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core::pose::full_model_info Namespace Reference

Classes

class  FullModelInfo
 Keep track of all information related to how a subpose 'fits in' to global modeling scheme. More...
 
class  FullModelParameters
 
class  SubMotifInfo
 Keep track of information about a submotif added to a pose. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< FullModelInfo
FullModelInfoOP
 
typedef
utility::pointer::shared_ptr
< FullModelParameters
FullModelParametersOP
 
typedef
utility::pointer::shared_ptr
< FullModelParameters const > 
FullModelParametersCOP
 
typedef
utility::pointer::shared_ptr
< SubMotifInfo
SubMotifInfoOP
 
typedef
utility::pointer::shared_ptr
< SubMotifInfo const > 
SubMotifInfoCOP
 

Enumerations

enum  FullModelParameterType {
  NO_TYPE = 0, CALC_RMS, CUTPOINT_OPEN, DOCK_DOMAIN,
  EXTRA_MINIMIZE, EXTRA_MINIMIZE_JUMP, FIXED_DOMAIN, INPUT_DOMAIN,
  JUMP, PREFERRED_ROOT, SAMPLE, WORKING,
  CYCLIZE_RES, TWOPRIME_RES, RNA_BULGE, ALIGNMENT_ANCHOR_RES,
  RNA_SAMPLE_SUGAR, RNA_SYN_CHI, RNA_ANTI_CHI, RNA_NORTH_SUGAR,
  RNA_SOUTH_SUGAR, RNA_TERMINAL, RNA_BLOCK_STACK_ABOVE, RNA_BLOCK_STACK_BELOW,
  FIVEPRIME_CAP, DISULFIDE, LAST_TYPE
}
 

Functions

FullModelInfo const & const_full_model_info (pose::Pose const &pose)
 
FullModelInfononconst_full_model_info (pose::Pose &pose)
 
bool full_model_info_defined (pose::Pose const &pose)
 
FullModelInfo const & make_sure_full_model_info_is_setup (pose::Pose &pose)
 
void set_full_model_info (pose::Pose &pose, FullModelInfoOP &full_model_info)
 
void update_full_model_info_from_pose (pose::Pose &pose)
 
std::ostream & operator<< (std::ostream &os, FullModelParameters const &t)
 
std::istream & operator>> (std::istream &is, FullModelParameters &t)
 
bool operator== (FullModelParameters const &a, FullModelParameters const &b)
 equal to operator More...
 
bool operator!= (FullModelParameters const &a, FullModelParameters const &b)
 equal to operator More...
 
void initialize_parameters (FullModelParameters &full_model_parameters)
 
void initialize_full_model_parameter_type_name ()
 
std::string to_string (FullModelParameterType const &full_model_parameter_type)
 
FullModelParameterType full_model_parameter_type_from_string (std::string const &name)
 
bool operator== (SubMotifInfoOP lhs, SubMotifInfoOP rhs)
 Equality comparator. More...
 
bool operator!= (SubMotifInfoOP lhs, SubMotifInfoOP rhs)
 Equality comparator. More...
 
std::ostream & operator<< (std::ostream &os, SubMotifInfoOP submotif_info)
 << operator More...
 
std::istream & operator>> (std::istream &is, SubMotifInfoOP submotif_info)
 << operator More...
 
utility::vector1< Sizereorder_moving_res_list_after_delete (utility::vector1< Size > const &moving_res_list, Size const res_to_delete)
 
utility::vector1< Sizereorder_res_list_after_delete (utility::vector1< Size > const &res_list, Size const res_to_delete)
 
utility::vector1< Sizereorder_moving_res_list_after_insert (utility::vector1< Size > const &moving_res_list, Size const &res_to_add)
 
utility::vector1< Sizereorder_res_list_after_prepend (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
 
utility::vector1< Sizereorder_res_list_after_append (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
 
void update_pdb_info_from_full_model_info (pose::Pose &pose)
 
void update_constraint_set_from_full_model_info (pose::Pose &pose)
 
void update_disulfides_from_full_model_info (pose::Pose &pose)
 
void update_pose_objects_from_full_model_info (pose::Pose &pose)
 
void update_res_list_in_full_model_info_and_pdb_info (pose::Pose &pose, utility::vector1< Size > const &res_list_new)
 
void reorder_full_model_info_after_delete (core::pose::Pose &pose, core::Size const res_to_delete)
 Keep track of RNA centroid information inside the pose. More...
 
void reorder_full_model_info_after_append (pose::Pose &pose, Size const res_to_add, Size const offset)
 
void reorder_full_model_info_after_prepend (pose::Pose &pose, Size const res_to_add, Size const offset)
 
utility::vector1< std::string > figure_out_conventional_segids_from_full_model_info (pose::Pose const &pose)
 
utility::vector1< char > figure_out_conventional_chains_from_full_model_info (pose::Pose const &pose)
 
utility::vector1< Sizefigure_out_chain_numbers_from_full_model_info (pose::Pose &pose)
 
utility::vector1< Sizeget_chains_full (pose::Pose const &pose)
 
utility::vector1< Sizeget_chains_from_cutpoint_open (utility::vector1< Size > const &cutpoint_open, Size const nres)
 
utility::vector1< Sizeget_cutpoint_open_from_chains (utility::vector1< Size > const &chains)
 
utility::vector1< Sizefigure_out_chain_numbers_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizefigure_out_dock_domain_map_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizeget_sample_res_for_pose (pose::Pose const &pose)
 
bool check_full_model_info_OK (pose::Pose const &pose)
 
utility::vector1< Size > const & get_res_list_from_full_model_info (pose::Pose &pose)
 
utility::vector1< Size > const & get_res_list_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizeget_res_list_const (pose::Pose const &pose)
 
utility::vector1
< utility::vector1< Size > > 
get_move_elements_from_full_model_info (pose::Pose &pose)
 
utility::vector1
< utility::vector1< Size > > 
get_move_elements_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizeget_moving_res_from_full_model_info (pose::Pose &pose)
 
utility::vector1< Sizeget_moving_res_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizeget_fixed_domain_from_full_model_info_const (pose::Pose const &pose)
 
utility::vector1< Sizeget_input_domain_from_full_model_info_const (pose::Pose const &pose)
 
core::Size sub_to_full (core::Size const i, core::pose::Pose const &pose)
 
utility::vector1< Sizesub_to_full (utility::vector1< Size > const &res_list, core::pose::Pose const &pose)
 
core::Size full_to_sub (core::Size const i, core::pose::Pose const &pose)
 
utility::vector1< Sizefull_to_sub (utility::vector1< Size > const &res_list, core::pose::Pose const &pose)
 
Size full_model_size (pose::Pose &pose)
 
void update_pose_domain_map_const (Pose const &pose, Size &pose_domain_number, utility::vector1< Size > &pose_domain_map)
 
void update_pose_domain_map (Pose &pose, Size &pose_domain_number, utility::vector1< Size > &pose_domain_map)
 
utility::vector1< Sizefigure_out_pose_domain_map (pose::Pose &pose)
 
utility::vector1< Sizefigure_out_pose_domain_map_const (pose::Pose const &pose)
 
core::conformation::Residue const & get_residue (Size const seqpos_in_full_model, pose::Pose const &pose, bool &found_residue)
 
core::conformation::Residue const & get_residue (Size const seqpos_in_full_model, pose::Pose const &pose)
 
utility::vector1< int > get_res_num_from_pdb_info (pose::Pose const &pose)
 
utility::vector1< char > get_chains_from_pdb_info (pose::Pose const &pose)
 
utility::vector1< std::string > get_segids_from_pdb_info (pose::Pose const &pose)
 
Size get_chain_for_full_model_resnum (Size const &resnum, pose::Pose const &pose)
 
Size get_chain_for_resnum (Size const &resnum, pose::Pose const &pose)
 
Size get_number_missing_residues_and_connections (pose::Pose &pose)
 Finds the number of missing residues in a pose. More...
 
Size get_number_missing_residues_and_connections (pose::Pose const &pose)
 What if you know your pose has a FMI but it has to be const? More...
 
Size get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< char > &missing_residues)
 Finds the number of missing residues in a pose. More...
 
Size get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< utility::vector1< Size > > &loop_suites)
 Finds the number of missing residues in a pose. More...
 
Size get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< char > &missing_residues, utility::vector1< utility::vector1< Size > > &loop_suites)
 Finds the number of missing residues in a pose. More...
 
bool check_all_residues_sampled (pose::Pose const &pose)
 
std::map< std::pair< Size,
Size >, std::pair< Size, Size > > 
get_preferred_jump_pair_for_docking_domains (FullModelInfo const &full_model_info)
 
utility::vector1< std::pair
< Size, Size > > 
get_chain_connections (pose::Pose const &pose)
 
utility::vector1< Sizeget_connection_domains (utility::vector1< std::pair< Size, Size > > const &chain_connections, Size const nchains)
 
bool check_sample_sugar_in_full_model_info (pose::Pose const &pose, Size const i)
 
void append_virtual_residue_to_full_model_info (pose::Pose &pose)
 
std::string get_current_global_sequence (pose::Pose const &pose)
 
void add_new_sequence_into_global_sequence (pose::Pose const &pose, std::string &current_global_sequence)
 
std::string get_current_global_sequence (utility::vector1< conformation::ResidueCOP > const &resvect, utility::vector1< Size > const &global_mapping, utility::vector1< Size > const &res_list, std::string const &native_sequence)
 
utility::vector1< core::Sizeget_connection_domains (utility::vector1< std::pair< core::Size, core::Size > > const &chain_connections, core::Size const nchains)
 

Variables

std::map
< FullModelParameterType,
std::string > 
full_model_parameter_type_name
 

Typedef Documentation

typedef utility::pointer::shared_ptr< FullModelInfo > core::pose::full_model_info::FullModelInfoOP
typedef utility::pointer::shared_ptr< FullModelParameters const > core::pose::full_model_info::FullModelParametersCOP
typedef utility::pointer::shared_ptr< SubMotifInfo const > core::pose::full_model_info::SubMotifInfoCOP
typedef utility::pointer::shared_ptr< SubMotifInfo > core::pose::full_model_info::SubMotifInfoOP

Enumeration Type Documentation

Enumerator
NO_TYPE 
CALC_RMS 
CUTPOINT_OPEN 
DOCK_DOMAIN 
EXTRA_MINIMIZE 
EXTRA_MINIMIZE_JUMP 
FIXED_DOMAIN 
INPUT_DOMAIN 
JUMP 
PREFERRED_ROOT 
SAMPLE 
WORKING 
CYCLIZE_RES 
TWOPRIME_RES 
RNA_BULGE 
ALIGNMENT_ANCHOR_RES 
RNA_SAMPLE_SUGAR 
RNA_SYN_CHI 
RNA_ANTI_CHI 
RNA_NORTH_SUGAR 
RNA_SOUTH_SUGAR 
RNA_TERMINAL 
RNA_BLOCK_STACK_ABOVE 
RNA_BLOCK_STACK_BELOW 
FIVEPRIME_CAP 
DISULFIDE 
LAST_TYPE 

Function Documentation

void core::pose::full_model_info::add_new_sequence_into_global_sequence ( pose::Pose const &  pose,
std::string &  current_global_sequence 
)
void core::pose::full_model_info::append_virtual_residue_to_full_model_info ( pose::Pose pose)
bool core::pose::full_model_info::check_all_residues_sampled ( pose::Pose const &  pose)
bool core::pose::full_model_info::check_full_model_info_OK ( pose::Pose const &  pose)
bool core::pose::full_model_info::check_sample_sugar_in_full_model_info ( pose::Pose const &  pose,
Size const  i 
)
FullModelInfo const & core::pose::full_model_info::const_full_model_info ( pose::Pose const &  pose)

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::FULL_MODEL_INFO.

Referenced by core::pose::rna::add_anti_chi_constraints(), core::pose::rna::add_chi_constraints(), add_new_sequence_into_global_sequence(), core::pose::rna::add_syn_chi_constraints(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::already_instantiated_in_pose(), append_virtual_residue_to_full_model_info(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::apply(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::AddMover::apply(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply(), core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), check_all_residues_sampled(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_intramolecular_submotif_jump(), check_full_model_info_OK(), check_sample_sugar_in_full_model_info(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::stepwise::monte_carlo::mover::DeleteMover::decide_to_keep_pose(), core::pose::definite_terminal_root(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_already_docked(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_attachment(), figure_out_conventional_chains_from_full_model_info(), figure_out_conventional_segids_from_full_model_info(), figure_out_dock_domain_map_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_from_scratch_delete_move_elements(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::figure_out_if_loop_involves_current_pose(), figure_out_pose_domain_map_const(), protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res(), core::io::rna::RNA_DataReader::fill_backbone_array(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses(), core::io::silent::SilentStruct::fill_other_struct_list(), core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::filter_pose_order(), core::scoring::rna::RNA_PartitionEnergy::finalize_total_energy(), core::pose::fix_up_residue_type_variants(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), full_to_sub(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_actual_moving_res(), protocols::stepwise::monte_carlo::mover::AddMover::get_add_res(), protocols::stepwise::monte_carlo::get_all_res_list(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments(), protocols::stepwise::modeler::protein::get_bridge_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), get_chains_full(), get_current_global_sequence(), core::pose::get_definite_terminal_root(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_dock_domains(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), protocols::stepwise::modeler::get_domain_boundary_suites(), get_fixed_domain_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_delete_move_elements(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), get_input_domain_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_delete_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), get_move_elements_from_full_model_info_const(), get_moving_res_from_full_model_info_const(), core::scoring::methods::IntermolEnergy::get_num_chains_frozen(), get_number_missing_residues_and_connections(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), get_res_list_from_full_model_info_const(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference(), get_residue(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose(), core::io::rna::get_rna_data_info(), get_sample_res_for_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_vary_loop_length_moves(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::has_precomputed_move(), protocols::stepwise::modeler::StepWiseModeler::initialize_constraints(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::is_addable_res(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles(), protocols::stepwise::modeler::StepWiseModeler::look_for_precompute_move(), protocols::stepwise::modeler::merge_in_other_pose(), core::scoring::loop_graph::LoopGraph::missing_residues(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::stepwise::modeler::rna::mutate_res_if_allowed(), core::scoring::loop_graph::LoopGraph::nmissing(), core::pose::operator<<(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::ordered_move_from_partition(), core::scoring::constraints::ConstraintIO::parse_residue(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::partitions_split_a_submotif(), core::pose::pdbslice(), core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::stepwise::monte_carlo::mover::read_checkpoint_log(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::remnant_would_be_deleted(), protocols::magnesium::remove_mg_bound_waters(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), core::scoring::methods::FreeDOF_Energy::residue_energy(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), core::scoring::rna::RNA_PartitionEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::scoring::rna::RNA_StubCoordinateEnergy::setup_for_scoring(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::share_chains(), core::pose::full_model_info::FullModelInfo::show_submotif_info_list(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), core::pose::stepwise_addable_pose_residue(), sub_to_full(), core::pose::full_model_info::FullModelInfo::submotif_info(), core::pose::full_model_info::FullModelInfo::submotif_info_containing_residues(), protocols::stepwise::modeler::switch_focus_among_poses_randomly(), protocols::stepwise::modeler::switch_focus_to_other_pose(), protocols::stepwise::modeler::test_merge_and_slice_with_two_helix_test_case(), core::scoring::loop_graph::LoopGraph::update(), core::pose::update_block_stack_variants(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_calc_rms_atom_id_map(), update_constraint_set_from_full_model_info(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), core::scoring::loop_graph::LoopGraph::update_loops(), update_pdb_info_from_full_model_info(), update_pose_domain_map_const(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local(), and update_res_list_in_full_model_info_and_pdb_info().

utility::vector1< Size > core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info ( pose::Pose pose)
utility::vector1< Size > core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info_const ( pose::Pose const &  pose)
utility::vector1< char > core::pose::full_model_info::figure_out_conventional_chains_from_full_model_info ( pose::Pose const &  pose)
utility::vector1< std::string > core::pose::full_model_info::figure_out_conventional_segids_from_full_model_info ( pose::Pose const &  pose)
utility::vector1< Size > core::pose::full_model_info::figure_out_dock_domain_map_from_full_model_info_const ( pose::Pose const &  pose)
utility::vector1< Size > core::pose::full_model_info::figure_out_pose_domain_map ( pose::Pose pose)
utility::vector1< Size > core::pose::full_model_info::figure_out_pose_domain_map_const ( pose::Pose const &  pose)
bool core::pose::full_model_info::full_model_info_defined ( pose::Pose const &  pose)

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::FULL_MODEL_INFO.

Referenced by core::scoring::methods::FreeDOF_Energy::accumulate_stack_energy(), core::pose::rna::add_anti_chi_constraints(), core::pose::rna::add_syn_anti_chi_constraints(), core::pose::rna::add_syn_chi_constraints(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), append_virtual_residue_to_full_model_info(), protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment(), check_sample_sugar_in_full_model_info(), core::pose::toolbox::AtomLevelDomainMap::disallow_movement_of_input_res(), core::scoring::methods::IntermolEnergy::eval_atom_derivative(), core::scoring::loop_graph::LoopCloseEnergy::eval_atom_derivative(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::figure_out_if_loop_involves_current_pose(), core::io::rna::RNA_DataReader::fill_backbone_array(), core::io::silent::SilentStruct::fill_other_struct_list(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(), core::scoring::methods::OtherPoseEnergy::finalize_total_energy(), core::scoring::methods::IntermolEnergy::finalize_total_energy(), core::scoring::rna::RNA_BulgeEnergy::finalize_total_energy(), core::scoring::loop_graph::LoopCloseEnergy::finalize_total_energy(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), get_res_list_const(), get_res_list_from_full_model_info_const(), get_residue(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::pose::toolbox::AtomLevelDomainMap::initialize(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), core::pose::operator<<(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::pdbslice(), core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment(), protocols::magnesium::remove_mg_bound_waters(), core::scoring::methods::FreeDOF_Energy::residue_energy(), core::scoring::loop_graph::LoopCloseEnergy::setup_for_derivatives(), core::scoring::rna::RNA_StubCoordinateEnergy::setup_for_scoring(), core::scoring::methods::FreeDOF_Energy::setup_for_scoring(), core::scoring::loop_graph::LoopCloseEnergy::setup_for_scoring(), core::pose::stepwise_addable_pose_residue(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), core::scoring::loop_graph::LoopCloseEnergy::update_loop_atoms_and_lengths(), and protocols::jd3::pose_outputters::SilentFilePoseOutputter::write_output().

FullModelParameterType core::pose::full_model_info::full_model_parameter_type_from_string ( std::string const &  name)
Size core::pose::full_model_info::full_model_size ( pose::Pose pose)
core::Size core::pose::full_model_info::full_to_sub ( core::Size const  i,
core::pose::Pose const &  pose 
)

References const_full_model_info(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_bulge_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_bulge_variants(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_res_variant(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::copy_rna_chi(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_cuts(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_cuts(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_gap_size_and_first_chain_break_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_gap_size_and_five_prime_chain_break_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_jump_partners(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_act_full_to_sub(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::monte_carlo::mover::ResampleMover::get_remodel_res(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), protocols::stepwise::monte_carlo::mover::DeleteMover::minimize_after_delete(), protocols::stepwise::modeler::rna::output_data(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_floating_base_jump_to_anchor(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), and protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::which_chain().

utility::vector1< Size > core::pose::full_model_info::full_to_sub ( utility::vector1< Size > const &  res_list,
core::pose::Pose const &  pose 
)
utility::vector1< std::pair< core::Size, core::Size > > core::pose::full_model_info::get_chain_connections ( pose::Pose const &  pose)
Size core::pose::full_model_info::get_chain_for_full_model_resnum ( Size const &  resnum,
pose::Pose const &  pose 
)
Size core::pose::full_model_info::get_chain_for_resnum ( Size const &  resnum,
pose::Pose const &  pose 
)
utility::vector1< Size > core::pose::full_model_info::get_chains_from_cutpoint_open ( utility::vector1< Size > const &  cutpoint_open,
Size const  nres 
)
utility::vector1< char > core::pose::full_model_info::get_chains_from_pdb_info ( pose::Pose const &  pose)
utility::vector1< Size > core::pose::full_model_info::get_chains_full ( pose::Pose const &  pose)
utility::vector1< core::Size > core::pose::full_model_info::get_connection_domains ( utility::vector1< std::pair< core::Size, core::Size > > const &  chain_connections,
core::Size const  nchains 
)
utility::vector1< Size > core::pose::full_model_info::get_connection_domains ( utility::vector1< std::pair< Size, Size > > const &  chain_connections,
Size const  nchains 
)
std::string core::pose::full_model_info::get_current_global_sequence ( pose::Pose const &  pose)
std::string core::pose::full_model_info::get_current_global_sequence ( utility::vector1< conformation::ResidueCOP > const &  resvect,
utility::vector1< Size > const &  global_mapping,
utility::vector1< Size > const &  res_list,
std::string const &  native_sequence 
)
utility::vector1< Size > core::pose::full_model_info::get_cutpoint_open_from_chains ( utility::vector1< Size > const &  chains)
utility::vector1< Size > core::pose::full_model_info::get_fixed_domain_from_full_model_info_const ( pose::Pose const &  pose)
utility::vector1< Size > core::pose::full_model_info::get_input_domain_from_full_model_info_const ( pose::Pose const &  pose)
utility::vector1< utility::vector1< Size > > core::pose::full_model_info::get_move_elements_from_full_model_info ( pose::Pose pose)
utility::vector1< utility::vector1< Size > > core::pose::full_model_info::get_move_elements_from_full_model_info_const ( pose::Pose const &  pose)
utility::vector1< Size > core::pose::full_model_info::get_moving_res_from_full_model_info ( pose::Pose pose)
utility::vector1< Size > core::pose::full_model_info::get_moving_res_from_full_model_info_const ( pose::Pose const &  pose)
Size core::pose::full_model_info::get_number_missing_residues_and_connections ( pose::Pose pose)
Size core::pose::full_model_info::get_number_missing_residues_and_connections ( pose::Pose const &  pose)

What if you know your pose has a FMI but it has to be const?

References get_number_missing_residues_and_connections().

Size core::pose::full_model_info::get_number_missing_residues_and_connections ( pose::Pose const &  pose,
utility::vector1< char > &  missing_residues 
)

Finds the number of missing residues in a pose.

This function returns the number of missing residues in the pose. The missing_residues vector is passed by nonconst reference, so its values can be modified and accessed by this function and the calling method.

References get_number_missing_residues_and_connections().

Size core::pose::full_model_info::get_number_missing_residues_and_connections ( pose::Pose const &  pose,
utility::vector1< utility::vector1< Size > > &  loop_suites 
)

Finds the number of missing residues in a pose.

This function returns the number of missing residues in the pose. The loop_suites vector is passed by nonconst reference, so its values can be modified and accessed by this function and the calling method.

References get_number_missing_residues_and_connections().

Size core::pose::full_model_info::get_number_missing_residues_and_connections ( pose::Pose const &  pose,
utility::vector1< char > &  missing_residues,
utility::vector1< utility::vector1< Size > > &  loop_suites 
)

Finds the number of missing residues in a pose.

This function returns the number of missing residues in the pose. The missing_res and loop_suites vectors are passed by nonconst reference, so their values can be modified and accessed by this function and the calling method.

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), figure_out_pose_domain_map_const(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::input_domain_map(), core::scoring::loop_graph::LoopGraph::update_loops(), and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by get_number_missing_residues_and_connections().

std::map< std::pair< Size, Size >, std::pair< Size, Size > > core::pose::full_model_info::get_preferred_jump_pair_for_docking_domains ( FullModelInfo const &  full_model_info)
utility::vector1< Size > core::pose::full_model_info::get_res_list_const ( pose::Pose const &  pose)
utility::vector1< Size > const & core::pose::full_model_info::get_res_list_from_full_model_info ( pose::Pose pose)
utility::vector1< Size > const & core::pose::full_model_info::get_res_list_from_full_model_info_const ( pose::Pose const &  pose)

References const_full_model_info(), full_model_info_defined(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::already_instantiated_in_pose(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), check_full_model_info_OK(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_already_docked(), figure_out_chain_numbers_from_full_model_info_const(), figure_out_conventional_chains_from_full_model_info(), figure_out_conventional_segids_from_full_model_info(), figure_out_dock_domain_map_from_full_model_info_const(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::monte_carlo::get_all_res_list(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), get_res_list_const(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_terminal_move_elements(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::has_precomputed_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles(), protocols::stepwise::modeler::merge_two_poses_using_full_model_info(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::partitions_split_a_submotif(), reorder_full_model_info_after_append(), reorder_full_model_info_after_delete(), reorder_full_model_info_after_prepend(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local().

utility::vector1< int > core::pose::full_model_info::get_res_num_from_pdb_info ( pose::Pose const &  pose)
core::conformation::Residue const& core::pose::full_model_info::get_residue ( Size const  seqpos_in_full_model,
pose::Pose const &  pose,
bool found_residue 
)
core::conformation::Residue const & core::pose::full_model_info::get_residue ( Size const  seqpos_in_full_model,
pose::Pose const &  pose 
)
utility::vector1< Size > core::pose::full_model_info::get_sample_res_for_pose ( pose::Pose const &  pose)
utility::vector1< std::string > core::pose::full_model_info::get_segids_from_pdb_info ( pose::Pose const &  pose)
void core::pose::full_model_info::initialize_full_model_parameter_type_name ( )
void core::pose::full_model_info::initialize_parameters ( FullModelParameters &  full_model_parameters)
FullModelInfo const & core::pose::full_model_info::make_sure_full_model_info_is_setup ( pose::Pose pose)
FullModelInfo & core::pose::full_model_info::nonconst_full_model_info ( pose::Pose pose)

Either returns a non-const reference to the FullModelInfo object already stored in the pose, or creates a new FullModelInfo object, places it in the pose, and returns a non-const reference to it.

References check_full_model_info_OK(), core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::FULL_MODEL_INFO.

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::monte_carlo::mover::AddOrDeleteMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::AddMover::do_append(), protocols::stepwise::monte_carlo::mover::AddMover::do_prepend(), core::import_pose::FullModelPoseBuilder::fill_full_model_info(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::scoring::methods::OtherPoseEnergy::finalize_total_energy(), full_model_size(), get_moving_res_from_full_model_info(), get_res_list_from_full_model_info(), make_sure_full_model_info_is_setup(), protocols::stepwise::modeler::merge_in_other_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), protocols::stepwise::monte_carlo::mover::set_up_params_for_move(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), core::io::silent::BinarySilentStruct::setup_other_poses(), protocols::stepwise::modeler::slice_out_pose(), protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_recursively(), protocols::stepwise::modeler::switch_focus_to_other_pose(), update_disulfides_from_full_model_info(), protocols::stepwise::monte_carlo::mover::FromScratchMover::update_full_model_info_and_switch_focus_to_new_pose(), and protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters().

bool core::pose::full_model_info::operator!= ( SubMotifInfoOP  lhs,
SubMotifInfoOP  rhs 
)

Equality comparator.

bool core::pose::full_model_info::operator!= ( FullModelParameters const &  a,
FullModelParameters const &  b 
)

equal to operator

not equal to operator

References protocols::match::upstream::b.

std::ostream& core::pose::full_model_info::operator<< ( std::ostream &  os,
SubMotifInfoOP  submotif_info 
)

<< operator

std::ostream& core::pose::full_model_info::operator<< ( std::ostream &  os,
FullModelParameters const &  t 
)
bool core::pose::full_model_info::operator== ( SubMotifInfoOP  lhs,
SubMotifInfoOP  rhs 
)

Equality comparator.

bool core::pose::full_model_info::operator== ( FullModelParameters const &  a,
FullModelParameters const &  b 
)

equal to operator

References core::pose::motif::a(), and protocols::match::upstream::b.

std::istream& core::pose::full_model_info::operator>> ( std::istream &  is,
SubMotifInfoOP  submotif_info 
)

<< operator

References protocols::kinmatch::str().

std::istream& core::pose::full_model_info::operator>> ( std::istream &  is,
FullModelParameters &  t 
)
void core::pose::full_model_info::reorder_full_model_info_after_append ( pose::Pose pose,
Size const  res_to_add,
Size const  offset 
)
void core::pose::full_model_info::reorder_full_model_info_after_delete ( pose::Pose pose,
Size const  res_to_delete 
)
void core::pose::full_model_info::reorder_full_model_info_after_prepend ( pose::Pose pose,
Size const  res_to_add,
Size const  offset 
)
utility::vector1<Size> core::pose::full_model_info::reorder_moving_res_list_after_delete ( utility::vector1< Size > const &  moving_res_list,
Size const  res_to_delete 
)
utility::vector1<Size> core::pose::full_model_info::reorder_moving_res_list_after_insert ( utility::vector1< Size > const &  moving_res_list,
Size const &  res_to_add 
)
utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_append ( utility::vector1< Size > const &  res_list,
Size const &  res_to_add,
Size const  offset = 1 
)
utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_delete ( utility::vector1< Size > const &  res_list,
Size const  res_to_delete 
)
utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_prepend ( utility::vector1< Size > const &  res_list,
Size const &  res_to_add,
Size const  offset = 1 
)
void core::pose::full_model_info::set_full_model_info ( pose::Pose pose,
FullModelInfoOP &  full_model_info 
)

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, and update_pdb_info_from_full_model_info().

Referenced by protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), append_virtual_residue_to_full_model_info(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::simple_moves::ResetFullModelInfoMover::apply(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag(), core::import_pose::RNA_HelixAssembler::fill_chain_info(), core::import_pose::FullModelPoseBuilder::fill_full_model_info(), core::io::silent::SilentStruct::full_model_info_into_pose(), core::pose::pdbslice(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_full_model_info(), protocols::stepwise::monte_carlo::mover::FromScratchMover::update_full_model_info_and_switch_focus_to_new_pose(), update_full_model_info_from_pose(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), and protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters().

core::Size core::pose::full_model_info::sub_to_full ( core::Size const  i,
core::pose::Pose const &  pose 
)
utility::vector1< Size > core::pose::full_model_info::sub_to_full ( utility::vector1< Size > const &  res_list,
core::pose::Pose const &  pose 
)
std::string core::pose::full_model_info::to_string ( FullModelParameterType const &  full_model_parameter_type)
void core::pose::full_model_info::update_constraint_set_from_full_model_info ( pose::Pose pose)
void core::pose::full_model_info::update_disulfides_from_full_model_info ( pose::Pose pose)
void core::pose::full_model_info::update_full_model_info_from_pose ( pose::Pose pose)
void core::pose::full_model_info::update_pdb_info_from_full_model_info ( pose::Pose pose)
void core::pose::full_model_info::update_pose_domain_map ( Pose pose,
Size pose_domain_number,
utility::vector1< Size > &  pose_domain_map 
)
void core::pose::full_model_info::update_pose_domain_map_const ( Pose const &  pose,
Size pose_domain_number,
utility::vector1< Size > &  pose_domain_map 
)
void core::pose::full_model_info::update_pose_objects_from_full_model_info ( pose::Pose pose)
void core::pose::full_model_info::update_res_list_in_full_model_info_and_pdb_info ( pose::Pose pose,
utility::vector1< Size > const &  res_list_new 
)

Variable Documentation

std::map< FullModelParameterType, std::string> core::pose::full_model_info::full_model_parameter_type_name