util.hh File Reference

utility functions for handling with symmetric conformations More...

#include <core/scoring/Energies.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/conformation/symmetry/SymmData.fwd.hh>
#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/PDBInfo.fwd.hh>
#include <core/types.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <utility/vector1.hh>
#include <string>

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

Functions
bool	core::pose::symmetry::is_symmetric (pose::Pose const &pose)
bool	core::pose::symmetry::is_symmetric (scoring::ScoreFunction const &scorefxn)
bool	core::pose::symmetry::is_symmetric (scoring::Energies const &energies)
void	core::pose::symmetry::make_score_function_consistent_with_symmetric_state_of_pose (pose::Pose const &pose, scoring::ScoreFunctionOP &scorefxn)
conformation::symmetry::SymmetryInfoCOP	core::pose::symmetry::symmetry_info (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)
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 with_virtual_atoms=true)
	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)
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)
numeric::xyzVector< core::Real >	core::pose::symmetry::get_symm_axis (core::pose::Pose &pose)
void	core::pose::symmetry::symmetrize_fold_tree (core::pose::Pose const &p, kinematics::FoldTree &f)
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)
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 sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_full_intracomponent_and_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_full_intracomponent_and_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_full_intracomponent_subpose (Pose const &pose, std::string sym_dof_name)
utility::vector1< Size >	core::pose::symmetry::get_full_intracomponent_resis (Pose const &pose, std::string sym_dof_name)
utility::vector1< std::string >	core::pose::symmetry::get_full_intracomponent_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_full_intracomponent_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_full_intracomponent_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
bool	core::pose::symmetry::intracomponent_contact (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	core::pose::symmetry::get_intracomponent_and_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_intracomponent_and_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_intracomponent_and_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	core::pose::symmetry::get_intracomponent_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_intracomponent_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_intracomponent_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	core::pose::symmetry::get_neighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_neighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_neighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	core::pose::symmetry::get_intracomponent_and_intraneighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_intracomponent_and_intraneighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_intracomponent_and_intraneighbor_resis (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< std::string >	core::pose::symmetry::get_intracomponent_and_interneighbor_subs (Pose const &pose, std::string sym_dof_name, Real contact_dist)
core::pose::Pose	core::pose::symmetry::get_intracomponent_and_interneighbor_subpose (Pose const &pose, std::string sym_dof_name, Real contact_dist)
utility::vector1< Size >	core::pose::symmetry::get_intracomponent_and_interneighbor_resis (Pose const &pose, std::string 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_multicomponent (core::pose::Pose const &pose)
bool	core::pose::symmetry::is_singlecomponent (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)

Detailed Description

utility functions for handling with symmetric conformations

Author

Ingemar Andre

Jacob Bale (balej.nosp@m.@uw..nosp@m.edu)