util.cc File Reference

Not particularly fancy, just minimizes a list of poses. More...

#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/align/util.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh>
#include <protocols/farna/util.hh>
#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/rna/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/copydofs/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/SequenceMapping.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/scoring/Energies.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzMatrix.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/stream_util.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::stepwise
	protocols::stepwise::modeler

Functions
static thread_local basic::Tracer	TR ("protocols.stepwise.modeler.util")
Size	protocols::stepwise::modeler::make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)
Size	protocols::stepwise::modeler::make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
Size	protocols::stepwise::modeler::find_jump_number_at_suite (kinematics::FoldTree const &fold_tree, Size const &moving_suite)
Size	protocols::stepwise::modeler::look_for_unique_jump_to_moving_res (kinematics::FoldTree const &fold_tree, Size const &i)
bool	protocols::stepwise::modeler::is_cutpoint_closed (pose::Pose const &pose, Size const seq_num)
utility::vector1< Size >	protocols::stepwise::modeler::get_cutpoint_closed (pose::Pose const &pose)
utility::vector1< Size >	protocols::stepwise::modeler::merge_vectors (utility::vector1< Size > const &vec1, utility::vector1< Size > const &vec2)
void	protocols::stepwise::modeler::get_jump_partners_from_pose (utility::vector1< Size > &jump_partners1, utility::vector1< Size > &jump_partners2, utility::vector1< std::string > &jump_atoms1, utility::vector1< std::string > &jump_atoms2, pose::Pose const &pose, utility::vector1< Size > const &working_res)
void	protocols::stepwise::modeler::get_endpoints_from_pose (utility::vector1< Size > &endpoints, pose::Pose const &pose, utility::vector1< Size > const &working_res)
utility::vector1< Size >	protocols::stepwise::modeler::map_to_local_numbering (utility::vector1< Size > const &vec, utility::vector1< Size > const &working_res)
std::map< Size, Size >	protocols::stepwise::modeler::get_res_map (utility::vector1< Size > const &working_res, utility::vector1< Size > const &source_res)
utility::vector1< Size >	protocols::stepwise::modeler::merge_disjoint_vectors (utility::vector1< Size > const &res_vector1, utility::vector1< Size > const &res_vector2)
bool	protocols::stepwise::modeler::find_root_without_virtual_ribose (kinematics::FoldTree const &f, pose::Pose const &pose)
bool	protocols::stepwise::modeler::effective_lower_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model)
bool	protocols::stepwise::modeler::effective_upper_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model, Size const nres_full)
bool	protocols::stepwise::modeler::definite_terminal_root (utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, Size const nres, Size const i)
bool	protocols::stepwise::modeler::definite_terminal_root (pose::Pose const &pose, Size const i)
Size	protocols::stepwise::modeler::find_first_root_residue (kinematics::FoldTree const &f, utility::vector1< Size > const &working_res_subset, utility::vector1< Size > const &working_res)
utility::vector1< Size >	protocols::stepwise::modeler::reorder_root_partition_res (utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map)
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< Size > const &root_partition_res)
void	protocols::stepwise::modeler::reroot (pose::Pose &pose, utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &preferred_root_res, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res)
void	protocols::stepwise::modeler::merge_in_other_pose_by_jump (pose::Pose &pose, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res)
void	protocols::stepwise::modeler::merge_in_other_pose_by_bond (pose::Pose &pose, pose::Pose const &pose2, Size const merge_res)
void	protocols::stepwise::modeler::merge_in_other_pose (pose::Pose &pose, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond)
utility::vector1< Size >	protocols::stepwise::modeler::merge_two_poses_using_full_model_info (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond)
utility::vector1< Size >	protocols::stepwise::modeler::merge_two_poses (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &working_res1, utility::vector1< Size > const &working_res2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond, bool const fix_first_pose)
utility::vector1< Size >	protocols::stepwise::modeler::apply_numbering (utility::vector1< Size > const &res, utility::vector1< Size > const &numbering)
utility::vector1< Size >	protocols::stepwise::modeler::get_other_residues (utility::vector1< Size > const &res, Size const &nres)
void	protocols::stepwise::modeler::slice_out_pose (pose::Pose &pose, pose::Pose &sliced_out_pose, utility::vector1< Size > const &residues_to_delete)
void	protocols::stepwise::modeler::slice (pose::Pose &sliced_out_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, FullModelInfo const &full_model_info)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, utility::vector1< Size > const &res_list, utility::vector1< Size > const &chains_in_full_model)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, FullModelInfo const &full_model_info)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, utility::vector1< Size > const &res_list, utility::vector1< Size > const &chains_in_full_model)
void	protocols::stepwise::modeler::fix_up_residue_type_variants_at_strand_end (pose::Pose &pose, Size const res)
void	protocols::stepwise::modeler::fix_up_residue_type_variants_at_strand_beginning (pose::Pose &pose, Size const res)
void	protocols::stepwise::modeler::fix_up_residue_type_variants_at_floating_base (pose::Pose &pose, Size const res)
void	protocols::stepwise::modeler::fix_up_residue_type_variants (pose::Pose &pose_to_fix)
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::switch_focus_to_other_pose (pose::Pose &pose, Size const &focus_pose_idx)
bool	protocols::stepwise::modeler::switch_focus_among_poses_randomly (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, bool force_switch)
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)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_chain_break_res (pose::Pose const &pose, kinematics::MoveMap const &mm)
bool	protocols::stepwise::modeler::check_for_input_domain (pose::Pose const &pose, utility::vector1< Size > const &partition_res)
Size	protocols::stepwise::modeler::primary_fixed_domain (pose::Pose const &pose, utility::vector1< Size > const &partition_res)
bool	protocols::stepwise::modeler::check_for_input_domain (pose::Pose const &pose)
void	protocols::stepwise::modeler::make_variants_match (pose::Pose &pose, pose::Pose const &reference_pose, Size const n, chemical::VariantType const variant_type)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res)
void	protocols::stepwise::modeler::figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res, utility::vector1< Size > &cutpoints_closed, utility::vector1< Size > &five_prime_chain_breaks, utility::vector1< Size > &three_prime_chain_breaks, utility::vector1< Size > &chain_break_gap_sizes)
utility::vector1< bool >	protocols::stepwise::modeler::get_partition_definition_by_jump (pose::Pose const &pose, Size const &jump_nr)
utility::vector1< bool >	protocols::stepwise::modeler::get_partition_definition (pose::Pose const &pose, Size const &moving_suite)
Size	protocols::stepwise::modeler::figure_out_reference_res_for_suite (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_partition_res_for_suite (pose::Pose const &pose, Size const moving_res, Size const reference_res)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump (pose::Pose const &pose, Size const jump_nr)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
utility::vector1< Size >	protocols::stepwise::modeler::figure_out_root_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
void	protocols::stepwise::modeler::figure_out_root_and_moving_partition_res (pose::Pose const &pose, Size const moving_res, utility::vector1< Size > &root_partition_res, utility::vector1< Size > &moving_partition_res)
bool	protocols::stepwise::modeler::revise_root_and_moving_res (pose::Pose &pose, Size &moving_res)
bool	protocols::stepwise::modeler::revise_root_and_moving_res_list (pose::Pose &pose, utility::vector1< Size > &moving_res_list)
Size	protocols::stepwise::modeler::split_pose (pose::Pose &pose, Size const moving_res, Size const reference_res)
void	protocols::stepwise::modeler::split_pose (pose::Pose &pose, utility::vector1< Size > const &moving_res_list)
void	protocols::stepwise::modeler::fix_protein_jump_atom (pose::Pose &pose, Size const res, std::string const atom_name)
void	protocols::stepwise::modeler::add_to_pose_list (utility::vector1< core::pose::PoseOP > &pose_list, pose::Pose const &pose, std::string const pose_tag)
bool	protocols::stepwise::modeler::is_protein (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_domain_boundary_suites (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_moving_res_including_domain_boundaries (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
utility::vector1< Size >	protocols::stepwise::modeler::get_all_working_moving_res (working_parameters::StepWiseWorkingParametersCOP working_parameters)
void	protocols::stepwise::modeler::virtualize_side_chains (pose::Pose &pose)
utility::vector1< Size >	protocols::stepwise::modeler::get_all_residues (pose::Pose const &pose)
Size	protocols::stepwise::modeler::find_downstream_connection_res (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res)
Size	protocols::stepwise::modeler::get_unique_connection_res (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res)
void	protocols::stepwise::modeler::map_constraints_from_original_pose (pose::Pose const &original_pose, pose::Pose &pose)

Detailed Description

Not particularly fancy, just minimizes a list of poses.

Detailed:

Author

Rhiju Das

Function Documentation

static thread_local basic::Tracer TR ( "protocols.stepwise.modeler.util"  )

static

Referenced by protocols::stepwise::modeler::fix_up_residue_type_variants_at_strand_beginning(), protocols::stepwise::modeler::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::modeler::get_domain_boundary_suites(), protocols::stepwise::modeler::merge_two_poses(), protocols::stepwise::modeler::reroot(), and protocols::stepwise::modeler::switch_focus_among_poses_randomly().