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util.cc File Reference
#include <core/pose/symmetry/util.hh>
#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/carbohydrates/GlycanTreeSet.hh>
#include <core/scoring/symmetry/SymmetricEnergies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/chains_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/fold_and_dock.OptionKeys.gen.hh>
#include <basic/pymol_chains.hh>
#include <core/id/AtomID.hh>
#include <numeric/random/random.hh>
#include <core/kinematics/Edge.hh>
#include <core/io/HeaderInformation.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <utility/vector1.hh>

Namespaces

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

Functions

static basic::Tracer core::pose::symmetry::TR ("core.pose.symmetry.util")
 
bool core::pose::symmetry::is_symmetric (scoring::Energies const &energies)
 
bool core::pose::symmetry::is_symmetric (pose::Pose const &pose)
 
bool core::pose::symmetry::is_mirror_symmetric (pose::Pose const &pose)
 
core::Size core::pose::symmetry::get_nres_asymmetric_unit (pose::Pose const &pose)
 Convenience function for the number of residues in a subunit. Will return the total size for a asymmetric pose. More...
 
conformation::symmetry::SymmetryInfoCOP core::pose::symmetry::symmetry_info (pose::Pose const &pose)
 
bool core::pose::symmetry::scorefxn_is_symmetric (conformation::Conformation const &conf)
 
bool core::pose::symmetry::scorefxn_is_symmetric (pose::Pose const &pose)
 
void core::pose::symmetry::make_symmetric_pose (pose::Pose &pose, conformation::symmetry::SymmetryInfo symmetry_info)
 
void core::pose::symmetry::make_symmetric_pose (pose::Pose &pose, conformation::symmetry::SymmData &symmdata, bool keep_pdb_info_labels)
 
void core::pose::symmetry::make_symmetric_pose (pose::Pose &pose, std::string symmdef_file)
 
void core::pose::symmetry::make_asymmetric_pose (pose::Pose &pose)
 
void core::pose::symmetry::extract_asymmetric_unit (core::pose::Pose const &pose_in, core::pose::Pose &pose_out, bool const with_virtual_atoms)
 extract the asu from a pose... unlike previous function symmetric clones are thrown out More...
 
core::pose::Pose core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose (pose::Pose const &pose)
 
void core::pose::symmetry::make_symmetric_pdb_info (pose::Pose const &pose, pose::PDBInfoOP pdb_info_src, pose::PDBInfoOP pdb_info_target, bool keep_pdb_info_labels)
 
void core::pose::symmetry::extract_asymmetric_unit_pdb_info (pose::Pose const &pose, pose::PDBInfoCOP pdb_info_src, pose::PDBInfoOP pdb_info_target)
 
void core::pose::symmetry::make_symmetric_movemap (pose::Pose const &pose, kinematics::MoveMap &movemap)
 
int core::pose::symmetry::find_symmetric_basejump_anchor (pose::Pose &pose)
 
void core::pose::symmetry::find_new_symmetric_jump_residues (core::pose::Pose &pose)
 
void core::pose::symmetry::rotate_anchor_to_x_axis (core::pose::Pose &pose)
 
void core::pose::symmetry::symmetrize_fold_tree (core::pose::Pose const &p, kinematics::FoldTree &f)
 Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric pose (p) More...
 
void core::pose::symmetry::set_asymm_unit_fold_tree (core::pose::Pose &p, kinematics::FoldTree const &f)
 
void core::pose::symmetry::partition_by_symm_jumps (utility::vector1< int > jump_numbers, core::kinematics::FoldTree const &ft, conformation::symmetry::SymmetryInfoCOP symm_info, ObjexxFCL::FArray1D_bool &partner1)
 
numeric::xyzVector< core::Realcore::pose::symmetry::get_symm_axis (core::pose::Pose &pose)
 
core::pose::Pose core::pose::symmetry::get_buildingblock_and_neighbor_subs (Pose const &pose_in, utility::vector1< Size > intra_subs)
 
core::pose::Pose core::pose::symmetry::get_subpose (Pose const &pose, utility::vector1< std::string > subs)
 
utility::vector1< Size > core::pose::symmetry::get_resis (Pose const &pose, utility::vector1< std::string > subs)
 
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_and_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_and_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_full_intracomponent_subpose (Pose const &pose, std::string const &sym_dof_name)
 
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_resis (Pose const &pose, std::string const &sym_dof_name)
 
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_full_intracomponent_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_full_intracomponent_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
bool core::pose::symmetry::intracomponent_contact (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_intracomponent_and_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_intracomponent_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_intracomponent_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< std::string > core::pose::symmetry::get_neighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_neighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_neighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_intraneighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_intracomponent_and_intraneighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_intraneighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< std::string > core::pose::symmetry::get_intracomponent_and_interneighbor_subs (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
core::pose::Pose core::pose::symmetry::get_intracomponent_and_interneighbor_subpose (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
utility::vector1< Size > core::pose::symmetry::get_intracomponent_and_interneighbor_resis (Pose const &pose, std::string const &sym_dof_name, Real contact_dist)
 
void core::pose::symmetry::make_residue_mask_symmetric (core::pose::Pose const &p, utility::vector1< bool > &msk)
 
kinematics::FoldTree core::pose::symmetry::sealed_symmetric_fold_tree (core::pose::Pose &pose)
 
int core::pose::symmetry::get_sym_aware_jump_num (core::pose::Pose const &pose, core::Size jump_num)
 
utility::vector1< std::string > core::pose::symmetry::sym_dof_names (core::pose::Pose const &pose)
 
int core::pose::symmetry::sym_dof_jump_num (core::pose::Pose const &pose, std::string const &jname)
 
std::string core::pose::symmetry::jump_num_sym_dof (core::pose::Pose const &pose, Size const &jnum)
 
utility::vector1< Size > core::pose::symmetry::get_symdof_subunits (core::pose::Pose const &pose, std::string const &jname)
 
utility::vector1< char > core::pose::symmetry::symmetric_components (core::pose::Pose const &pose)
 
bool core::pose::symmetry::is_singlecomponent (core::pose::Pose const &pose)
 
bool core::pose::symmetry::is_multicomponent (core::pose::Pose const &pose)
 
Size core::pose::symmetry::get_component_lower_bound (core::pose::Pose const &pose, char c)
 
Size core::pose::symmetry::get_component_upper_bound (core::pose::Pose const &pose, char c)
 
char core::pose::symmetry::get_component_of_residue (core::pose::Pose const &pose, Size ir)
 
char core::pose::symmetry::get_subunit_name_to_component (core::pose::Pose const &pose, std::string const &vname)
 
utility::vector1< char > const & core::pose::symmetry::get_jump_name_to_components (core::pose::Pose const &pose, std::string const &jname)
 
utility::vector1< Size > const & core::pose::symmetry::get_jump_name_to_subunits (core::pose::Pose const &pose, std::string const &jname)
 
std::string core::pose::symmetry::get_resnum_to_subunit_component (core::pose::Pose const &pose, Size const &resnum)
 
utility::vector1< std::string > core::pose::symmetry::get_full_intracomponent_subs (core::pose::Pose const &pose, std::string const &jname)