StepWiseUtil.cc File Reference

#include <protocols/stepwise/StepWiseUtil.hh>
#include <protocols/stepwise/sampling/protein/StepWiseProteinUtil.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Util.hh>
#include <protocols/stepwise/sampling/general/StepWisePoseAligner.hh>
#include <protocols/farna/RNA_ProtocolUtil.hh>
#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/rna/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/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/FullModelInfoUtil.hh>
#include <protocols/stepwise/full_model_info/FullModelInfoSetupFromCommandLine.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/rna/RNA_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/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/Energies.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzMatrix.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.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

Functions
Size	protocols::stepwise::make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)
Size	protocols::stepwise::make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
Size	protocols::stepwise::find_jump_number_at_suite (kinematics::FoldTree const &fold_tree, Size const &moving_suite)
Size	protocols::stepwise::look_for_unique_jump_to_moving_res (kinematics::FoldTree const &fold_tree, Size const &i)
bool	protocols::stepwise::is_cutpoint_closed (pose::Pose const &pose, Size const seq_num)
utility::vector1< Size >	protocols::stepwise::get_cutpoint_closed (pose::Pose const &pose)
bool	protocols::stepwise::is_close_chain_break (pose::Pose const &pose)
void	protocols::stepwise::output_boolean (std::string const &tag, bool boolean, std::ostream &TR)
void	protocols::stepwise::output_boolean (bool boolean, std::ostream &TR)
void	protocols::stepwise::output_movemap (kinematics::MoveMap const &mm, Size const total_residue, std::ostream &TR)
void	protocols::stepwise::figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const &fixed_res, bool const move_takeoff_torsions, bool const move_jumps_between_chains)
void	protocols::stepwise::pdbslice (core::pose::Pose &new_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
void	protocols::stepwise::pdbslice (core::pose::Pose &pose, utility::vector1< core::Size > const &slice_res)
Real	protocols::stepwise::superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< Size, Size > const &res_map)
	Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map. Simple wrapper around superimpose_pose using IDs. More...
id::AtomID_Map< id::AtomID >	protocols::stepwise::create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)
id::AtomID_Map< id::AtomID >	protocols::stepwise::create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)
utility::vector1< Size > const	protocols::stepwise::convert_to_working_res (utility::vector1< Size > const &res_vector, utility::vector1< Size > const &working_res)
core::scoring::constraints::ConstraintSetOP	protocols::stepwise::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)
utility::vector1< std::string >	protocols::stepwise::load_s_and_l ()
std::string	protocols::stepwise::get_file_name (std::string const &silent_file, std::string const &tag)
void	protocols::stepwise::check_scorefxn_has_constraint_terms_if_pose_has_constraints (pose::Pose const &pose, core::scoring::ScoreFunctionOP &scorefxn)
utility::vector1< Size >	protocols::stepwise::merge_vectors (utility::vector1< Size > const &vec1, utility::vector1< Size > const &vec2)
void	protocols::stepwise::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
void	protocols::stepwise::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
void	protocols::stepwise::get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
void	protocols::stepwise::translate (pose::Pose &pose, Vector const shift, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	protocols::stepwise::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)
void	protocols::stepwise::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	protocols::stepwise::get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)
void	protocols::stepwise::translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i, utility::vector1< Size > const moving_res, bool const do_not_rotate)
void	protocols::stepwise::translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)
void	protocols::stepwise::superimpose_at_fixed_res (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms_rmsd, bool skip_bulges)
Real	protocols::stepwise::superimpose_at_fixed_res_and_get_all_atom_rmsd (pose::Pose &pose, pose::Pose const &native_pose, bool skip_bulges)
void	protocols::stepwise::superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms, bool skip_bulges=false)
Real	protocols::stepwise::superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose)
Size	protocols::stepwise::get_number_missing_residue_connections (pose::Pose &pose)
bool	protocols::stepwise::is_at_terminus (core::pose::Pose const &pose, Size const i)
void	protocols::stepwise::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::get_endpoints_from_pose (utility::vector1< Size > &endpoints, pose::Pose const &pose, utility::vector1< Size > const &working_res)
utility::vector1< Size >	protocols::stepwise::map_to_local_numbering (utility::vector1< Size > const &vec, utility::vector1< Size > const &working_res)
std::map< Size, Size >	protocols::stepwise::get_res_map (utility::vector1< Size > const &working_res, utility::vector1< Size > const &source_res)
utility::vector1< Size >	protocols::stepwise::merge_disjoint_vectors (utility::vector1< Size > const &res_vector1, utility::vector1< Size > const &res_vector2)
void	protocols::stepwise::remove_upper_terminus (core::conformation::ResidueOP &rsd)
void	protocols::stepwise::remove_lower_terminus (core::conformation::ResidueOP &rsd)
bool	protocols::stepwise::find_root_without_virtual_ribose (kinematics::FoldTree const &f, pose::Pose const &pose)
bool	protocols::stepwise::definite_terminal_root (pose::Pose const &pose, Size const i)
void	protocols::stepwise::try_reroot_at_fixed_domain (pose::Pose &pose)
Size	protocols::stepwise::find_first_root_residue (kinematics::FoldTree const &f, utility::vector1< Size > const &working_res_subset, utility::vector1< Size > const &working_res)
void	protocols::stepwise::reroot_based_on_full_model_info (pose::Pose &pose, utility::vector1< Size > const &root_partition_res)
void	protocols::stepwise::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::merge_in_other_pose_by_bond (pose::Pose &pose, pose::Pose const &pose2, Size const merge_res)
void	protocols::stepwise::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::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::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::apply_numbering (utility::vector1< Size > const &res, utility::vector1< Size > const &numbering)
utility::vector1< Size >	protocols::stepwise::get_other_residues (utility::vector1< Size > const &res, Size const &nres)
void	protocols::stepwise::slice_out_pose (pose::Pose &pose, pose::Pose &sliced_out_pose, utility::vector1< Size > const &residues_to_delete)
void	protocols::stepwise::slice (pose::Pose &sliced_out_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)
Size	protocols::stepwise::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::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)
Size	protocols::stepwise::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::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::check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)
Size	protocols::stepwise::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::fix_up_residue_type_variants_at_strand_end (pose::Pose &pose, Size const res)
void	protocols::stepwise::fix_up_residue_type_variants_at_strand_beginning (pose::Pose &pose, Size const res)
void	protocols::stepwise::fix_up_residue_type_variants_at_floating_base (pose::Pose &pose, Size const res)
void	protocols::stepwise::fix_up_residue_type_variants (pose::Pose &pose_to_fix)
void	protocols::stepwise::fix_up_jump_atoms (pose::Pose &pose)
void	protocols::stepwise::fix_up_jump_atoms_and_residue_type_variants (pose::Pose &pose_to_fix)
void	protocols::stepwise::switch_focus_to_other_pose (pose::Pose &pose, Size const &focus_pose_idx)
bool	protocols::stepwise::switch_focus_among_poses_randomly (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, bool force_switch)
void	protocols::stepwise::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::figure_out_moving_chain_break_res (pose::Pose const &pose, kinematics::MoveMap const &mm)
bool	protocols::stepwise::check_for_fixed_domain (pose::Pose const &pose, utility::vector1< Size > const &partition_res)
Size	protocols::stepwise::primary_fixed_domain (pose::Pose const &pose, utility::vector1< Size > const &partition_res)
bool	protocols::stepwise::check_for_fixed_domain (pose::Pose const &pose)
void	protocols::stepwise::make_variants_match (pose::Pose &pose, pose::Pose const &reference_pose, Size const &n, chemical::VariantType const variant_type)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_cutpoints_closed (pose::Pose const &pose, utility::vector1< Size > moving_partition_pos)
void	protocols::stepwise::figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< Size > moving_partition_pos, 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::get_partition_definition_by_jump (pose::Pose const &pose, Size const &jump_nr)
utility::vector1< bool >	protocols::stepwise::get_partition_definition (pose::Pose const &pose, Size const &moving_suite)
Size	protocols::stepwise::figure_out_reference_res_for_suite (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_partition_res_for_suite (pose::Pose const &pose, Size const moving_res, Size const reference_res)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_partition_res_for_jump (pose::Pose const &pose, Size const jump_nr)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::stepwise::figure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
utility::vector1< Size >	protocols::stepwise::figure_out_root_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)
void	protocols::stepwise::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::revise_root_and_moving_res (pose::Pose &pose, Size &moving_res)
bool	protocols::stepwise::revise_root_and_moving_res_list (pose::Pose &pose, utility::vector1< Size > &moving_res_list)
Size	protocols::stepwise::split_pose (pose::Pose &pose, Size const moving_res, Size const reference_res)
void	protocols::stepwise::split_pose (pose::Pose &pose, utility::vector1< Size > const &moving_res_list)
void	protocols::stepwise::fix_protein_jump_atom (pose::Pose &pose, Size const res, std::string const atom_name)

Variables
static numeric::random::RandomGenerator	RG (539155021)
static basic::Tracer	TR ("protocols.stepwise.StepWiseUtil")

Variable Documentation

numeric::random::RandomGenerator RG(539155021)

static

Referenced by protocols::stepwise::switch_focus_among_poses_randomly().

basic::Tracer TR("protocols.stepwise.StepWiseUtil")

static

Referenced by protocols::stepwise::figure_out_moving_residues(), protocols::stepwise::fix_up_residue_type_variants_at_strand_beginning(), protocols::stepwise::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::merge_two_poses(), protocols::stepwise::output_movemap(), and protocols::stepwise::switch_focus_among_poses_randomly().