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Rosetta
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Various utilities to accomodated PDB input issues. More...
#include <core/io/pose_from_sfr/chirality_resolution.fwd.hh>#include <core/io/ResidueInformation.fwd.hh>#include <core/types.hh>#include <core/chemical/ResidueType.fwd.hh>#include <core/conformation/Residue.fwd.hh>#include <string>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::io | |
| core::io::pose_from_sfr | |
Functions | |
| void | core::io::pose_from_sfr::check_and_correct_sister_atoms (core::conformation::ResidueOP &rsd) |
| due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms (like OP1 <--> OP2, or H41 <--> H42) in PDBs is totally wacky. This is an attempt to regularize... and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize. More... | |
| void | core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_chirality (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name, std::string const &parent_name, std::string const &cousin_name) |
| void | core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_outgroup (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name, std::string const &outgroup_name) |
| void | core::io::pose_from_sfr::flip_atom_xyz (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name) |
| int | core::io::pose_from_sfr::sgn (Real const &x) |
| int | core::io::pose_from_sfr::get_chirality_sign (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_parent, Vector const &xyz_cousin) |
| int | core::io::pose_from_sfr::get_closest_sister (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_outgroup) |
| core::Real | core::io::pose_from_sfr::bonding_distance_threshold (std::string element1, std::string element2) |
| Get theshold distance below which two atoms are considered bonded. (1.2*covalent) More... | |
| core::Real | core::io::pose_from_sfr::score_mapping (NameBimap const &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type) |
| Scoring scheme for the heuristic PDB renaming. More... | |
| void | core::io::pose_from_sfr::remap_names_on_geometry (NameBimap &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type) |
| Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names. More... | |
Various utilities to accomodated PDB input issues.
1.9.1