Rosetta  2021.07
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util.cc File Reference
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/MirrorSymmetricConformation.hh>
#include <core/conformation/symmetry/VirtualCoordinate.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/util.hh>
#include <core/kinematics/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/kinematics/Edge.hh>
#include <core/id/AtomID.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::conformation
 
 core::conformation::symmetry
 

Functions

static std::string const core::conformation::symmetry::chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcba")
 
std::string core::conformation::symmetry::get_chain_id_string ()
 
static basic::Tracer core::conformation::symmetry::TR ("core.conformation.symmetry.util")
 
void core::conformation::symmetry::calculate_inverting_virtuals (core::kinematics::FoldTree const &ft, Conformation const &conf, SymmetryInfo const &symm_info, utility::vector1< bool > &mirrored_subs, utility::vector1< std::pair< bool, bool > > &mirrored_jumps)
 A very specific helper function that counts the number of mirror ops from root->each subunit More...
 
Size core::conformation::symmetry::fold_tree_entry_point (core::kinematics::FoldTree const &ft, Size lb_resi=0, Size ub_resi=0)
 
Size core::conformation::symmetry::process_residue_request (conformation::Conformation const &src_conf, std::string input, Size lb_resi=0, Size ub_resi=0)
 
bool core::conformation::symmetry::is_jump_intracomponent (std::map< char, std::pair< Size, Size > > chain2range, Size up, Size dn)
 
char core::conformation::symmetry::which_component (std::map< char, std::pair< Size, Size > > chain2range, Size resi)
 
core::kinematics::FoldTree core::conformation::symmetry::get_component_contiguous_foldtree (core::kinematics::FoldTree const &f_orig, std::map< char, std::pair< Size, Size > > const &)
 
std::map< char, std::pair
< Size, Size > > 
core::conformation::symmetry::get_chain2range (Conformation const &src_conf, std::map< core::Size, char > src_conf2pdb_chain)
 
bool core::conformation::symmetry::is_symmetric (conformation::Conformation const &conf)
 
bool core::conformation::symmetry::is_mirror_symmetric (conformation::Conformation const &conf)
 
bool core::conformation::symmetry::is_symmetric (conformation::symmetry::SymmetryInfo const &symminfo)
 
conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< core::Size, char > src_conf2pdb_chain)
 
kinematics::FoldTree core::conformation::symmetry::set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< core::Size, char > src_conf2pdb_chain)
 
kinematics::FoldTree core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer (kinematics::FoldTree symm_f, conformation::symmetry::SymmetryInfo symmetry_info, kinematics::FoldTree monomer_f)
 
void core::conformation::symmetry::recenter (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata)
 
void core::conformation::symmetry::shift_jump_numbers_in_dofs (conformation::Conformation &conformation, Size shift)
 
kinematics::FoldTree core::conformation::symmetry::get_asymm_unit_fold_tree (core::conformation::Conformation const &conf)
 
void core::conformation::symmetry::symmetrize_fold_tree (core::conformation::Conformation const &conf, kinematics::FoldTree &f)
 Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric conformation (conf) More...
 
void core::conformation::symmetry::set_asymm_unit_fold_tree (core::conformation::Conformation &conf, kinematics::FoldTree const &f)
 
int core::conformation::symmetry::residue_center_of_mass (conformation::Conformation const &conformation, int const start, int const stop)
 
int core::conformation::symmetry::return_nearest_residue (conformation::Conformation const &conformation, int const begin, int const end, Vector center)
 
std::string core::conformation::symmetry::show_foldtree (core::conformation::symmetry::SymmetricConformation const &symm_conf, SymmData const &symmdata, std::map< char, std::pair< Size, Size > > const &chain2range)