src/core/io/pdb/file_data.hh File Reference

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

Classes
class	core::io::pdb::AtomInformation
	Atom_information contain information for individual atom. only fields that predent in file will be initialazed, other will have default value. That class basicaly reflect structure of 'ATOM' line in PDB file format. More...
class	core::io::pdb::ResidueInformation
	Intermediate format for easy construction of core::conformation::Residue objects. Subset of data from "ATOM" lines that is shared by all atoms in a residue. More...
class	core::io::pdb::FileData
	FileData class. Hold data created from PDB file. More...
Namespaces
namespace	core
	A class for defining atom parameters, known as atom_types.
namespace	core::io
namespace	core::io::pdb
Typedefs
typedef std::string	core::io::pdb::String
	Record type, represent one line in pdb file.
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 &, bool write_fold_tree)
	Writes.
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.
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_as_is1 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing)
bool	core::io::pdb::is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCAPs 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)
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, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices)

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Detailed Description

Author:

Sergey Lyskov