file_data.cc File Reference

#include <core/io/pdb/Field.hh>
#include <core/io/pdb/HeaderInformation.hh>
#include <core/io/pdb/file_data.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/types.hh>
#include <core/io/pdb/file_data_options.hh>
#include <core/io/pdb/pdb_dynamic_reader.hh>
#include <core/io/pdb/pdb_dynamic_reader_options.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/io/raw_data/DisulfideFile.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/util.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <numeric/random/random.hh>
#include <utility/string_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <fstream>
#include <sstream>
#include <cstdlib>
#include <cstdio>
#include <utility>
#include <ObjexxFCL/format.hh>
#include <utility/vector1.hh>
#include <core/pose/util.tmpl.hh>

Go to the source code of this file.

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::io
	core::io::pdb

Constant Groups
	core
	A class for defining atom parameters, known as atom_types.
	core::io
	core::io::pdb

Functions
static basic::Tracer	core::io::pdb::TR ("core.io.pdb.file_data")
static numeric::random::RandomGenerator	core::io::pdb::RG (231411)
static string const	core::io::pdb::chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz")
std::ostream &	core::io::pdb::operator<< (std::ostream &os, FileData const &fd)
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)
std::string	core::io::pdb::local_strip_whitespace (std::string const &name)
void	core::io::pdb::write_additional_pdb_data (std::ostream &out, pose::Pose const &pose, io::pdb::FileData const &, bool write_fold_tree)
	Writes. More...
void	core::io::pdb::build_pose_from_pdb_as_is (pose::Pose &pose, std::string const &filename)
	Builds a pose into <pose>, without repacking or optimizing hydrogens; using the fullatom ResidueTypeSet. More...
void	core::io::pdb::build_pose_from_pdb_as_is (pose::Pose &pose, std::string const &filename, PDB_DReaderOptions const &pdr_options)
	Builds a pose into <pose>, without repacking or optimizing hydrogens; using the fullatom ResidueTypeSet and a set of options. More...
void	core::io::pdb::build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
void	core::io::pdb::build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, PDB_DReaderOptions const &pdr_options)
void	core::io::pdb::build_pose_as_is1 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, FileDataOptions const &options)
bool	core::io::pdb::is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCOPs const &rsd_type_list, std::map< std::string, Vector > const &xyz, std::map< std::string, double > const &rtemp, utility::vector1< Size > &UA_res_nums, utility::vector1< std::string > &UA_res_names, utility::vector1< std::string > &UA_atom_names, utility::vector1< numeric::xyzVector< Real > > &UA_coords, utility::vector1< core::Real > &UA_temps)
bool	core::io::pdb::is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCOPs const &rsd_type_list, std::map< std::string, Vector > const &xyz, std::map< std::string, double > const &rtemp, utility::vector1< Size > &UA_res_nums, utility::vector1< std::string > &UA_res_names, utility::vector1< std::string > &UA_atom_names, utility::vector1< numeric::xyzVector< Real > > &UA_coords, utility::vector1< core::Real > &UA_temps, FileDataOptions const &options)
void	core::io::pdb::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices)
void	core::io::pdb::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices, FileDataOptions const &options)
void	core::io::pdb::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices)
void	core::io::pdb::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices, FileDataOptions const &options)

Detailed Description

Author

Sergey Lyskov

Definition in file file_data.cc.