Rosetta Core  2014.35
Namespaces | Functions | Variables
file_data.cc File Reference

Method definitions for FileData and related classes. More...

#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/io/pdb/file_data_options.hh>
#include <core/io/pdb/file_data_fixup.hh>
#include <core/io/pdb/pdb_dynamic_reader.hh>
#include <core/io/pdb/pdb_dynamic_reader_options.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/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/chemical/types.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pose/ncbb/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/cryst/util.hh>
#include <basic/options/option.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 <basic/Tracer.hh>
#include <numeric/random/random.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 <ObjexxFCL/format.hh>
#include <boost/lexical_cast.hpp>
#include <fstream>
#include <sstream>
#include <cstdlib>
#include <cstdio>
#include <utility>

Namespaces

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

Functions

std::ostream & core::io::pdb::operator<< (std::ostream &os, FileData const &fd)
 
void core::io::pdb::fill_name_map (core::io::pdb::NameBimap &name_map, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type, FileDataOptions const &options)
 
void core::io::pdb::write_additional_pdb_data (std::ostream &out, pose::Pose const &pose, io::pdb::FileData const &fd, bool write_fold_tree=false)
 Adds data to the end of a pdb that are not a standard part of the pdb format. 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 full-atom 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 full-atom 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)
 
void core::io::pdb::fixup_rinfo_based_on_residue_type_set (utility::vector1< ResidueInformation > &rinfos, chemical::ResidueTypeSet const &residue_set)
 

Variables

static basic::Tracer core::io::pdb::TR ("core.io.pdb.file_data")
 
static
numeric::random::RandomGenerator 
core::io::pdb::RG (231411)
 

Detailed Description

Method definitions for FileData and related classes.

Author
Sergey Lyskov