file_data.hh File Reference

Declarations for FileData and related classes. More...

#include <core/io/pdb/Field.fwd.hh>
#include <core/io/pdb/HeaderInformation.hh>
#include <core/io/pdb/file_data.fwd.hh>
#include <core/io/pdb/file_data_fixup.fwd.hh>
#include <core/io/pdb/file_data_options.fwd.hh>
#include <core/io/pdb/pdb_dynamic_reader_options.fwd.hh>
#include <core/types.hh>
#include <core/id/AtomID_Mask.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Remarks.hh>
#include <core/pose/CrystInfo.hh>
#include <core/pose/Pose.fwd.hh>
#include <numeric/xyzVector.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/vector1.hh>
#include <iostream>
#include <map>
#include <string>

Classes
class	core::io::pdb::AtomInformation
	A class that contains information for individual atoms. More...
class	core::io::pdb::ResidueInformation
	Intermediate format for easy construction of core::conformation::Residue objects. More...
struct	core::io::pdb::LinkInformation
	A structure for storing information from PDB LINK records. More...
class	core::io::pdb::FileData
	FileData class. Hold data created from PDB file. More...

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

Typedefs
typedef std::string	core::io::pdb::String
typedef std::vector < AtomInformation >	core::io::pdb::AtomChain

Functions
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)
void	core::io::pdb::fill_name_map (core::io::pdb::NameBimap &name_map, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type, FileDataOptions const &options)

Detailed Description

Declarations for FileData and related classes.

Author

Sergey Lyskov