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

#include <file_data.hh>

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 &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...

ResidueInformation	get_residue_information (core::pose::Pose const &pose, core::uint const seqpos, bool use_PDB=true, bool renumber_chains=false) const
	Return the PDB resName, chainID, resSeq, and iCode for the given Rosetta sequence position. More...

void	append_residue (core::conformation::Residue const &rsd, core::Size &atom_index, core::pose::Pose const &pose, bool preserve_crystinfo=false)
	Append pdb information to FileData for a single residue. More...

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

void	init_from_pose (core::pose::Pose const &pose, FileDataOptions const &options)
	Fill FileData object 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 object using information from given Pose object, for a specified subset of residues. More...

bool	update_atom_information_based_on_occupancy (AtomInformation &ai, FileDataOptions const &options) const

void	randomize_missing_coords (AtomInformation &ai) const
	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...

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::string	filename

std::string	modeltag

HeaderInformationOP	header

pose::RemarksOP	remarks

utility::vector1< std::pair < std::string, std::string > >	heterogen_names

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

std::map< std::string, utility::vector1 < LinkInformation > >	link_map

pose::CrystInfo	crystinfo

std::vector< AtomChain >	chains

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

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

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

Constructor & Destructor Documentation

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

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,
		bool	preserve_crystinfo = `false`
	)

Append pdb information to FileData for a single residue.

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.

References options.

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.

References core::io::pdb::ResidueInformation::atoms, chains, core::io::pdb::convert_atom_name(), core::io::pdb::convert_res_name(), core::io::pdb::AtomInformation::name, core::io::pdb::AtomInformation::resName, core::io::pdb::AtomInformation::temperature, core::io::pdb::ResidueInformation::temps, update_atom_information_based_on_occupancy(), core::io::pdb::AtomInformation::x, core::io::pdb::ResidueInformation::xyz, core::io::pdb::AtomInformation::y, and core::io::pdb::AtomInformation::z.

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().

Referenced by dump_pdb(), core::pose::Pose::dump_pdb(), core::import_pose::atom_tree_diffs::dump_reference_pose(), and core::pose::Pose::dump_scored_pdb().

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 into PDB format and save it to 'file_name' file.

Returns: true if operation was completed without error, false otherwise.

References dump_pdb(), Error(), and file.

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 into 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().

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!

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!

References header.

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

ResidueInformation core::io::pdb::FileData::get_residue_information	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		bool	use_PDB = `true`,
		bool	renumber_chains = `false`
	)		const

Return the PDB resName, chainID, resSeq, and iCode for the given Rosetta sequence position.

References core::pose::Pose::chain(), core::conformation::Conformation::chain_endings(), chr_chains(), core::pose::Pose::conformation(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::io::pdb::ResidueInformation::resName, runtime_assert, and core::io::pdb::TR.

Referenced by append_residue(), and init_from_pose().

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

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 object using information from given Pose object.

Read atoms/residue information from Pose object and put it in FileData object.

References options.

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 object using information from given Pose object and a set of options.

Read atoms/residue information from Pose object and put it in FileData object using options defined in FileDataOptions.

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

Fill FileData object 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.

Note: The alternative of constructing new subposes for output only would be unnecessary/less efficient (?)

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

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

prepare the HeaderInformation data structure;

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.

Author: Labonte

References carbohydrate_residue_type_base_names, and key.

Referenced by store_heterogen_names().

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

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::RG, core::io::pdb::TR, numeric::random::RandomGenerator::uniform(), core::io::pdb::AtomInformation::x, core::io::pdb::AtomInformation::y, and core::io::pdb::AtomInformation::z.

Referenced by update_atom_information_based_on_occupancy().

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!

References header.

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

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