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protocols::stepwise::modeler Namespace Reference

Namespaces

 align
 
 movemap
 
 options
 
 packer
 
 polar_hydrogens
 
 precomputed
 
 protein
 
 rna
 
 working_parameters
 

Classes

class  StepWiseConnectionSampler
 
class  StepWiseMinimizer
 
class  StepWiseModeler
 

Typedefs

typedef utility::pointer::shared_ptr< StepWiseConnectionSampler > StepWiseConnectionSamplerOP
 
typedef utility::pointer::shared_ptr< StepWiseConnectionSampler const > StepWiseConnectionSamplerCOP
 
typedef utility::pointer::shared_ptr< StepWiseMinimizer > StepWiseMinimizerOP
 
typedef utility::pointer::shared_ptr< StepWiseMinimizer const > StepWiseMinimizerCOP
 
typedef utility::pointer::shared_ptr< StepWiseModeler > StepWiseModelerOP
 
typedef utility::pointer::shared_ptr< StepWiseModeler const > StepWiseModelerCOP
 
typedef std::map< std::string, core::pose::PoseOP > PoseList
 

Enumerations

enum  MinimizerMode { THERMAL_SAMPLER , TRADITIONAL_MINIMIZER }
 

Functions

core::scoring::constraints::ConstraintSetOP constraint_set_slice (core::scoring::constraints::ConstraintSetOP &cst_set, utility::vector1< core::Size > const &slice_res, pose::Pose const &pose, pose::Pose const &full_pose)
 
void check_scorefxn_has_constraint_terms_if_pose_has_constraints (pose::Pose const &pose, core::scoring::ScoreFunctionOP &scorefxn)
 
void output_boolean (std::string const &tag, bool boolean, std::ostream &outstream)
 
void output_boolean (bool boolean, std::ostream &outstream)
 
void output_rna_movemap_header (core::Size const &spacing, std::ostream &outstream)
 
void output_protein_movemap_header (core::Size const &spacing, std::ostream &outstream)
 
void output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose, std::ostream &outstream)
 
core::scoring::ScoreFunctionOP get_minimize_scorefxn (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, options::StepWiseModelerOptionsCOP options)
 
core::scoring::ScoreFunctionCOP initialize_sample_scorefxn (core::scoring::ScoreFunctionCOP scorefxn, pose::Pose const &pose, options::StepWiseModelerOptionsCOP options)
 
core::scoring::ScoreFunctionCOP initialize_pack_scorefxn (core::scoring::ScoreFunctionCOP sample_scorefxn, pose::Pose const &)
 
core::scoring::ScoreFunctionCOP initialize_o2prime_pack_scorefxn (core::scoring::ScoreFunctionCOP const &scorefxn)
 
Real add_these (core::Size const final_idx, utility::vector1< Real > const &factors)
 
void freeze_waters (core::pose::Pose const &pose, core::kinematics::MoveMap &mm)
 
Size make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, core::Size const &moving_suite)
 
Size make_cut_at_moving_suite (pose::Pose &pose, core::Size const &moving_suite)
 
Size find_jump_number_at_suite (kinematics::FoldTree const &fold_tree, core::Size const &moving_suite)
 
Size look_for_unique_jump_to_moving_res (kinematics::FoldTree const &fold_tree, core::Size const &i)
 
bool is_cutpoint_closed (pose::Pose const &pose, core::Size const seq_num)
 
utility::vector1< core::Size > get_cutpoint_closed (pose::Pose const &pose)
 
utility::vector1< core::Size > merge_vectors (utility::vector1< core::Size > const &vec1, utility::vector1< core::Size > const &vec2)
 
void get_jump_partners_from_pose (utility::vector1< core::Size > &jump_partners1, utility::vector1< core::Size > &jump_partners2, utility::vector1< std::string > &jump_atoms1, utility::vector1< std::string > &jump_atoms2, pose::Pose const &pose, utility::vector1< core::Size > const &working_res)
 
void get_endpoints_from_pose (utility::vector1< core::Size > &endpoints, pose::Pose const &pose, utility::vector1< core::Size > const &working_res)
 
utility::vector1< core::Size > map_to_local_numbering (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res)
 
std::map< core::Size, core::Size > get_res_map (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &source_res)
 
utility::vector1< core::Size > merge_disjoint_vectors (utility::vector1< core::Size > const &res_vector1, utility::vector1< core::Size > const &res_vector2)
 
bool find_root_without_virtual_ribose (kinematics::FoldTree const &f, pose::Pose const &pose)
 
Size find_first_root_residue (kinematics::FoldTree const &f, utility::vector1< core::Size > const &working_res_subset, utility::vector1< core::Size > const &working_res)
 
void reroot_based_on_full_model_info (pose::Pose &pose)
 
void reroot_based_on_full_model_info (pose::Pose &pose, utility::vector1< core::Size > const &root_partition_res)
 
void merge_in_other_pose_by_jump (pose::Pose &pose, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res)
 
void merge_in_other_pose_by_bond (pose::Pose &pose, pose::Pose const &pose2, core::Size const merge_res)
 
void merge_in_other_pose (pose::Pose &pose, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond)
 
utility::vector1< core::Size > merge_two_poses_using_full_model_info (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond)
 
utility::vector1< core::Size > merge_two_poses (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< core::Size > const &working_res1, utility::vector1< core::Size > const &working_res2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond, bool const fix_first_pose)
 
void declare_chemical_bonds_at_cutpoints (pose::Pose &pose, pose::Pose const &source_pose, utility::vector1< core::Size > const &working_res)
 
void declare_chemical_bonds_at_cutpoints (pose::Pose &pose, pose::Pose const &source_pose, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &source_working_res)
 
utility::vector1< core::Size > apply_numbering (utility::vector1< core::Size > const &res, utility::vector1< core::Size > const &numbering)
 
utility::vector1< core::Size > get_other_residues (utility::vector1< core::Size > const &res, core::Size const &nres)
 
void slice_out_pose (pose::Pose &pose, pose::Pose &sliced_out_pose, utility::vector1< core::Size > const &residues_to_delete)
 
void slice (pose::Pose &sliced_out_pose, pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
 
Size check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, FullModelInfo const &full_model_info)
 
Size check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element)
 
Size check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &chains_in_full_model)
 
Size check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, FullModelInfo const &full_model_info)
 
Size check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element)
 
Size check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &chains_in_full_model)
 
void fix_up_jump_atoms (pose::Pose &pose)
 
void fix_up_jump_atoms_and_residue_type_variants (pose::Pose &pose_to_fix)
 
void check_scores_from_parts (std::string const &tag, Real const original_score, pose::Pose &pose, pose::PoseOP original_pose_clone, utility::vector1< PoseOP > const &other_pose_list, core::scoring::ScoreFunctionCOP scorefxn)
 
void switch_focus_to_other_pose (pose::Pose &pose, core::Size const &focus_pose_idx, core::scoring::ScoreFunctionCOP scorefxn)
 
bool switch_focus_among_poses_randomly (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, bool force_switch)
 
void test_merge_and_slice_with_two_helix_test_case (utility::vector1< core::pose::PoseOP > const &input_poses, core::scoring::ScoreFunctionOP scorefxn)
 
utility::vector1< core::Size > figure_out_moving_chain_break_res (pose::Pose const &pose, kinematics::MoveMap const &mm)
 TODO: generalize to cyclized chainbreaks. More...
 
bool check_for_input_domain (pose::Pose const &pose, utility::vector1< core::Size > const &partition_res)
 
Size primary_fixed_domain (pose::Pose const &pose, utility::vector1< core::Size > const &partition_res)
 
bool check_for_input_domain (pose::Pose const &pose)
 
void make_variants_match (pose::Pose &pose, pose::Pose const &reference_pose, core::Size const n, chemical::VariantType const variant_type)
 
utility::vector1< core::Size > figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Size > figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Size > figure_out_moving_cutpoints_closed (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)
 
void figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res, utility::vector1< core::Size > &cutpoints_closed, utility::vector1< core::Size > &five_prime_chain_breaks, utility::vector1< core::Size > &three_prime_chain_breaks, utility::vector1< core::Size > &chain_break_gap_sizes)
 TODO: generalize to cyclized chainbreaks. More...
 
utility::vector1< bool > get_partition_definition_by_jump (pose::Pose const &pose, core::Size const &jump_nr)
 
utility::vector1< bool > get_partition_definition_by_chemical_edge (pose::Pose const &pose, core::kinematics::Edge const &edge)
 
utility::vector1< bool > get_partition_definition (pose::Pose const &pose, core::Size const &moving_suite)
 
Size figure_out_reference_res_for_suite (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Size > figure_out_moving_partition_res_for_suite (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
utility::vector1< core::Size > figure_out_moving_partition_res_for_jump (pose::Pose const &pose, core::Size const jump_nr)
 
utility::vector1< core::Size > figure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Size > figure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Size > figure_out_root_partition_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
void figure_out_root_and_moving_partition_res (pose::Pose const &pose, core::Size const moving_res, utility::vector1< core::Size > &root_partition_res, utility::vector1< core::Size > &moving_partition_res)
 
Size get_possible_root (pose::Pose const &pose, utility::vector1< Size > const &partition_res, bool const disallow_cutpoint_closed_upper)
 
bool revise_root_and_moving_res (pose::Pose &pose, core::Size &moving_res)
 
bool revise_root_and_moving_res_list (pose::Pose &pose, utility::vector1< core::Size > &moving_res_list)
 
Size split_pose (pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
 
void split_pose (pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)
 
void fix_protein_jump_atom (pose::Pose &pose, core::Size const res, std::string const &atom_name)
 
void add_to_pose_list (utility::vector1< core::pose::PoseOP > &pose_list, pose::Pose const &pose, std::string const &pose_tag)
 
bool is_protein (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Size > get_domain_boundary_suites (pose::Pose const &pose)
 
utility::vector1< core::Size > get_domain_boundary_res (pose::Pose const &pose)
 
utility::vector1< core::Size > get_moving_res_including_domain_boundaries (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Size > get_all_working_moving_res (working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
void virtualize_side_chains (pose::Pose &pose)
 
utility::vector1< core::Size > get_all_residues (pose::Pose const &pose)
 
Size find_downstream_connection_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)
 
Size get_unique_connection_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)
 

Typedef Documentation

◆ PoseList

typedef std::map< std::string, core::pose::PoseOP > protocols::stepwise::modeler::PoseList

◆ StepWiseConnectionSamplerCOP

typedef utility::pointer::shared_ptr< StepWiseConnectionSampler const > protocols::stepwise::modeler::StepWiseConnectionSamplerCOP

◆ StepWiseConnectionSamplerOP

typedef utility::pointer::shared_ptr< StepWiseConnectionSampler > protocols::stepwise::modeler::StepWiseConnectionSamplerOP

◆ StepWiseMinimizerCOP

typedef utility::pointer::shared_ptr< StepWiseMinimizer const > protocols::stepwise::modeler::StepWiseMinimizerCOP

◆ StepWiseMinimizerOP

typedef utility::pointer::shared_ptr< StepWiseMinimizer > protocols::stepwise::modeler::StepWiseMinimizerOP

◆ StepWiseModelerCOP

typedef utility::pointer::shared_ptr< StepWiseModeler const > protocols::stepwise::modeler::StepWiseModelerCOP

◆ StepWiseModelerOP

typedef utility::pointer::shared_ptr< StepWiseModeler > protocols::stepwise::modeler::StepWiseModelerOP

Enumeration Type Documentation

◆ MinimizerMode

enum protocols::stepwise::modeler::MinimizerMode
Enumerator
THERMAL_SAMPLER 
TRADITIONAL_MINIMIZER 

Function Documentation

◆ add_these()

Real protocols::stepwise::modeler::add_these ( core::Size const  final_idx,
utility::vector1< Real > const &  factors 
)

References protocols::hybridization::val.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_clustering().

◆ add_to_pose_list()

void protocols::stepwise::modeler::add_to_pose_list ( utility::vector1< core::pose::PoseOP > &  pose_list,
pose::Pose const &  pose,
std::string const &  pose_tag 
)

References core::pose::Pose::clone(), and core::pose::tag_into_pose().

◆ apply_numbering()

utility::vector1< core::Size > protocols::stepwise::modeler::apply_numbering ( utility::vector1< core::Size > const &  res,
utility::vector1< core::Size > const &  numbering 
)

Referenced by slice_out_pose().

◆ check_for_input_domain() [1/2]

bool protocols::stepwise::modeler::check_for_input_domain ( pose::Pose const &  pose)

References core::pose::Pose::size().

◆ check_for_input_domain() [2/2]

bool protocols::stepwise::modeler::check_for_input_domain ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  partition_res 
)

References core::pose::full_model_info::get_fixed_domain_from_full_model_info_const().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::decide_to_keep_pose().

◆ check_jump_to_next_residue_in_chain() [1/3]

Size protocols::stepwise::modeler::check_jump_to_next_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element 
)

References check_jump_to_next_residue_in_chain(), and core::pose::Pose::size().

◆ check_jump_to_next_residue_in_chain() [2/3]

Size protocols::stepwise::modeler::check_jump_to_next_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element,
FullModelInfo const &  full_model_info 
)

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

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments().

◆ check_jump_to_next_residue_in_chain() [3/3]

Size protocols::stepwise::modeler::check_jump_to_next_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  chains_in_full_model 
)

References core::kinematics::Edge::CHEMICAL, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::jump_nr(), core::kinematics::Edge::label(), core::kinematics::FoldTree::residue_is_in_fold_tree(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), and core::kinematics::Edge::start().

Referenced by check_jump_to_next_residue_in_chain(), and slice().

◆ check_jump_to_previous_residue_in_chain() [1/3]

Size protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element 
)

References check_jump_to_previous_residue_in_chain(), and core::pose::Pose::size().

◆ check_jump_to_previous_residue_in_chain() [2/3]

Size protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element,
FullModelInfo const &  full_model_info 
)

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

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments().

◆ check_jump_to_previous_residue_in_chain() [3/3]

Size protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain ( pose::Pose const &  pose,
core::Size const  i,
utility::vector1< core::Size > const &  current_element,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  chains_in_full_model 
)

References core::kinematics::Edge::CHEMICAL, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::jump_nr(), core::kinematics::Edge::label(), core::kinematics::FoldTree::residue_is_in_fold_tree(), and core::kinematics::FoldTree::root().

Referenced by check_jump_to_previous_residue_in_chain(), and slice().

◆ check_scorefxn_has_constraint_terms_if_pose_has_constraints()

void protocols::stepwise::modeler::check_scorefxn_has_constraint_terms_if_pose_has_constraints ( pose::Pose const &  pose,
core::scoring::ScoreFunctionOP &  scorefxn 
)

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), and core::scoring::coordinate_constraint.

Referenced by get_minimize_scorefxn(), and initialize_sample_scorefxn().

◆ check_scores_from_parts()

void protocols::stepwise::modeler::check_scores_from_parts ( std::string const &  tag,
Real const  original_score,
pose::Pose &  pose,
pose::PoseOP  original_pose_clone,
utility::vector1< PoseOP > const &  other_pose_list,
core::scoring::ScoreFunctionCOP  scorefxn 
)

References core::pose::Pose::energies(), core::scoring::intermol, core::scoring::loop_close, protocols::hybridization::score, core::scoring::Energies::total_energies(), core::pose::TR(), and core::scoring::loop_graph::LoopGraph::update().

◆ constraint_set_slice()

core::scoring::constraints::ConstraintSetOP protocols::stepwise::modeler::constraint_set_slice ( core::scoring::constraints::ConstraintSetOP &  cst_set,
utility::vector1< core::Size > const &  slice_res,
pose::Pose const &  pose,
pose::Pose const &  full_pose 
)

References core::pose::Pose::size().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_constraints().

◆ declare_chemical_bonds_at_cutpoints() [1/2]

void protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints ( pose::Pose &  pose,
pose::Pose const &  source_pose,
utility::vector1< core::Size > const &  working_res 
)

References declare_chemical_bonds_at_cutpoints(), and core::pose::Pose::size().

◆ declare_chemical_bonds_at_cutpoints() [2/2]

void protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints ( pose::Pose &  pose,
pose::Pose const &  source_pose,
utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  source_working_res 
)

References core::chemical::CUTPOINT_LOWER, core::pose::declare_cutpoint_chemical_bond(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by declare_chemical_bonds_at_cutpoints(), merge_two_poses(), and slice().

◆ figure_out_moving_chain_break_res()

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_chain_break_res ( pose::Pose const &  pose,
kinematics::MoveMap const &  mm 
)

TODO: generalize to cyclized chainbreaks.

References core::id::BB, core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), get_cutpoint_closed(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::partition_by_residue(), and core::pose::Pose::size().

Referenced by protocols::rna::denovo::movers::RNA_Minimizer::apply().

◆ figure_out_moving_chain_breaks()

void protocols::stepwise::modeler::figure_out_moving_chain_breaks ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res,
utility::vector1< core::Size > &  cutpoints_closed,
utility::vector1< core::Size > &  five_prime_chain_breaks,
utility::vector1< core::Size > &  three_prime_chain_breaks,
utility::vector1< core::Size > &  chain_break_gap_sizes 
)

TODO: generalize to cyclized chainbreaks.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info_const(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_TNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by figure_out_moving_cutpoints_closed(), protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

◆ figure_out_moving_cutpoints_closed()

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_cutpoints_closed ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)

References figure_out_moving_chain_breaks().

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler(), and figure_out_moving_cutpoints_closed_from_moving_res().

◆ figure_out_moving_cutpoints_closed_from_moving_res() [1/2]

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res ( pose::Pose const &  pose,
core::Size const  moving_res 
)

References figure_out_moving_cutpoints_closed(), and protocols::toolbox::rigid_body::figure_out_moving_partition_res().

Referenced by protocols::recces::scratch::ThermalMinimizer::apply(), protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks(), and protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

◆ figure_out_moving_cutpoints_closed_from_moving_res() [2/2]

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References figure_out_moving_cutpoints_closed(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), and merge_vectors().

Referenced by protocols::stepwise::modeler::protein::get_bridge_res().

◆ figure_out_moving_partition_res() [1/2]

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res ( pose::Pose const &  pose,
core::Size const  moving_res 
)

References figure_out_root_and_moving_partition_res().

Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack(), and protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler().

◆ figure_out_moving_partition_res() [2/2]

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References protocols::toolbox::rigid_body::figure_out_moving_partition_res(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), and core::chemical::VIRTUAL_RNA_RESIDUE.

◆ figure_out_moving_partition_res_for_jump()

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump ( pose::Pose const &  pose,
core::Size const  jump_nr 
)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), get_partition_definition_by_jump(), and core::pose::Pose::size().

◆ figure_out_moving_partition_res_for_suite()

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res_for_suite ( pose::Pose const &  pose,
core::Size const  moving_res,
core::Size const  reference_res 
)

References get_partition_definition(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::figure_out_reference_res().

◆ figure_out_reference_res_for_suite()

core::Size protocols::stepwise::modeler::figure_out_reference_res_for_suite ( pose::Pose const &  pose,
core::Size const  moving_res 
)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::get_parent_residue().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::figure_out_reference_res().

◆ figure_out_root_and_moving_partition_res()

void protocols::stepwise::modeler::figure_out_root_and_moving_partition_res ( pose::Pose const &  pose,
core::Size const  moving_res,
utility::vector1< core::Size > &  root_partition_res,
utility::vector1< core::Size > &  moving_partition_res 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), get_partition_definition(), get_partition_definition_by_jump(), core::kinematics::FoldTree::jump_nr(), protocols::mean_field::min(), and core::pose::Pose::size().

Referenced by protocols::stepwise::screener::PartitionContactScreener::check_screen(), figure_out_moving_partition_res(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::ordered_move_from_partition(), revise_root_and_moving_res(), and protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly().

◆ figure_out_root_partition_res()

utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_root_partition_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References protocols::toolbox::rigid_body::figure_out_moving_partition_res(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), protocols::stepwise::modeler::align::StepWiseClusterer::check_for_closeness(), protocols::rna::AlignmentEnergy::eval_atom_derivative(), protocols::rna::AlignmentEnergy::finalize_total_energy(), and protocols::stepwise::modeler::align::get_rmsd().

◆ find_downstream_connection_res()

Size protocols::stepwise::modeler::find_downstream_connection_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_h2o, core::pose::Pose::annotated_sequence(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::pose::Pose::residue_type(), and core::pose::TR().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_actual_moving_res(), and get_unique_connection_res().

◆ find_first_root_residue()

Size protocols::stepwise::modeler::find_first_root_residue ( kinematics::FoldTree const &  f,
utility::vector1< core::Size > const &  working_res_subset,
utility::vector1< core::Size > const &  working_res 
)

References core::kinematics::FoldTree::nres(), and core::kinematics::FoldTree::possible_root().

Referenced by merge_two_poses().

◆ find_jump_number_at_suite()

core::Size protocols::stepwise::modeler::find_jump_number_at_suite ( kinematics::FoldTree const &  fold_tree,
core::Size const &  moving_suite 
)

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by make_cut_at_moving_suite().

◆ find_root_without_virtual_ribose()

bool protocols::stepwise::modeler::find_root_without_virtual_ribose ( kinematics::FoldTree const &  f,
pose::Pose const &  pose 
)

References core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::possible_root(), core::pose::Pose::residue_type(), and core::chemical::VIRTUAL_RIBOSE.

◆ fix_protein_jump_atom()

void protocols::stepwise::modeler::fix_protein_jump_atom ( pose::Pose &  pose,
core::Size const  res,
std::string const &  atom_name 
)

References core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::is_protein(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::upstream_atom(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries().

◆ fix_up_jump_atoms()

void protocols::stepwise::modeler::fix_up_jump_atoms ( pose::Pose &  pose)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs().

Referenced by fix_up_jump_atoms_and_residue_type_variants().

◆ fix_up_jump_atoms_and_residue_type_variants()

void protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants ( pose::Pose &  pose_to_fix)

References core::scoring::rna::clear_rna_scoring_info(), core::pose::rna::secstruct_legacy::clear_rna_secstruct_legacy_info(), fix_up_jump_atoms(), core::pose::fix_up_residue_type_variants(), and core::pose::full_model_info::update_constraint_set_from_full_model_info().

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::apply(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), and protocols::stepwise::monte_carlo::mover::FromScratchMover::apply().

◆ freeze_waters()

void protocols::stepwise::modeler::freeze_waters ( core::pose::Pose const &  pose,
core::kinematics::MoveMap &  mm 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), protocols::magnesium::get_water_res(), and core::kinematics::MoveMap::set_jump().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::get_move_map_and_atom_level_domain_map().

◆ get_all_residues()

utility::vector1< core::Size > protocols::stepwise::modeler::get_all_residues ( pose::Pose const &  pose)

References core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::packer::StepWisePacker::figure_out_neighbors(), protocols::stepwise::modeler::StepWiseMinimizer::let_neighboring_side_chains_minimize(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose(), and protocols::stepwise::modeler::packer::StepWisePacker::reset().

◆ get_all_working_moving_res()

utility::vector1< core::Size > protocols::stepwise::modeler::get_all_working_moving_res ( working_parameters::StepWiseWorkingParametersCOP  working_parameters)

References merge_vectors().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize_packer(), and protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root().

◆ get_cutpoint_closed()

utility::vector1< core::Size > protocols::stepwise::modeler::get_cutpoint_closed ( pose::Pose const &  pose)

References is_cutpoint_closed(), and core::pose::Pose::size().

Referenced by figure_out_moving_chain_break_res().

◆ get_domain_boundary_res()

utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_res ( pose::Pose const &  pose)

References core::pose::Pose::fold_tree(), get_domain_boundary_suites(), and core::kinematics::FoldTree::get_parent_residue().

Referenced by get_moving_res_including_domain_boundaries().

◆ get_domain_boundary_suites()

utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_suites ( pose::Pose const &  pose)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::size(), and core::pose::TR().

Referenced by get_domain_boundary_res().

◆ get_endpoints_from_pose()

void protocols::stepwise::modeler::get_endpoints_from_pose ( utility::vector1< core::Size > &  endpoints,
pose::Pose const &  pose,
utility::vector1< core::Size > const &  working_res 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::size().

Referenced by merge_two_poses().

◆ get_jump_partners_from_pose()

void protocols::stepwise::modeler::get_jump_partners_from_pose ( utility::vector1< core::Size > &  jump_partners1,
utility::vector1< core::Size > &  jump_partners2,
utility::vector1< std::string > &  jump_atoms1,
utility::vector1< std::string > &  jump_atoms2,
pose::Pose const &  pose,
utility::vector1< core::Size > const &  working_res 
)

References core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::upstream_atom(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by merge_two_poses().

◆ get_minimize_scorefxn()

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::get_minimize_scorefxn ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
options::StepWiseModelerOptionsCOP  options 
)

References core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::chainbreak, check_scorefxn_has_constraint_terms_if_pose_has_constraints(), core::scoring::coordinate_constraint, core::scoring::elec_dens_atomwise, core::scoring::elec_dens_fast, core::scoring::linear_chainbreak, and core::scoring::rna_chem_map.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::setup_scorefxns().

◆ get_moving_res_including_domain_boundaries()

utility::vector1< core::Size > protocols::stepwise::modeler::get_moving_res_including_domain_boundaries ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References get_domain_boundary_res(), and merge_vectors().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

◆ get_other_residues()

utility::vector1< core::Size > protocols::stepwise::modeler::get_other_residues ( utility::vector1< core::Size > const &  res,
core::Size const &  nres 
)

Referenced by get_unique_connection_res(), revise_root_and_moving_res_list(), and slice_out_pose().

◆ get_partition_definition()

utility::vector1< bool > protocols::stepwise::modeler::get_partition_definition ( pose::Pose const &  pose,
core::Size const &  moving_suite 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_residue(), and core::pose::Pose::size().

Referenced by figure_out_moving_partition_res_for_suite(), figure_out_root_and_moving_partition_res(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

◆ get_partition_definition_by_chemical_edge()

utility::vector1< bool > protocols::stepwise::modeler::get_partition_definition_by_chemical_edge ( pose::Pose const &  pose,
core::kinematics::Edge const &  edge 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_residue(), core::pose::Pose::size(), and core::kinematics::Edge::start().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements().

◆ get_partition_definition_by_jump()

utility::vector1< bool > protocols::stepwise::modeler::get_partition_definition_by_jump ( pose::Pose const &  pose,
core::Size const &  jump_nr 
)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::partition_by_jump().

Referenced by figure_out_moving_partition_res_for_jump(), figure_out_root_and_moving_partition_res(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), and protocols::stepwise::modeler::rna::get_partition_definition_floating_base().

◆ get_possible_root()

Size protocols::stepwise::modeler::get_possible_root ( pose::Pose const &  pose,
utility::vector1< Size > const &  partition_res,
bool const  disallow_cutpoint_closed_upper 
)

References core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::possible_root(), and core::pose::Pose::residue_type().

Referenced by revise_root_and_moving_res().

◆ get_res_map()

std::map< core::Size, core::Size > protocols::stepwise::modeler::get_res_map ( utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  source_res 
)

Referenced by protocols::stepwise::modeler::rna::sugar::convert_sugar_modeling_to_residue_alternative_set(), protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion(), and merge_two_poses().

◆ get_unique_connection_res()

Size protocols::stepwise::modeler::get_unique_connection_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)

References find_downstream_connection_res(), core::pose::Pose::fold_tree(), get_other_residues(), core::kinematics::FoldTree::root(), and core::pose::Pose::size().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply().

◆ initialize_o2prime_pack_scorefxn()

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_o2prime_pack_scorefxn ( core::scoring::ScoreFunctionCOP const &  scorefxn)

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::free_2HOprime, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_sr_bb_sc, and core::scoring::lk_nonpolar.

Referenced by protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::O2PrimePacker().

◆ initialize_pack_scorefxn()

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_pack_scorefxn ( core::scoring::ScoreFunctionCOP  sample_scorefxn,
pose::Pose const &   
)

References core::scoring::ch_bond, core::scoring::methods::EnergyMethodOptions::clone(), core::scoring::methods::EnergyMethodOptions::etable_options(), core::scoring::fa_sol, core::scoring::fa_stack, core::scoring::facts_elec, core::scoring::facts_sasa, core::scoring::facts_solv, core::scoring::free_2HOprime, core::scoring::free_base, core::scoring::free_dof, core::scoring::free_side_chain, core::scoring::free_suite, core::scoring::geom_sol, core::scoring::geom_sol_fast, core::scoring::lk_ball, core::scoring::lk_nonpolar, core::scoring::lk_polar, core::scoring::etable::EtableOptions::no_lk_polar_desolvation, core::scoring::occ_sol_fitted, and core::scoring::rna_chem_map.

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

◆ initialize_sample_scorefxn()

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_sample_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn,
pose::Pose const &  pose,
options::StepWiseModelerOptionsCOP  options 
)

References core::scoring::chainbreak, check_scorefxn_has_constraint_terms_if_pose_has_constraints(), core::scoring::elec_dens_atomwise, core::scoring::fa_rep, core::scoring::linear_chainbreak, core::scoring::mg_lig, core::scoring::mg_sol, core::scoring::rna_chem_map, and core::scoring::rna_mg_point.

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

◆ is_cutpoint_closed()

bool protocols::stepwise::modeler::is_cutpoint_closed ( pose::Pose const &  pose,
core::Size const  seq_num 
)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint_flanked_by_bridge_res(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), get_cutpoint_closed(), protocols::stepwise::legacy::modeler::protein::is_close_chain_break(), and protocols::stepwise::modeler::rna::remove_chain_break_variants().

◆ is_protein()

bool protocols::stepwise::modeler::is_protein ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), and core::pose::Pose::residue_type().

Referenced by protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info(), protocols::loops::Loop::is_terminal(), core::pose::Pose::omega(), output_movemap(), core::pose::Pose::phi(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::pose::Pose::psi(), core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and protocols::electron_density::DockPDBIntoDensityMover::setMultiNative().

◆ look_for_unique_jump_to_moving_res()

core::Size protocols::stepwise::modeler::look_for_unique_jump_to_moving_res ( kinematics::FoldTree const &  fold_tree,
core::Size const &  i 
)

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), protocols::stepwise::modeler::rna::get_anchor_res(), and protocols::stepwise::modeler::rna::get_partition_definition_floating_base().

◆ make_cut_at_moving_suite() [1/2]

core::Size protocols::stepwise::modeler::make_cut_at_moving_suite ( core::kinematics::FoldTree &  fold_tree,
core::Size const &  moving_suite 
)

References find_jump_number_at_suite(), and core::kinematics::FoldTree::new_jump().

◆ make_cut_at_moving_suite() [2/2]

core::Size protocols::stepwise::modeler::make_cut_at_moving_suite ( pose::Pose &  pose,
core::Size const &  moving_suite 
)

References core::kinematics::Edge::CHEMICAL, find_jump_number_at_suite(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::Edge::label(), and core::pose::Pose::size().

Referenced by split_pose().

◆ make_variants_match()

void protocols::stepwise::modeler::make_variants_match ( pose::Pose &  pose,
pose::Pose const &  reference_pose,
core::Size const  n,
chemical::VariantType const  variant_type 
)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::packer::SideChainCopier::apply(), and protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants().

◆ map_to_local_numbering()

utility::vector1< core::Size > protocols::stepwise::modeler::map_to_local_numbering ( utility::vector1< core::Size > const &  vec,
utility::vector1< core::Size > const &  working_res 
)

Referenced by merge_two_poses().

◆ merge_disjoint_vectors()

utility::vector1< core::Size > protocols::stepwise::modeler::merge_disjoint_vectors ( utility::vector1< core::Size > const &  res_vector1,
utility::vector1< core::Size > const &  res_vector2 
)

Referenced by merge_two_poses().

◆ merge_in_other_pose()

void protocols::stepwise::modeler::merge_in_other_pose ( pose::Pose &  pose,
pose::Pose const &  pose2,
core::Size const  lower_merge_res,
core::Size const  upper_merge_res,
bool const  connect_residues_by_bond 
)

References core::pose::full_model_info::FullModelInfo::add_submotif_info(), core::pose::Pose::conformation(), core::pose::full_model_info::const_full_model_info(), merge_two_poses_using_full_model_info(), core::pose::full_model_info::nonconst_full_model_info(), core::pose::full_model_info::FullModelInfo::set_res_list(), core::pose::full_model_info::update_pose_objects_from_full_model_info(), and core::pose::full_model_info::FullModelInfo::update_submotif_info_list().

Referenced by merge_in_other_pose_by_bond(), and merge_in_other_pose_by_jump().

◆ merge_in_other_pose_by_bond()

void protocols::stepwise::modeler::merge_in_other_pose_by_bond ( pose::Pose &  pose,
pose::Pose const &  pose2,
core::Size const  merge_res 
)

References merge_in_other_pose().

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose().

◆ merge_in_other_pose_by_jump()

void protocols::stepwise::modeler::merge_in_other_pose_by_jump ( pose::Pose &  pose,
pose::Pose const &  pose2,
core::Size const  lower_merge_res,
core::Size const  upper_merge_res 
)

References merge_in_other_pose().

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose().

◆ merge_two_poses()

utility::vector1< core::Size > protocols::stepwise::modeler::merge_two_poses ( pose::Pose &  pose,
pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< core::Size > const &  working_res1,
utility::vector1< core::Size > const &  working_res2,
core::Size const  lower_merge_res,
core::Size const  upper_merge_res,
bool const  connect_residues_by_bond,
bool const  fix_first_pose 
)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::C_METHYLAMIDATION, core::conformation::Residue::clone(), core::pose::copydofs::copy_dofs_match_atom_names(), declare_chemical_bonds_at_cutpoints(), core::chemical::rna::default_jump_atom(), find_first_root_residue(), core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), get_endpoints_from_pose(), get_jump_partners_from_pose(), get_res_map(), core::import_pose::get_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::LOWER_TERMINUS_VARIANT, map_to_local_numbering(), merge_disjoint_vectors(), core::chemical::N_ACETYLATION, core::pose::remove_variant_type_from_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::stepwise::modeler::align::superimpose_pose_legacy(), core::chemical::THREE_PRIME_PHOSPHATE, core::pose::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by merge_two_poses_using_full_model_info().

◆ merge_two_poses_using_full_model_info()

utility::vector1< core::Size > protocols::stepwise::modeler::merge_two_poses_using_full_model_info ( pose::Pose &  pose,
pose::Pose const &  pose1,
pose::Pose const &  pose2,
core::Size const  lower_merge_res,
core::Size const  upper_merge_res,
bool const  connect_residues_by_bond 
)

References core::pose::full_model_info::get_res_list_from_full_model_info_const(), and merge_two_poses().

Referenced by merge_in_other_pose(), and test_merge_and_slice_with_two_helix_test_case().

◆ merge_vectors()

utility::vector1< core::Size > protocols::stepwise::modeler::merge_vectors ( utility::vector1< core::Size > const &  vec1,
utility::vector1< core::Size > const &  vec2 
)

Referenced by figure_out_moving_cutpoints_closed_from_moving_res(), get_all_working_moving_res(), protocols::stepwise::modeler::protein::get_bridge_res(), and get_moving_res_including_domain_boundaries().

◆ output_boolean() [1/2]

void protocols::stepwise::modeler::output_boolean ( bool  boolean,
std::ostream &  outstream 
)

References protocols::comparative_modeling::features::A.

Referenced by output_movemap().

◆ output_boolean() [2/2]

void protocols::stepwise::modeler::output_boolean ( std::string const &  tag,
bool  boolean,
std::ostream &  outstream 
)

References protocols::comparative_modeling::features::A.

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::output_bool_list(), protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(), protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list().

◆ output_movemap()

void protocols::stepwise::modeler::output_movemap ( kinematics::MoveMap const &  mm,
core::pose::Pose const &  pose,
std::ostream &  outstream 
)

References protocols::comparative_modeling::features::A, core::id::BB, core::id::CHI, core::kinematics::FoldTree::downstream_jump_residue(), core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), core::kinematics::MoveMap::get_jump(), core::chemical::element::I, core::chemical::ResidueTypeBase::is_protein(), is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::MoveMap::jump_id_begin(), core::kinematics::MoveMap::jump_id_end(), output_boolean(), output_protein_movemap_header(), output_rna_movemap_header(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::get_move_map_and_atom_level_domain_map(), and protocols::rna::movers::ErraserMinimizerMover::process_entire_pose().

◆ output_protein_movemap_header()

void protocols::stepwise::modeler::output_protein_movemap_header ( core::Size const &  spacing,
std::ostream &  outstream 
)

References protocols::comparative_modeling::features::A.

Referenced by output_movemap().

◆ output_rna_movemap_header()

void protocols::stepwise::modeler::output_rna_movemap_header ( core::Size const &  spacing,
std::ostream &  outstream 
)

References protocols::comparative_modeling::features::A.

Referenced by output_movemap().

◆ primary_fixed_domain()

Size protocols::stepwise::modeler::primary_fixed_domain ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  partition_res 
)

References core::pose::full_model_info::get_fixed_domain_from_full_model_info_const().

Referenced by revise_root_and_moving_res().

◆ reroot_based_on_full_model_info() [1/2]

void protocols::stepwise::modeler::reroot_based_on_full_model_info ( pose::Pose &  pose)

References reroot_based_on_full_model_info(), and core::pose::Pose::size().

◆ reroot_based_on_full_model_info() [2/2]

void protocols::stepwise::modeler::reroot_based_on_full_model_info ( pose::Pose &  pose,
utility::vector1< core::Size > const &  root_partition_res 
)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::chemical::CUTPOINT_UPPER, core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::full_model_info::FullModelInfo::preferred_root_res(), core::pose::reroot(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::TR(), and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by reroot_based_on_full_model_info(), revise_root_and_moving_res(), and revise_root_and_moving_res_list().

◆ revise_root_and_moving_res()

bool protocols::stepwise::modeler::revise_root_and_moving_res ( pose::Pose &  pose,
core::Size &  moving_res 
)

References figure_out_root_and_moving_partition_res(), core::pose::Pose::fold_tree(), core::pose::get_definite_terminal_root(), core::kinematics::FoldTree::get_parent_residue(), get_possible_root(), primary_fixed_domain(), reroot_based_on_full_model_info(), and core::pose::TR().

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res(), and revise_root_and_moving_res_list().

◆ revise_root_and_moving_res_list()

bool protocols::stepwise::modeler::revise_root_and_moving_res_list ( pose::Pose &  pose,
utility::vector1< core::Size > &  moving_res_list 
)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::Pose::fold_tree(), get_other_residues(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::jump_nr(), reroot_based_on_full_model_info(), core::pose::Pose::residue_type(), revise_root_and_moving_res(), core::kinematics::FoldTree::root(), and core::pose::Pose::size().

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

◆ slice()

void protocols::stepwise::modeler::slice ( pose::Pose &  sliced_out_pose,
pose::Pose const &  pose,
utility::vector1< core::Size > const &  slice_res 
)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), check_jump_to_next_residue_in_chain(), check_jump_to_previous_residue_in_chain(), core::kinematics::Edge::CHEMICAL, core::conformation::Conformation::clear(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::pose::copydofs::copy_dofs_match_atom_names(), declare_chemical_bonds_at_cutpoints(), core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_root(), core::chemical::ResidueType::is_virtual_residue(), core::kinematics::FoldTree::jump_nr(), core::kinematics::Edge::label(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::num_jump(), core::pose::remove_variant_type_from_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), protocols::stepwise::modeler::align::superimpose_pose_legacy(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), core::chemical::UPPER_TERMINUS_VARIANT, core::kinematics::FoldTree::upstream_atom(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::denovo_design::components::DivideAndConqueror::all_permutations(), protocols::denovo_design::components::BuildPhases::BuildPhases(), protocols::denovo_design::components::SolutionPredicate::check_basic_connectivity(), protocols::denovo_design::components::SolutionPredicate::check_for_unpaired_segments(), protocols::denovo_design::components::SolutionPredicate::check_template_poses(), protocols::denovo_design::components::DivideAndConqueror::compute_all_units(), protocols::denovo_design::components::StructureSlicePredicate::operator()(), protocols::denovo_design::components::operator<<(), and slice_out_pose().

◆ slice_out_pose()

void protocols::stepwise::modeler::slice_out_pose ( pose::Pose &  pose,
pose::Pose &  sliced_out_pose,
utility::vector1< core::Size > const &  residues_to_delete 
)

References apply_numbering(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, get_other_residues(), core::pose::full_model_info::nonconst_full_model_info(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::full_model_info::FullModelInfo::set_res_list(), protocols::scoring::set_vdw_cached_rep_screen_info_from_pose(), core::pose::Pose::size(), slice(), core::pose::full_model_info::update_pose_objects_from_full_model_info(), and core::pose::full_model_info::FullModelInfo::update_submotif_info_list().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::magnesium::remove_mg_bound_waters(), and test_merge_and_slice_with_two_helix_test_case().

◆ split_pose() [1/2]

core::Size protocols::stepwise::modeler::split_pose ( pose::Pose &  pose,
core::Size const  moving_res,
core::Size const  reference_res 
)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::jump(), core::kinematics::FoldTree::jump_nr(), make_cut_at_moving_suite(), core::pose::Pose::residue_type(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_translation(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by protocols::simple_ddg::DdgFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::stepwise::modeler::packer::StepWisePacker::do_prepack(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker::get_base_atr_rep_score(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score(), and protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface().

◆ split_pose() [2/2]

void protocols::stepwise::modeler::split_pose ( pose::Pose &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::get_parent_residue().

◆ switch_focus_among_poses_randomly()

bool protocols::stepwise::modeler::switch_focus_among_poses_randomly ( pose::Pose &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
bool  force_switch 
)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::other_pose_list(), core::scoring::rg, switch_focus_to_other_pose(), and core::pose::TR().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply_legacy(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), and protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus().

◆ switch_focus_to_other_pose()

void protocols::stepwise::modeler::switch_focus_to_other_pose ( pose::Pose &  pose,
core::Size const &  focus_pose_idx,
core::scoring::ScoreFunctionCOP  scorefxn 
)

References core::pose::Pose::clone(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::full_model_info::const_full_model_info(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, core::pose::full_model_info::nonconst_full_model_info(), core::scoring::other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), core::pose::full_model_info::FullModelInfo::set_other_pose_list(), protocols::scoring::set_vdw_cached_rep_screen_info_from_pose(), and core::pose::TR().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), and switch_focus_among_poses_randomly().

◆ test_merge_and_slice_with_two_helix_test_case()

void protocols::stepwise::modeler::test_merge_and_slice_with_two_helix_test_case ( utility::vector1< core::pose::PoseOP > const &  input_poses,
core::scoring::ScoreFunctionOP  scorefxn 
)

References core::pose::full_model_info::const_full_model_info(), core::pose::Pose::dump_pdb(), merge_two_poses_using_full_model_info(), core::pose::full_model_info::FullModelInfo::res_list(), and slice_out_pose().

◆ virtualize_side_chains()

void protocols::stepwise::modeler::virtualize_side_chains ( pose::Pose &  pose)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::VIRTUAL_O2PRIME_HYDROGEN, and core::chemical::VIRTUAL_SIDE_CHAIN.

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose().

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