PoseFromSFRBuilder.cc File Reference

#include <core/io/pose_from_sfr/PoseFromSFRBuilder.hh>
#include <core/io/pose_from_sfr/chirality_resolution.hh>
#include <core/io/StructFileRepOptions.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/HeaderInformation.hh>
#include <core/io/NomenclatureManager.hh>
#include <core/io/ResidueInformation.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/NamedAtomID_Map.hh>
#include <core/io/raw_data/DisulfideFile.hh>
#include <core/io/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/PoseResidueTypeSet.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>
#include <core/chemical/types.hh>
#include <core/chemical/rings/RingConformerSet.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/parametric/Parameters.hh>
#include <core/conformation/parametric/ParametersSet.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/datacache/ObserverCache.hh>
#include <core/pose/datacache/CacheableObserverType.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/ncbb/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/Pose.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/cryst/util.hh>
#include <core/simple_metrics/util.hh>
#include <core/simple_metrics/SimpleMetricData.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/string_util.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <sstream>
#include <cstdlib>
#include <cstdio>
#include <algorithm>
#include <vector>
#include <boost/tokenizer.hpp>

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

Functions
static basic::Tracer	core::io::pose_from_sfr::TR ("core.io.pose_from_sfr.PoseFromSFRBuilder")
bool	core::io::pose_from_sfr::missing_O2prime (utility::vector1< core::io::AtomInformation > const &atoms)
bool	core::io::pose_from_sfr::is_connected (core::conformation::Conformation const &conf, core::Size ii, std::string const &ii_atm, core::Size jj, std::string const &jj_atm)
void	core::io::pose_from_sfr::show_residue_connections (core::conformation::Conformation const &conf, core::Size i)
std::string	core::io::pose_from_sfr::convert_atom_name (std::string const &res_name, std::string const &atom_name)
	for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard) More...
std::string	core::io::pose_from_sfr::convert_res_name (std::string const &name)
void	core::io::pose_from_sfr::create_working_data (StructFileRepOptions const &options, StructFileRep const &sfr, utility::vector1< core::io::ResidueInformation > &rinfos)
bool	core::io::pose_from_sfr::update_atom_information_based_on_occupancy (StructFileRepOptions const &options, AtomInformation &ai)
void	core::io::pose_from_sfr::randomize_missing_coords (AtomInformation &ai)
	randomize missing density More...