Rosetta 3.4
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Friends
core::io::pdb::FileData Class Reference

FileData class. Hold data created from PDB file. More...

#include <file_data.hh>

Collaboration diagram for core::io::pdb::FileData:
Collaboration graph
[legend]

List of all members.

Public Types

typedef std::map< std::string,
double > 
ResidueTemps
typedef std::map< std::string,
ResidueTemps
Temps
typedef std::map< std::string,
Vector
ResidueCoords
typedef std::map< std::string,
ResidueCoords
Coords
typedef utility::vector1
< std::string > 
Strings

Public Member Functions

 FileData ()
 ~FileData ()
 empty destructor in C++ file to reduce number of necessary includes.
void init_from_pose (core::pose::Pose const &pose)
 Fill FileData structure using information from given pose object.
void init_from_pose (core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_indices)
 Fill FileData structure using information from given pose object, for a specified subset of residues.
void randomize_missing_coords (AtomInformation &ai)
 randomize missing density
void create_working_data (utility::vector1< ResidueInformation > &rinfo)
 Convert FileData in to set of residues, sequences, coordinats etc.
void append_residue (core::conformation::Residue const &rsd, core::Size &atom_index, core::pose::Pose const &pose)
 appends pdb information for a single residue

Static Public Member Functions

static void dump_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &tag="", bool write_fold_tree=false)
 Writes <pose> to a given stream in PDB file format.
static bool dump_pdb (core::pose::Pose const &pose, std::string const &file_name, std::string const &tag="", bool write_fold_tree=false)
 Writes <pose> to a PDB file, returns false if an error occurs.
static void dump_pdb (core::pose::Pose const &pose, std::ostream &out, utility::vector1< core::Size > const &residue_indices, std::string const &tag="")

Public Attributes

std::vector< AtomChainchains
 only one data member, that should not preserve any 'state' - so it is public.
pose::RemarksOP remarks
std::string filename
std::string modeltag

Friends

std::ostream & operator<< (std::ostream &os, FileData const &)
 Debug printing.

Detailed Description

FileData class. Hold data created from PDB file.


Member Typedef Documentation

typedef std::map< std::string, ResidueCoords > core::io::pdb::FileData::Coords
typedef std::map< std::string, Vector > core::io::pdb::FileData::ResidueCoords
typedef std::map< std::string, double > core::io::pdb::FileData::ResidueTemps
typedef std::map< std::string, ResidueTemps > core::io::pdb::FileData::Temps

Constructor & Destructor Documentation

core::io::pdb::FileData::FileData ( ) [inline]
core::io::pdb::FileData::~FileData ( )

empty destructor in C++ file to reduce number of necessary includes.


Member Function Documentation

void core::io::pdb::FileData::append_residue ( core::conformation::Residue const &  rsd,
core::Size atom_index,
core::pose::Pose const &  pose 
)
void core::io::pdb::FileData::create_working_data ( utility::vector1< ResidueInformation > &  rinfo)
void core::io::pdb::FileData::dump_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
utility::vector1< core::Size > const &  residue_indices,
std::string const &  tag = "" 
) [static]

Convert given Pose object in to PDB format and send it to the given stream. only the residues corresponding to indices in 'residue_indices' will be output

References core::io::pdb::PDB_DReader::createPDBData(), init_from_pose(), and core::io::pdb::write_additional_pdb_data().

bool core::io::pdb::FileData::dump_pdb ( core::pose::Pose const &  pose,
std::string const &  file_name,
std::string const &  tag = "",
bool  write_fold_tree = false 
) [static]

Writes <pose> to a PDB file, returns false if an error occurs.

Convert given Pose object in to PDB format and save it to 'file_name' file. return: true if operation was completed without error, false other wise.

References core::io::pdb::dump_pdb().

void core::io::pdb::FileData::dump_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
std::string const &  tag = "",
bool  write_fold_tree = false 
) [static]

Writes <pose> to a given stream in PDB file format.

Convert given Pose object in to PDB format and send it to the given stream.

References core::io::pdb::PDB_DReader::createPDBData(), init_from_pose(), and core::io::pdb::write_additional_pdb_data().

void core::io::pdb::FileData::init_from_pose ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  residue_indices 
)

Fill FileData structure using information from given pose object, for a specified subset of residues.

a lightweight, direct way of limiting pose pdb output to a subset of residues the alternative of constructing new subposes for output only would be unnecessary/less efficient (?)

References core::sequence::end, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void core::io::pdb::FileData::init_from_pose ( core::pose::Pose const &  pose)

Fill FileData structure using information from given pose object.

init FileData structure from pose object. read atoms/residue information from Pose object and put it in FileData object.

References core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by dump_pdb(), and core::io::pdb::pose_from_pose().

void core::io::pdb::FileData::randomize_missing_coords ( AtomInformation ai)

randomize missing density

The missing density regions in the input pdb should have 0.000 in the placeholders this routine puts random coordinates wherever there is 0.000 for mainchain atoms. tex - that's a stupid way of defining missing density, as atoms can be at the origin for other reasons. This has been updated to check for occupancy to define missing density rather than atoms located at the origin.

References core::io::pdb::AtomInformation::name, core::io::pdb::AtomInformation::occupancy, core::io::pdb::AtomInformation::resName, core::io::pdb::AtomInformation::resSeq, core::io::pdb::AtomInformation::x, core::io::pdb::AtomInformation::y, and core::io::pdb::AtomInformation::z.


Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
FileData const &  fd 
) [friend]

Debug printing.

Debug/Info function. Output FileData object to TR like stream in human redable format.


Member Data Documentation

only one data member, that should not preserve any 'state' - so it is public.

Referenced by core::io::pdb::PDB_DReader::createFileData(), core::io::pdb::PDB_DReader::createRecords(), and core::io::pdb::operator<<().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines