util.cc File Reference

#include <core/pose/full_model_info/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/rna/util.hh>
#include <core/chemical/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/id/SequenceMapping.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/FullModelParameters.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/loop_graph/LoopGraph.hh>
#include <utility/stream_util.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/vector1.functions.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/Tracer.hh>
#include <string>
#include <map>

Namespaces
	core
	A class for reading in the atom type properties.
	core::pose
	core::pose::full_model_info

Functions
static THREAD_LOCAL basic::Tracer	TR ("core.pose.full_model_info.util")
utility::vector1< Size >	core::pose::full_model_info::reorder_moving_res_list_after_delete (utility::vector1< Size > const &moving_res_list, Size const &res_to_delete)
utility::vector1< Size >	core::pose::full_model_info::reorder_res_list_after_delete (utility::vector1< Size > const &res_list, Size const &res_to_delete)
utility::vector1< Size >	core::pose::full_model_info::reorder_moving_res_list_after_insert (utility::vector1< Size > const &moving_res_list, Size const &res_to_add)
utility::vector1< Size >	core::pose::full_model_info::reorder_res_list_after_prepend (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
utility::vector1< Size >	core::pose::full_model_info::reorder_res_list_after_append (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
void	core::pose::full_model_info::update_pdb_info_from_full_model_info (pose::Pose &pose)
void	core::pose::full_model_info::update_constraint_set_from_full_model_info (pose::Pose &pose)
void	core::pose::full_model_info::update_disulfides_from_full_model_info (pose::Pose &pose)
void	core::pose::full_model_info::update_pose_objects_from_full_model_info (pose::Pose &pose)
void	core::pose::full_model_info::update_res_list_in_full_model_info_and_pdb_info (pose::Pose &pose, utility::vector1< Size > const &res_list_new)
void	core::pose::full_model_info::reorder_full_model_info_after_delete (core::pose::Pose &pose, core::Size const res_to_delete)
	Keep track of RNA centroid information inside the pose. More...
void	core::pose::full_model_info::reorder_full_model_info_after_append (pose::Pose &pose, Size const res_to_add, Size const offset)
void	core::pose::full_model_info::reorder_full_model_info_after_prepend (pose::Pose &pose, Size const res_to_add, Size const offset)
utility::vector1< char >	core::pose::full_model_info::figure_out_conventional_chains_from_full_model_info (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info (pose::Pose &pose)
utility::vector1< Size >	core::pose::full_model_info::get_chains_full (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_chains_from_cutpoint_open (utility::vector1< Size > const &cutpoint_open, Size const nres)
utility::vector1< Size >	core::pose::full_model_info::get_cutpoint_open_from_chains (utility::vector1< Size > const &chains)
utility::vector1< Size >	core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::figure_out_dock_domain_map_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_sample_res_for_pose (pose::Pose const &pose)
bool	core::pose::full_model_info::check_full_model_info_OK (pose::Pose const &pose)
utility::vector1< Size > const &	core::pose::full_model_info::get_res_list_from_full_model_info (pose::Pose &pose)
utility::vector1< Size > const &	core::pose::full_model_info::get_res_list_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_res_list_const (pose::Pose const &pose)
utility::vector1 < utility::vector1< Size > >	core::pose::full_model_info::get_move_elements_from_full_model_info (pose::Pose &pose)
utility::vector1 < utility::vector1< Size > >	core::pose::full_model_info::get_move_elements_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_moving_res_from_full_model_info (pose::Pose &pose)
utility::vector1< Size >	core::pose::full_model_info::get_fixed_domain_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_input_domain_from_full_model_info_const (pose::Pose const &pose)
core::Size	core::pose::full_model_info::sub_to_full (core::Size const i, core::pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::sub_to_full (utility::vector1< Size > const &res_list, core::pose::Pose const &pose)
core::Size	core::pose::full_model_info::full_to_sub (core::Size const i, core::pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::full_to_sub (utility::vector1< Size > const &res_list, core::pose::Pose const &pose)
Size	core::pose::full_model_info::full_model_size (pose::Pose &pose)
void	core::pose::full_model_info::update_pose_domain_map_const (Pose const &pose, Size &pose_domain_number, utility::vector1< Size > &pose_domain_map)
void	core::pose::full_model_info::update_pose_domain_map (Pose &pose, Size &pose_domain_number, utility::vector1< Size > &pose_domain_map)
utility::vector1< Size >	core::pose::full_model_info::figure_out_pose_domain_map (pose::Pose &pose)
utility::vector1< Size >	core::pose::full_model_info::figure_out_pose_domain_map_const (pose::Pose const &pose)
core::conformation::Residue const &	core::pose::full_model_info::get_residue (Size const seqpos_in_full_model, pose::Pose const &pose, bool &found_residue)
core::conformation::Residue const &	core::pose::full_model_info::get_residue (Size const seqpos_in_full_model, pose::Pose const &pose)
utility::vector1< int >	core::pose::full_model_info::get_res_num_from_pdb_info (pose::Pose const &pose)
utility::vector1< char >	core::pose::full_model_info::get_chains_from_pdb_info (pose::Pose const &pose)
Size	core::pose::full_model_info::get_chain_for_full_model_resnum (Size const &resnum, pose::Pose const &pose)
Size	core::pose::full_model_info::get_chain_for_resnum (Size const &resnum, pose::Pose const &pose)
Size	core::pose::full_model_info::get_number_missing_residues_and_connections (pose::Pose &pose)
	Finds the number of missing residues in a pose. More...
Size	core::pose::full_model_info::get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< char > &missing_residues)
	Finds the number of missing residues in a pose. More...
Size	core::pose::full_model_info::get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< utility::vector1< Size > > &loop_suites)
	Finds the number of missing residues in a pose. More...
Size	core::pose::full_model_info::get_number_missing_residues_and_connections (pose::Pose const &pose, utility::vector1< char > &missing_residues, utility::vector1< utility::vector1< Size > > &loop_suites)
	Finds the number of missing residues in a pose. More...
bool	core::pose::full_model_info::check_all_residues_sampled (pose::Pose const &pose)
std::map< std::pair< Size, Size >, std::pair< Size, Size > >	core::pose::full_model_info::get_preferred_jump_pair_for_docking_domains (FullModelInfo const &full_model_info)
utility::vector1< std::pair < Size, Size > >	core::pose::full_model_info::get_chain_connections (pose::Pose const &pose)
utility::vector1< Size >	core::pose::full_model_info::get_connection_domains (utility::vector1< std::pair< Size, Size > > const &chain_connections, Size const nchains)
bool	core::pose::full_model_info::check_sample_sugar_in_full_model_info (pose::Pose const &pose, Size const i)

Function Documentation

static THREAD_LOCAL basic::Tracer TR ( "core.pose.full_model_info.util"  )

static