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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::Sizeget_cutpoint_closed (pose::Pose const &pose)
 
utility::vector1< core::Sizemerge_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::Sizemap_to_local_numbering (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res)
 
std::map< core::Size, core::Sizeget_res_map (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &source_res)
 
utility::vector1< core::Sizemerge_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::Sizemerge_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::Sizemerge_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::Sizeapply_numbering (utility::vector1< core::Size > const &res, utility::vector1< core::Size > const &numbering)
 
utility::vector1< core::Sizeget_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::Sizefigure_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::Sizefigure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Sizefigure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Sizefigure_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< boolget_partition_definition_by_jump (pose::Pose const &pose, core::Size const &jump_nr)
 
utility::vector1< boolget_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::Sizefigure_out_moving_partition_res_for_suite (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
utility::vector1< core::Sizefigure_out_moving_partition_res_for_jump (pose::Pose const &pose, core::Size const jump_nr)
 
utility::vector1< core::Sizefigure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Sizefigure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Sizefigure_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)
 
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::Sizeget_domain_boundary_suites (pose::Pose const &pose)
 
utility::vector1< core::Sizeget_domain_boundary_res (pose::Pose const &pose)
 
utility::vector1< core::Sizeget_moving_res_including_domain_boundaries (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
 
utility::vector1< core::Sizeget_all_working_moving_res (working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
void virtualize_side_chains (pose::Pose &pose)
 
utility::vector1< core::Sizeget_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)
 
void add_to_pose_list (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose const &pose, std::string const &pose_tag)
 

Typedef Documentation

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

Enumeration Type Documentation

Enumerator
THERMAL_SAMPLER 
TRADITIONAL_MINIMIZER 

Function Documentation

Real protocols::stepwise::modeler::add_these ( core::Size const  final_idx,
utility::vector1< Real > const &  factors 
)
void protocols::stepwise::modeler::add_to_pose_list ( utility::vector1< core::pose::PoseOP > &  pose_list,
core::pose::Pose const &  pose,
std::string const &  pose_tag 
)
void protocols::stepwise::modeler::add_to_pose_list ( utility::vector1< core::pose::PoseOP > &  pose_list,
pose::Pose const &  pose,
std::string const &  pose_tag 
)
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().

bool protocols::stepwise::modeler::check_for_input_domain ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  partition_res 
)
bool protocols::stepwise::modeler::check_for_input_domain ( pose::Pose const &  pose)
core::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 
)
core::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 
)
core::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 
)
core::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 
)
core::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 
)
core::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 
)
void protocols::stepwise::modeler::check_scorefxn_has_constraint_terms_if_pose_has_constraints ( pose::Pose const &  pose,
core::scoring::ScoreFunctionOP scorefxn 
)
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 
)
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 
)
void protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints ( pose::Pose pose,
pose::Pose const &  source_pose,
utility::vector1< core::Size > const &  working_res 
)
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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_chain_break_res ( pose::Pose const &  pose,
kinematics::MoveMap const &  mm 
)
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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_cutpoints_closed ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res ( pose::Pose const &  pose,
core::Size const  moving_res 
)
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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res ( pose::Pose const &  pose,
core::Size const  moving_res 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump ( pose::Pose const &  pose,
core::Size const  jump_nr 
)
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 
)
core::Size protocols::stepwise::modeler::figure_out_reference_res_for_suite ( pose::Pose const &  pose,
core::Size const  moving_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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::figure_out_root_partition_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)
core::Size protocols::stepwise::modeler::find_downstream_connection_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)
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 
)
core::Size protocols::stepwise::modeler::find_jump_number_at_suite ( kinematics::FoldTree const &  fold_tree,
core::Size const &  moving_suite 
)
bool protocols::stepwise::modeler::find_root_without_virtual_ribose ( kinematics::FoldTree const &  f,
pose::Pose const &  pose 
)
void protocols::stepwise::modeler::fix_protein_jump_atom ( pose::Pose pose,
core::Size const  res,
std::string const &  atom_name 
)
void protocols::stepwise::modeler::fix_up_jump_atoms ( pose::Pose pose)
void protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants ( pose::Pose pose_to_fix)
void protocols::stepwise::modeler::freeze_waters ( core::pose::Pose const &  pose,
core::kinematics::MoveMap mm 
)
utility::vector1< core::Size > protocols::stepwise::modeler::get_all_residues ( pose::Pose const &  pose)
utility::vector1< core::Size > protocols::stepwise::modeler::get_all_working_moving_res ( working_parameters::StepWiseWorkingParametersCOP  working_parameters)
utility::vector1< core::Size > protocols::stepwise::modeler::get_cutpoint_closed ( pose::Pose const &  pose)
utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_res ( pose::Pose const &  pose)
utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_suites ( pose::Pose const &  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 
)
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 
)
core::scoring::ScoreFunctionOP protocols::stepwise::modeler::get_minimize_scorefxn ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scorefxn,
options::StepWiseModelerOptionsCOP  options 
)
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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::get_other_residues ( utility::vector1< core::Size > const &  res,
core::Size const &  nres 
)
utility::vector1< bool > protocols::stepwise::modeler::get_partition_definition ( pose::Pose const &  pose,
core::Size const &  moving_suite 
)
utility::vector1< bool > protocols::stepwise::modeler::get_partition_definition_by_jump ( pose::Pose const &  pose,
core::Size const &  jump_nr 
)
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 
)
core::Size protocols::stepwise::modeler::get_unique_connection_res ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_partition_res 
)
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_o2prime_pack_scorefxn ( core::scoring::ScoreFunctionCOP const &  scorefxn)
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_pack_scorefxn ( core::scoring::ScoreFunctionCOP  sample_scorefxn,
pose::Pose const &   
)
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_sample_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn,
pose::Pose const &  pose,
options::StepWiseModelerOptionsCOP  options 
)
bool protocols::stepwise::modeler::is_cutpoint_closed ( pose::Pose const &  pose,
core::Size const  seq_num 
)
bool protocols::stepwise::modeler::is_protein ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res_list 
)
core::Size protocols::stepwise::modeler::look_for_unique_jump_to_moving_res ( kinematics::FoldTree const &  fold_tree,
core::Size const &  i 
)
core::Size protocols::stepwise::modeler::make_cut_at_moving_suite ( core::kinematics::FoldTree fold_tree,
core::Size const &  moving_suite 
)
core::Size protocols::stepwise::modeler::make_cut_at_moving_suite ( pose::Pose pose,
core::Size const &  moving_suite 
)
void protocols::stepwise::modeler::make_variants_match ( pose::Pose pose,
pose::Pose const &  reference_pose,
core::Size const  n,
chemical::VariantType const  variant_type 
)
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().

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().

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 
)
void protocols::stepwise::modeler::merge_in_other_pose_by_bond ( pose::Pose pose,
pose::Pose const &  pose2,
core::Size const  merge_res 
)
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 
)
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 
)
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 
)
utility::vector1< core::Size > protocols::stepwise::modeler::merge_vectors ( utility::vector1< core::Size > const &  vec1,
utility::vector1< core::Size > const &  vec2 
)
void protocols::stepwise::modeler::output_boolean ( std::string const &  tag,
bool  boolean,
std::ostream &  outstream 
)
void protocols::stepwise::modeler::output_boolean ( bool  boolean,
std::ostream &  outstream 
)
void protocols::stepwise::modeler::output_movemap ( kinematics::MoveMap const &  mm,
core::pose::Pose const &  pose,
std::ostream &  outstream 
)
void protocols::stepwise::modeler::output_protein_movemap_header ( core::Size const &  spacing,
std::ostream &  outstream 
)
void protocols::stepwise::modeler::output_rna_movemap_header ( core::Size const &  spacing,
std::ostream &  outstream 
)
Size protocols::stepwise::modeler::primary_fixed_domain ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  partition_res 
)
void protocols::stepwise::modeler::reroot_based_on_full_model_info ( pose::Pose pose)
void protocols::stepwise::modeler::reroot_based_on_full_model_info ( pose::Pose pose,
utility::vector1< core::Size > const &  root_partition_res 
)
bool protocols::stepwise::modeler::revise_root_and_moving_res ( pose::Pose pose,
core::Size moving_res 
)
bool protocols::stepwise::modeler::revise_root_and_moving_res_list ( pose::Pose pose,
utility::vector1< core::Size > &  moving_res_list 
)
void protocols::stepwise::modeler::slice ( pose::Pose sliced_out_pose,
pose::Pose const &  pose,
utility::vector1< core::Size > const &  slice_res 
)
void protocols::stepwise::modeler::slice_out_pose ( pose::Pose pose,
pose::Pose sliced_out_pose,
utility::vector1< core::Size > const &  residues_to_delete 
)
core::Size protocols::stepwise::modeler::split_pose ( pose::Pose pose,
core::Size const  moving_res,
core::Size const  reference_res 
)
void protocols::stepwise::modeler::split_pose ( pose::Pose pose,
utility::vector1< core::Size > const &  moving_res_list 
)
bool protocols::stepwise::modeler::switch_focus_among_poses_randomly ( pose::Pose pose,
core::scoring::ScoreFunctionCOP  scorefxn,
bool  force_switch 
)
void protocols::stepwise::modeler::switch_focus_to_other_pose ( pose::Pose pose,
core::Size const &  focus_pose_idx,
core::scoring::ScoreFunctionCOP  scorefxn 
)
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 
)
void protocols::stepwise::modeler::virtualize_side_chains ( pose::Pose pose)