file_data_fixup.cc File Reference

#include <core/io/pdb/file_data_fixup.hh>
#include <core/io/pdb/file_data.hh>
#include <core/types.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ElementSet.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/Element.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/numeric.functions.hh>
#include <ObjexxFCL/format.hh>
#include <boost/graph/vf2_sub_graph_iso.hpp>
#include <boost/graph/mcgregor_common_subgraphs.hpp>
#include <fstream>
#include <sstream>
#include <cstdlib>
#include <cstdio>
#include <utility>

Classes
class	core::io::pdb::GeometricRenameIsomorphismCallback
class	core::io::pdb::GeometricRenameVerticiesEquivalent
	Will consider two verticies equivalent if they have the same element. More...

Namespaces
	core
	A class for reading in the atom type properties.
	core::io
	core::io::pdb

Typedefs
typedef boost::undirected_graph < AtomInformation >	core::io::pdb::AtomInfoGraph
typedef AtomInfoGraph::vertex_descriptor	core::io::pdb::AIVD

Functions
std::string	core::io::pdb::convert_res_name (std::string const &name)
std::string	core::io::pdb::convert_atom_name (std::string const &res_name, std::string atom_name)
	for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard) More...
void	core::io::pdb::convert_nucleic_acid_residue_info_to_standard (utility::vector1< ResidueInformation > &all_rinfo, bool const force_RNA)
bool	core::io::pdb::is_potential_old_DNA (std::string const &res_name)
bool	core::io::pdb::is_old_RNA (std::string const &res_name)
bool	core::io::pdb::is_NA (std::string const &res_name)
bool	core::io::pdb::missing_O2prime (utility::vector1< AtomInformation > const &atoms)
void	core::io::pdb::convert_nucleic_acid_atom_names_to_standard (ResidueInformation &rinfo, bool const force_RNA=false)
	This is a pretty good framework and could allow for other crazy nucleic acid atom name schemes. More...
void	core::io::pdb::convert_nucleic_acid_atom_name_to_standard (AtomInformation &atom_info)
void	core::io::pdb::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::pdb::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::pdb::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::pdb::flip_atom_xyz (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name)
int	core::io::pdb::sgn (Real const &x)
int	core::io::pdb::get_chirality_sign (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_parent, Vector const &xyz_cousin)
int	core::io::pdb::get_closest_sister (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_outgroup)
core::Real	core::io::pdb::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::pdb::score_mapping (NameBimap const &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type)
	Scoring scheme for the heuristic PDB renaming. More...
void	core::io::pdb::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...

Variables
static basic::Tracer	TR ("core.io.pdb.file_data_fixup")

Detailed Description

Author

Rhiju Das

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

Variable Documentation

basic::Tracer TR("core.io.pdb.file_data_fixup")

static