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

#include <StepWiseConnectionSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::StepWiseConnectionSampler:

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, 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...
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 Strings &	info ()
	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::Size >	protein_cutpoints_closed_
utility::vector1 < core::pose::PoseOP >	protein_ccd_poses_
utility::vector1 < protein::loop_close::StepWiseProteinCCD_CloserOP >	protein_ccd_closers_
utility::vector1< core::Size >	rna_five_prime_chain_breaks_
utility::vector1< core::Size >	rna_three_prime_chain_breaks_
utility::vector1< core::Size >	rna_chain_break_gap_sizes_
utility::vector1 < rna::checker::RNA_ChainClosableGeometryCheckerOP >	rna_chain_closable_geometry_checkers_
utility::vector1< core::Size >	rna_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 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. 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_

)

References protocols::moves::Mover::set_native_pose().

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

)

References residue_alternative_sets_.

Referenced by presample_virtual_sugars().

void protocols::stepwise::modeler::StepWiseConnectionSampler::apply ( core::pose::Pose &  )

overridevirtual

Main Method.

Implements protocols::moves::MoverForPoseList.

References clusterer_, get_max_ntries(), initialize_pose(), initialize_sampler(), initialize_screeners(), initialize_useful_info(), moving_ligand_, options_, pose_list_, protocols::stepwise::StepWiseSampleAndScreen::run(), sampler_, screeners_, protocols::stepwise::StepWiseSampleAndScreen::set_max_ntries(), protocols::stepwise::StepWiseSampleAndScreen::set_num_random_samples(), protocols::stepwise::StepWiseSampleAndScreen::set_verbose(), and protocols::TR().

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

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

References protocols::stepwise::modeler::figure_out_moving_partition_res_for_suite(), protocols::stepwise::modeler::figure_out_reference_res_for_suite(), figure_out_reference_res_with_rigid_body_rotamer(), moving_partition_res_, moving_res_, moving_res_list_, reference_res_, and rigid_body_modeler_.

Referenced by initialize_useful_info().

void protocols::stepwise::modeler::StepWiseConnectionSampler::figure_out_reference_res_with_rigid_body_rotamer ( core::pose::Pose const &  pose )

private

References moving_partition_res_, moving_res_, reference_res_, and rigid_body_rotamer_.

Referenced by figure_out_reference_res().

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::get_full_bond_sampler ( )

private

Size protocols::stepwise::modeler::StepWiseConnectionSampler::get_max_ntries ( )

private

References kic_modeler_, protocols::mean_field::max(), options_, protein_connection_, rigid_body_modeler_, and rna_chain_closure_checkers_.

Referenced by apply().

utility::vector1< core::conformation::ResidueOP > protocols::stepwise::modeler::StepWiseConnectionSampler::get_moving_rsd_list ( ) const

private

References moving_res_, protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet::pose(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet::pose_list(), residue_alternative_sets_, rigid_body_modeler_, and which_residue_alternative_set_is_moving_residue().

Referenced by initialize_xyz_grid_parameters().

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

References base_centroid_checker_, options_, rigid_body_modeler_, and working_parameters_.

Referenced by initialize_checkers().

utility::vector1< PoseOP > & protocols::stepwise::modeler::StepWiseConnectionSampler::get_pose_list

(

)

References pose_list_.

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

sampler::copy_dofs::ResidueAlternativeStepWiseSamplerCombOP protocols::stepwise::modeler::StepWiseConnectionSampler::get_rsd_alternatives_rotamer ( )

private

References residue_alternative_sets_, and rigid_body_rotamer_.

Referenced by initialize_full_rigid_body_sampler(), initialize_rna_bond_sampler(), and initialize_tna_bond_sampler().

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_carbohydrate_bond_sampler ( core::pose::Pose const &  pose )

private

References core::chemical::rna::CHI, moving_res_, moving_res_list_, core::chemical::ResidueType::n_ring_conformer_sets(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), and core::chemical::ResidueType::ring_conformer_set().

Referenced by initialize_sampler().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers ( core::pose::Pose const &  pose )

private

References core::pose::add_variant_type_to_pose_residue(), core::pose::rna::add_virtual_O2Prime_hydrogen(), base_centroid_checker_, core::pose::Pose::clone(), clusterer_, protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res(), protocols::stepwise::modeler::get_moving_res_including_domain_boundaries(), get_num_pose_kept(), core::chemical::ResidueType::is_carbohydrate(), protocols::stepwise::modeler::protein::just_protein(), kic_modeler_, master_packer_, moving_partition_res_, moving_res_, moving_res_list_, options_, protein_ccd_closers_, protein_ccd_poses_, protein_connection_, protein_cutpoints_closed_, protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates(), core::pose::remove_variant_type_from_pose_residue(), residue_alternative_sets_, core::pose::Pose::residue_type(), rigid_body_modeler_, rna_atr_rep_checker_, rna_chain_break_gap_sizes_, rna_chain_closable_geometry_checkers_, rna_chain_closure_checkers_, rna_cutpoints_closed_, rna_five_prime_chain_breaks_, rna_three_prime_chain_breaks_, scorefxn_, screening_pose_, protocols::TR(), user_input_VDW_bin_checker_, VDW_bin_checker_, virt_sugar_screening_pose_, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RIBOSE, and working_parameters_.

Referenced by initialize_screeners().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_euler_angle_grid_parameters ( )

private

References moving_ligand_, options_, rigid_body_rotamer_, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_centroid_bin_size(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_euler_angle_bin_size(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_euler_z_bin_size(), STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE, and protocols::TR().

Referenced by initialize_sampler().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_full_rigid_body_sampler ( )

private

References core::pose::copydofs::copy_dofs(), get_rsd_alternatives_rotamer(), options_, rigid_body_rotamer_, and sampler_.

Referenced by initialize_sampler().

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler ( core::pose::Pose const &  pose )

private

References core::id::BB, core::chemical::rna::CHI, core::chemical::ResidueType::mainchain_atoms(), moving_res_, moving_res_list_, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), and protocols::TR().

Referenced by initialize_sampler().

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_ligand_bond_sampler ( core::pose::Pose const &  pose )

private

References core::chemical::rna::CHI, moving_res_, moving_res_list_, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), rigid_body_rotamer_, and protocols::TR().

Referenced by initialize_sampler().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_moving_residue_pose_list ( core::pose::Pose const &  pose )

private

References core::pose::Pose::clone(), core::chemical::ResidueTypeBase::is_RNA(), moving_partition_res_, moving_res_, options_, residue_alternative_sets_, core::pose::Pose::residue_type(), rigid_body_modeler_, protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list(), and which_residue_alternative_set_is_moving_residue().

Referenced by presample_virtual_sugars().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose ( core::pose::Pose &  pose )

private

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_h2o, protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), core::pose::add_variant_type_to_pose_residue(), presample_virtual_sugars(), core::pose::Pose::residue_type(), rna_cutpoints_closed_, core::pose::Pose::size(), and core::chemical::VIRTUAL_RESIDUE_VARIANT.

Referenced by apply().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners ( core::pose::Pose &  pose )

private

References base_centroid_checker_, clusterer_, core::chemical::DEOXY_O2PRIME, protocols::moves::Mover::get_native_pose(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_RNA(), kic_modeler_, master_packer_, moving_partition_res_, moving_res_, moving_res_list_, options_, protein_ccd_closers_, protein_ccd_poses_, protein_connection_, reference_res_, core::pose::Pose::residue_type(), rigid_body_modeler_, rna_atr_rep_checker_, rna_chain_closable_geometry_checkers_, rna_chain_closure_checkers_, rna_cutpoints_closed_, rna_five_prime_chain_breaks_, scorefxn_, screeners_, screening_pose_, tag_definition_, user_input_VDW_bin_checker_, VDW_bin_checker_, virt_sugar_atr_rep_screen_, virt_sugar_screening_pose_, and working_parameters_.

Referenced by initialize_screeners().

StepWiseSamplerSizedOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_sampler ( core::pose::Pose const &  pose )

private

References protocols::stepwise::sampler::protein::get_basic_protein_sampler(), input_streams_, protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples(), moving_res_list_, options_, protein_cutpoints_closed_, and working_parameters_.

Referenced by initialize_sampler().

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

References base_centroid_checker_, core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_polymer(), max_distance_squared_, moving_res_, moving_res_base_stub_, protein_connection_, core::pose::Pose::residue_type(), rigid_body_rotamer_, rna_chain_closable_geometry_checkers_, rna_five_prime_chain_breaks_, screeners_, tag_definition_, user_input_VDW_bin_checker_, VDW_bin_checker_, and virt_sugar_screening_pose_.

Referenced by initialize_screeners().

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

References get_rsd_alternatives_rotamer(), kic_modeler_, moving_res_list_, options_, rna_cutpoints_closed_, sampler_, protocols::stepwise::sampler::rna::setup_sampler(), and working_parameters_.

Referenced by initialize_sampler().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler ( core::pose::Pose const &  pose )

private

References core::pose::Pose::clone(), initialize_carbohydrate_bond_sampler(), initialize_euler_angle_grid_parameters(), initialize_full_rigid_body_sampler(), initialize_generic_polymer_bond_sampler(), initialize_ligand_bond_sampler(), initialize_protein_bond_sampler(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), initialize_xyz_grid_parameters(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_TNA(), moving_ligand_, moving_res_, pose_list_, protein_connection_, core::pose::Pose::residue_type(), rigid_body_modeler_, sampler_, and protocols::TR().

Referenced by apply().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_screeners ( core::pose::Pose &  pose )

private

References initialize_checkers(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), core::chemical::ResidueTypeBase::is_polymer(), moving_res_, core::pose::Pose::residue_type(), rigid_body_modeler_, and screeners_.

Referenced by apply().

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_tna_bond_sampler ( core::pose::Pose const &  pose )

private

References get_rsd_alternatives_rotamer(), kic_modeler_, moving_res_list_, options_, rna_cutpoints_closed_, sampler_, protocols::stepwise::sampler::rna::setup_sampler(), and working_parameters_.

Referenced by initialize_sampler().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info ( core::pose::Pose const &  pose )

private

References core::pose::Pose::aa(), core::chemical::aa_vrt, protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks(), figure_out_reference_res(), protocols::toolbox::rigid_body::figure_out_reference_res_for_jump(), protocols::stepwise::modeler::is_protein(), kic_modeler_, moving_partition_res_, moving_res_, moving_res_list_, options_, protein_connection_, rigid_body_modeler_, rna_chain_break_gap_sizes_, rna_cutpoints_closed_, rna_five_prime_chain_breaks_, and rna_three_prime_chain_breaks_.

Referenced by apply().

void protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_xyz_grid_parameters ( )

private

References get_moving_rsd_list(), protocols::stepwise::modeler::rna::rigid_body::initialize_xyz_parameters(), max_distance_squared_, moving_ligand_, options_, rigid_body_rotamer_, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_centroid_bin_max(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_centroid_bin_min(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_max_distance(), protocols::TR(), and truly_floating_base().

Referenced by initialize_sampler().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::presample_virtual_sugars ( core::pose::Pose &  pose )

private

References add_residue_alternative_set(), initialize_moving_residue_pose_list(), protocols::stepwise::modeler::rna::sugar::instantiate_any_virtual_sugars(), moving_res_, options_, rigid_body_modeler_, scorefxn_, and working_parameters_.

Referenced by initialize_pose().

void protocols::stepwise::modeler::StepWiseConnectionSampler::set_input_streams ( utility::vector1< protein::InputStreamWithResidueInfoOP > const &  input_streams )

inline

References input_streams_.

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

void protocols::stepwise::modeler::StepWiseConnectionSampler::set_master_packer ( packer::StepWiseMasterPackerOP  master_packer )

inline

References master_packer_.

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

void protocols::stepwise::modeler::StepWiseConnectionSampler::set_options

(

options::StepWiseModelerOptionsCOP

options

)

References options_.

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

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

References scorefxn_.

Referenced by protocols::stepwise::modeler::StepWiseModeler::do_sampling().

void protocols::stepwise::modeler::StepWiseConnectionSampler::set_user_input_VDW_bin_checker

(

rna::checker::RNA_VDW_BinCheckerOP const &

user_input_VDW_bin_checker

)

References user_input_VDW_bin_checker_.

Size protocols::stepwise::modeler::StepWiseConnectionSampler::truly_floating_base ( )

private

References moving_res_, reference_res_, and rna_cutpoints_closed_.

Referenced by initialize_xyz_grid_parameters().

Size protocols::stepwise::modeler::StepWiseConnectionSampler::which_residue_alternative_set_is_moving_residue ( ) const

private

References moving_res_, and residue_alternative_sets_.

Referenced by get_moving_rsd_list(), and initialize_moving_residue_pose_list().

Member Data Documentation

rna::checker::RNA_BaseCentroidCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::base_centroid_checker_

private

Referenced by get_num_pose_kept(), initialize_checkers(), initialize_pose_level_screeners(), and initialize_residue_level_screeners().

align:: StepWiseClustererOP protocols::stepwise::modeler::StepWiseConnectionSampler::clusterer_

private

Referenced by apply(), initialize_checkers(), and initialize_pose_level_screeners().

rna::StepWiseRNA_CountStruct protocols::stepwise::modeler::StepWiseConnectionSampler::count_data_

private

utility::vector1< protein::InputStreamWithResidueInfoOP > protocols::stepwise::modeler::StepWiseConnectionSampler::input_streams_

private

Referenced by initialize_protein_bond_sampler(), and set_input_streams().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::kic_modeler_

private

Referenced by get_max_ntries(), initialize_checkers(), initialize_pose_level_screeners(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), and initialize_useful_info().

packer::StepWiseMasterPackerOP protocols::stepwise::modeler::StepWiseConnectionSampler::master_packer_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), and set_master_packer().

core::Real protocols::stepwise::modeler::StepWiseConnectionSampler::max_distance_squared_

private

Referenced by initialize_residue_level_screeners(), and initialize_xyz_grid_parameters().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::moving_ligand_ = false

private

Referenced by apply(), initialize_euler_angle_grid_parameters(), initialize_sampler(), and initialize_xyz_grid_parameters().

utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_partition_res_

private

Referenced by figure_out_reference_res(), figure_out_reference_res_with_rigid_body_rotamer(), initialize_checkers(), initialize_moving_residue_pose_list(), initialize_pose_level_screeners(), and initialize_useful_info().

core::Size const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_

private

Referenced by figure_out_reference_res(), figure_out_reference_res_with_rigid_body_rotamer(), get_moving_rsd_list(), initialize_carbohydrate_bond_sampler(), initialize_checkers(), initialize_generic_polymer_bond_sampler(), initialize_ligand_bond_sampler(), initialize_moving_residue_pose_list(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), initialize_sampler(), initialize_screeners(), initialize_useful_info(), presample_virtual_sugars(), truly_floating_base(), and which_residue_alternative_set_is_moving_residue().

core::kinematics::Stub protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_base_stub_

private

Referenced by initialize_residue_level_screeners().

utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseConnectionSampler::moving_res_list_

private

Referenced by figure_out_reference_res(), initialize_carbohydrate_bond_sampler(), initialize_checkers(), initialize_generic_polymer_bond_sampler(), initialize_ligand_bond_sampler(), initialize_pose_level_screeners(), initialize_protein_bond_sampler(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), and initialize_useful_info().

options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseConnectionSampler::options_

private

Referenced by apply(), get_max_ntries(), get_num_pose_kept(), initialize_checkers(), initialize_euler_angle_grid_parameters(), initialize_full_rigid_body_sampler(), initialize_moving_residue_pose_list(), initialize_pose_level_screeners(), initialize_protein_bond_sampler(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), initialize_useful_info(), initialize_xyz_grid_parameters(), presample_virtual_sugars(), and set_options().

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseConnectionSampler::pose_list_

private

Referenced by apply(), get_pose_list(), initialize_sampler(), and set_pose_list().

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

Referenced by initialize_checkers(), and initialize_pose_level_screeners().

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseConnectionSampler::protein_ccd_poses_

private

Referenced by initialize_checkers(), and initialize_pose_level_screeners().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::protein_connection_

private

Referenced by get_max_ntries(), initialize_checkers(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), initialize_sampler(), and initialize_useful_info().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::protein_cutpoints_closed_

private

Referenced by initialize_checkers(), and initialize_protein_bond_sampler().

core::Size protocols::stepwise::modeler::StepWiseConnectionSampler::reference_res_

private

Referenced by figure_out_reference_res(), figure_out_reference_res_with_rigid_body_rotamer(), initialize_pose_level_screeners(), and truly_floating_base().

utility::vector1< sampler::copy_dofs::ResidueAlternativeSet > protocols::stepwise::modeler::StepWiseConnectionSampler::residue_alternative_sets_

private

Referenced by add_residue_alternative_set(), get_moving_rsd_list(), get_rsd_alternatives_rotamer(), initialize_checkers(), initialize_moving_residue_pose_list(), and which_residue_alternative_set_is_moving_residue().

bool protocols::stepwise::modeler::StepWiseConnectionSampler::rigid_body_modeler_

private

Referenced by figure_out_reference_res(), get_max_ntries(), get_moving_rsd_list(), get_num_pose_kept(), initialize_checkers(), initialize_moving_residue_pose_list(), initialize_pose_level_screeners(), initialize_sampler(), initialize_screeners(), initialize_useful_info(), and presample_virtual_sugars().

sampler::rigid_body::RigidBodyStepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rigid_body_rotamer_

private

Referenced by figure_out_reference_res_with_rigid_body_rotamer(), get_rsd_alternatives_rotamer(), initialize_euler_angle_grid_parameters(), initialize_full_rigid_body_sampler(), initialize_ligand_bond_sampler(), initialize_residue_level_screeners(), and initialize_xyz_grid_parameters().

rna::checker::RNA_AtrRepCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rna_atr_rep_checker_

private

Referenced by initialize_checkers(), and initialize_pose_level_screeners().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_break_gap_sizes_

private

Referenced by initialize_checkers(), and initialize_useful_info().

utility::vector1< rna::checker::RNA_ChainClosableGeometryCheckerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_closable_geometry_checkers_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), and initialize_residue_level_screeners().

utility::vector1< rna::checker::RNA_ChainClosureCheckerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_chain_closure_checkers_

private

Referenced by get_max_ntries(), initialize_checkers(), and initialize_pose_level_screeners().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_cutpoints_closed_

private

Referenced by initialize_checkers(), initialize_pose(), initialize_pose_level_screeners(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), initialize_useful_info(), and truly_floating_base().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_five_prime_chain_breaks_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), and initialize_useful_info().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseConnectionSampler::rna_three_prime_chain_breaks_

private

Referenced by initialize_checkers(), and initialize_useful_info().

rna::checker::RNA_AtrRepCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::rna_virt_sugar_atr_rep_checker_

private

sampler::StepWiseSamplerOP protocols::stepwise::modeler::StepWiseConnectionSampler::sampler_

private

Referenced by apply(), initialize_full_rigid_body_sampler(), initialize_rna_bond_sampler(), initialize_sampler(), and initialize_tna_bond_sampler().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseConnectionSampler::scorefxn_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), presample_virtual_sugars(), and set_scorefxn().

utility::vector1< screener::StepWiseScreenerOP > protocols::stepwise::modeler::StepWiseConnectionSampler::screeners_

private

Referenced by apply(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), and initialize_screeners().

core::pose::PoseOP protocols::stepwise::modeler::StepWiseConnectionSampler::screening_pose_

private

Referenced by initialize_checkers(), and initialize_pose_level_screeners().

screener::TagDefinitionOP protocols::stepwise::modeler::StepWiseConnectionSampler::tag_definition_

private

Referenced by initialize_pose_level_screeners(), and initialize_residue_level_screeners().

rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::user_input_VDW_bin_checker_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), initialize_residue_level_screeners(), and set_user_input_VDW_bin_checker().

rna::checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::StepWiseConnectionSampler::VDW_bin_checker_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), and initialize_residue_level_screeners().

bool const protocols::stepwise::modeler::StepWiseConnectionSampler::virt_sugar_atr_rep_screen_

private

Referenced by initialize_pose_level_screeners().

core::pose::PoseOP protocols::stepwise::modeler::StepWiseConnectionSampler::virt_sugar_screening_pose_

private

Referenced by initialize_checkers(), initialize_pose_level_screeners(), and initialize_residue_level_screeners().

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseConnectionSampler::working_parameters_

private

Referenced by get_num_pose_kept(), initialize_checkers(), initialize_pose_level_screeners(), initialize_protein_bond_sampler(), initialize_rna_bond_sampler(), initialize_tna_bond_sampler(), and presample_virtual_sugars().

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

• src/protocols/stepwise/modeler/StepWiseConnectionSampler.hh
• src/protocols/stepwise/modeler/StepWiseConnectionSampler.cc