein_packer (core::pose::Pose &pose)
 
core::Size which_residue_alternative_set_is_moving_residue () const
 
utility::vector1
< core::conformation::ResidueOP
get_moving_rsd_list () const
 
core::Size truly_floating_base ()
 
void check_working_parameters (core::pose::Pose const &pose)
 
bool presample_virtual_sugars (core::pose::Pose &pose)
 

Private Attributes

working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
utility::vector1< core::Size >
const 
moving_res_list_
 
core::Size const moving_res_
 
utility::vector1< core::Size >
const 
moving_partition_res_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
options::StepWiseModelerOptionsCOP options_
 
utility::vector1
< core::pose::PoseOP
pose_list_
 
bool rigid_body_modeler_
 
bool moving_ligand_ = false
 
core::Size reference_res_
 
bool kic_modeler_
 
bool protein_connection_
 
sampler::rigid_body::RigidBodyStepWiseSamplerOP rigid_body_rotamer_
 
sampler::StepWiseSamplerOP sampler_
 
utility::vector1
< screener::StepWiseScreenerOP
screeners_
 
screener::TagDefinitionOP tag_definition_
 
utility::vector1
< sampler::copy_dofs::ResidueAlternativeSet
residue_alternative_sets_
 
packer::StepWiseMasterPackerOP master_packer_
 
core::pose::PoseOP protein_atr_rep_screening_pose_
 
rna::checker::RNA_AtrRepCheckerOP rna_atr_rep_checker_
 
rna::checker::RNA_AtrRepCheckerOP rna_virt_sugar_atr_rep_checker_
 
rna::checker::RNA_VDW_BinCheckerOP VDW_bin_checker_
 
rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
 
utility::vector1< core::Sizeprotein_cutpoints_closed_
 
utility::vector1
< core::pose::PoseOP
protein_ccd_poses_
 
utility::vector1
< protein::loop_close::StepWiseProteinCCD_CloserOP
protein_ccd_closers_
 
utility::vector1< core::Sizerna_five_prime_chain_breaks_
 
utility::vector1< core::Sizerna_three_prime_chain_breaks_
 
utility::vector1< core::Sizerna_chain_break_gap_sizes_
 
utility::vector1
< rna::checker::RNA_ChainClosableGeometryCheckerOP
rna_chain_closable_geometry_checkers_
 
utility::vector1< core::Sizerna_cutpoints_closed_
 
utility::vector1
< rna::checker::RNA_ChainClosureCheckerOP
rna_chain_closure_checkers_
 
rna::checker::RNA_BaseCentroidCheckerOP base_centroid_checker_
 
core::pose::PoseOP screening_pose_
 
core::pose::PoseOP virt_sugar_screening_pose_
 
align::StepWiseClustererOP clusterer_
 
core::kinematics::Stub moving_res_base_stub_
 
core::Real max_distance_squared_
 
utility::vector1
< protein::InputStreamWithResidueInfoOP
input_streams_
 
bool const virt_sugar_atr_rep_screen_
 
rna::StepWiseRNA_CountStruct count_data_
 

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::StepWiseConnectionSampler::StepWiseConnectionSampler ( )
private
protocols::stepwise::modeler::StepWiseConnectionSampler::StepWiseConnectionSampler ( working_parameters::StepWiseWorkingParametersCOP working_parameters_)
protocols::stepwise::modeler::StepWiseConnectionSampler::~StepWiseConnectionSampler ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::StepWiseConnectionSampler::add_residue_alternative_set ( sampler::copy_dofs::ResidueAlternativeSet const &  residue_alternative_set)
void protocols::stepwise::modeler::StepWiseConnectionSampler::apply ( core::pose::Pose )
overridevirtual
void protocols::stepwise::modeler::StepWiseConnectionSampler::check_working_parameters ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::figure_out_reference_res ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::figure_out_reference_res_with_rigid_body_rotamer ( core::pose::Pose const &  pose)
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::get_full_bond_sampler ( )
private
Size protocols::stepwise::modeler::StepWiseConnectionSampler::get_max_ntries ( )
private
utility::vector1< core::conformation::ResidueOP > protocols::stepwise::modeler::StepWiseConnectionSampler::get_moving_rsd_list ( ) const
private
std::string protocols::stepwise::modeler::StepWiseConnectionSampler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Size protocols::stepwise::modeler::StepWiseConnectionSampler::get_num_pose_kept ( )
private
utility::vector1< PoseOP > & protocols::stepwise::modeler::StepWiseConnectionSampler::get_pose_list ( )
sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP protocols::stepwise::modeler::StepWiseConnectionSampler::get_rsd_alternatives_rotamer ( )
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_carbohydrate_bond_sampler ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_euler_angle_grid_parameters ( )
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_full_rigid_body_sampler ( )
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler ( core::pose::Pose const &  pose)
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_ligand_bond_sampler ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_moving_residue_pose_list ( core::pose::Pose const &  pose)
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners ( core::pose::Pose pose)
private
StepWiseSamplerSizedOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_sampler ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_packer ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_rigid_body_rotamer ( )
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_rna_bond_sampler ( core::pose::Pose const &  pose)
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_screeners ( core::pose::Pose pose)
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_tna_bond_sampler ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_xyz_grid_parameters ( )
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::presample_virtual_sugars ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseConnectionSampler::set_input_streams ( utility::vector1< protein::InputStreamWithResidueInfoOP > const &  input_streams)
inline
void protocols::stepwise::modeler::StepWiseConnectionSampler::set_master_packer ( packer::StepWiseMasterPackerOP  master_packer)
inline
void protocols::stepwise::modeler::StepWiseConnectionSampler::set_options ( options::StepWiseModelerOptionsCOP  options)
void protocols::stepwise::modeler::StepWiseConnectionSampler::set_pose_list ( utility::vector1< core::pose::PoseOP > &  pose_list)

References pose_list_.

void protocols::stepwise::modeler::StepWiseConnectionSampler::set_scorefxn ( core::scoring::ScoreFunctionCOP const &  scorefxn)
inline
void protocols::stepwise::modeler::StepWiseConnectionSampler::set_user_input_VDW_bin_checker ( rna::checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker)
Size protocols::stepwise::modeler::StepWiseConnectionSampler::truly_floating_base ( )
private
Size protocols::stepwise::modeler::StepWiseConnectionSampler::which_residue_alternative_set_is_moving_residue ( ) const
private

Member Data Documentation

rna::checker::RNA_BaseCentroidCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::base_centroid_checker_
private
align:: StepWiseClustererOP protocols::stepwise::modeler::StepWiseConnectionSampler::clusterer_
private
rna::StepWiseRNA_CountStruct protocols::stepwise::modeler::StepWiseConnectionSampler::count_data_
private
utility::vector1< protein::InputStreamWithResidueInfoOP > protocols::stepwise::modeler::StepWiseConnectionSampler::input_streams_
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::kic_modeler_
private
packer::StepWiseMasterPackerOP protocols::stepwise::modeler::StepWiseConnectionSampler::master_packer_
private
core::Real protocols::stepwise::modeler::StepWiseConnectionSampler::max_distance_squared_
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::moving_ligand_ = false
private
utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_partition_res_
private
core::Size const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_
private
core::kinematics::Stub protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_base_stub_
private
utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_list_
private
options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseConnectionSampler::options_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseConnectionSampler::pose_list_
private
core::pose::PoseOP protocols::stepwise::modeler::StepWiseConnectionSampler::protein_atr_rep_screening_pose_
private
utility::vector1< protein::loop_close::StepWiseProteinCCD_CloserOP > protocols::stepwise::modeler::StepWiseConnectionSampler::protein_ccd_closers_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseConnectionSampler::protein_ccd_poses_
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::protein_connection_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::protein_cutpoints_closed_
private
core::Size protocols::stepwise::modeler::StepWiseConnectionSampler::reference_res_
private
utility::vector1< sampler::copy_dofs::ResidueAlternativeSet > protocols::stepwise::modeler::StepWiseConnectionSampler::residue_alternative_sets_
private
bool protocols::stepwise::modeler::StepWiseConnectionSampler::rigid_body_modeler_
private
sampler::rigid_body::RigidBodyStepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rigid_body_rotamer_
private
rna::checker::RNA_AtrRepCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rna_atr_rep_checker_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_break_gap_sizes_
private
utility::vector1< rna::checker::RNA_ChainClosableGeometryCheckerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_closable_geometry_checkers_
private
utility::vector1< rna::checker::RNA_ChainClosureCheckerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_closure_checkers_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_cutpoints_closed_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_five_prime_chain_breaks_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_three_prime_chain_breaks_
private
rna::checker::RNA_AtrRepCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rna_virt_sugar_atr_rep_checker_
private
sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::sampler_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseConnectionSampler::scorefxn_
private
utility::vector1< screener::StepWiseScreenerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::screeners_
private
core::pose::PoseOP protocols::stepwise::modeler::StepWiseConnectionSampler::screening_pose_
private
screener::TagDefinitionOP protocols::stepwise::modeler::StepWiseConnectionSampler::tag_definition_
private
rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::user_input_VDW_bin_checker_
private
rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::VDW_bin_checker_
private
bool const protocols::stepwise::modeler::StepWiseConnectionSampler::virt_sugar_atr_rep_screen_
private
core::pose::PoseOP protocols::stepwise::modeler::StepWiseConnectionSampler::virt_sugar_screening_pose_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseConnectionSampler::working_parameters_
private

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