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

#include <file_data.hh>

Collaboration diagram for core::io::pdb::FileData:

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. More...

void	initialize_header_information ()

HeaderInformationOP	header_information () const

void	store_header_record (Record &R)

void	finalize_header_information ()
	The header records can span multiple lines while the pdb_dynamic_parser is done line-wise. Finalizing the header information ensures that all the information is fully processed. More...

void	fill_header_records (std::vector< Record > &VR) const
	Make sure to call finalize_header_information before calling this. More...

void	store_link_record (Record &record)
	Store (non-standard) polymer linkages in a map. More...

void	store_heterogen_names (std::string const &hetID, std::string const &text)
	Store heterogen name information in a map. More...

void	parse_heterogen_name_for_carbohydrate_residues (std::string const &text)
	Parse heterogen name data for a given carbohydrate and save the particular base (non-variant) ResidueType needed in a map. More...

void	init_from_pose (core::pose::Pose const &pose)
	Fill FileData structure using information from given pose object. More...

void	init_from_pose (core::pose::Pose const &pose, FileDataOptions const &options)
	Fill FileData structure using information from given pose object and a set of options. More...

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. More...

void	randomize_missing_coords (AtomInformation &ai)
	randomize missing density More...

void	create_working_data (utility::vector1< ResidueInformation > &rinfo)
	Convert FileData into set of residues, sequences, coordinates etc. More...

void	create_working_data (utility::vector1< ResidueInformation > &rinfo, FileDataOptions const &options)
	Convert FileData into set of residues, sequences, coordinates etc. using a set of options. More...

void	append_residue (core::conformation::Residue const &rsd, core::Size &atom_index, core::pose::Pose const &pose)
	appends pdb information for a single residue More...

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. More...

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. More...

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< AtomChain >	chains

pose::RemarksOP	remarks

HeaderInformationOP	header

std::string	filename

std::string	modeltag

std::map< std::string, LinkInformation >	links

std::map< std::string, std::string >	heterogen_names

std::map< std::string, std::string >	carbohydrate_residue_type_base_names

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

Detailed Description

FileData class. Hold data created from PDB file.

Definition at line 153 of file file_data.hh.

Member Typedef Documentation

typedef std::map< std::string, ResidueCoords > core::io::pdb::FileData::Coords

Definition at line 268 of file file_data.hh.

typedef std::map< std::string, Vector > core::io::pdb::FileData::ResidueCoords

Definition at line 267 of file file_data.hh.

typedef std::map< std::string, double > core::io::pdb::FileData::ResidueTemps

Definition at line 265 of file file_data.hh.

typedef utility::vector1< std::string > core::io::pdb::FileData::Strings

Definition at line 269 of file file_data.hh.

typedef std::map< std::string, ResidueTemps > core::io::pdb::FileData::Temps

Definition at line 266 of file file_data.hh.

Constructor & Destructor Documentation

core::io::pdb::FileData::FileData ( )

inline

Definition at line 156 of file file_data.hh.

core::io::pdb::FileData::~FileData ( )

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

Definition at line 163 of file file_data.cc.

Member Function Documentation

void core::io::pdb::FileData::append_residue	(	core::conformation::Residue const &	rsd,
		core::Size &	atom_index,
		core::pose::Pose const &	pose
	)

appends pdb information for a single residue

Definition at line 168 of file file_data.cc.

Referenced by init_from_pose().

void core::io::pdb::FileData::create_working_data ( utility::vector1< ResidueInformation > & rinfo)

Convert FileData into set of residues, sequences, coordinates etc.

Convert FileData in to set of residues, sequences, coordinates. this is a convenience function, no magic done here. Well, maybe a little.

Definition at line 577 of file file_data.cc.

Referenced by core::io::pdb::build_pose_as_is1().

void core::io::pdb::FileData::create_working_data	(	utility::vector1< ResidueInformation > &	rinfo,
		FileDataOptions const &	options
	)

Convert FileData into set of residues, sequences, coordinates etc. using a set of options.

Convert FileData in to set of residues, sequences, coordinates. this is a convenience function, no magic done here. Well, maybe a little.

Definition at line 588 of file file_data.cc.

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.

Definition at line 448 of file file_data.cc.

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

Referenced by dump_pdb(), core::pose::Pose::dump_pdb(), protocols::jd2::PDBJobOutputter::dump_pose(), protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::pose::Pose::dump_scored_pdb(), and protocols::checkpoint::CheckPointer::recover_checkpoint().

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.

Definition at line 467 of file file_data.cc.

References dump_pdb().

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

Definition at line 488 of file file_data.cc.

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

void core::io::pdb::FileData::fill_header_records ( std::vector< Record > & VR) const

Make sure to call finalize_header_information before calling this.

Populate the header records from the data in the HeaderInformation

Remarks: HeaderInformation must be created explicitly before it can be filled!

Definition at line 297 of file file_data.cc.

References header.

Referenced by core::io::pdb::PDB_DReader::createRecords().

void core::io::pdb::FileData::finalize_header_information ( )

The header records can span multiple lines while the pdb_dynamic_parser is done line-wise. Finalizing the header information ensures that all the information is fully processed.

finalize storing records from the data in the HeaderInformation

Remarks: HeaderInformation must be created explicitly before it can be filled!

Definition at line 306 of file file_data.cc.

References header.

Referenced by core::io::pdb::PDB_DReader::createFileData().

HeaderInformationOP core::io::pdb::FileData::header_information ( ) const

Definition at line 283 of file file_data.cc.

References header.

Referenced by core::io::pdb::build_pose_as_is1(), and core::io::pdb::PDB_DReader::createRecords().

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.

Definition at line 269 of file file_data.cc.

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

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

Fill FileData structure using information from given pose object and a set of options.

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

Definition at line 401 of file file_data.cc.

References append_residue(), chains, header, core::pose::Pose::pdb_info(), core::io::pdb::FileDataOptions::preserve_header(), remarks, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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 (?)

Definition at line 429 of file file_data.cc.

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

void core::io::pdb::FileData::initialize_header_information ( )

prepare the HeaderInformation data structure;

Definition at line 278 of file file_data.cc.

References header.

Referenced by core::io::pdb::PDB_DReader::createFileData().

void core::io::pdb::FileData::parse_heterogen_name_for_carbohydrate_residues ( std::string const & text)

Parse heterogen name data for a given carbohydrate and save the particular base (non-variant) ResidueType needed in a map.

The standard PDB HETNAM record is insufficient for indicating the type of carbohydrate residue found at each position of the sequence. The PDB format only allows one heterogen name per 3-letter code. To work around this, a PDB file containing carbohydrates will need to be made "Rosetta-ready". 3-letter codes will need to be converted from, e.g., GLC, which implies the vague "ALPHA-D-GLUCOSE", to Glc. When Rosetta reads in a "sentence case" code such as this, it will check a resID-to-ResidueType map to determine which type of alpha-D-glucose to use, e.g., ->4)-alpha-D-glucopyranosyl or ->6)-alpha-D-glucopyranosyl or ->4)-alpha-D-glucofuranosyl, etc. This function fills that map from a "Rosetta-ready" HETNAM text field, which includes the resID information (in the same order as in an ATOM or HETATOM record) followed by a space and the base (non-variant) ResidueType.

Definition at line 383 of file file_data.cc.

References carbohydrate_residue_type_base_names, protocols::loops::chainID, protocols::loops::iCode, and protocols::loops::resSeq.

Referenced by store_heterogen_names().

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.

Definition at line 662 of file file_data.cc.

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

Referenced by create_working_data().

void core::io::pdb::FileData::store_header_record ( Record & R)

Store information in the header record into the HeaderInformation

Remarks: HeaderInformation must be created explicitly before it can be filled!

Definition at line 290 of file file_data.cc.

References header.

Referenced by core::io::pdb::PDB_DReader::createFileData().

void core::io::pdb::FileData::store_heterogen_names	(	std::string const &	hetID,
		std::string const &	text
	)

Store heterogen name information in a map.

Remarks: heterogen "names" for carbohydrates (from "Rosetta-ready" PDB files) instead have the name field parsed to extract the base (non-variant) ResidueType needed for a particular residue.

Definition at line 341 of file file_data.cc.

References heterogen_names, parse_heterogen_name_for_carbohydrate_residues(), strip_whitespace(), and core::io::pdb::TR().

Referenced by core::io::pdb::PDB_DReader::createFileData().

void core::io::pdb::FileData::store_link_record ( Record & record)

Store (non-standard) polymer linkages in a map.

Definition at line 314 of file file_data.cc.

References links, core::io::pdb::LinkInformation::name1_, and core::io::pdb::TR().

Referenced by core::io::pdb::PDB_DReader::createFileData().