core::io Namespace Reference

Namespaces
	carbohydrates
	external
	mmcif
	mmtf
	nmr
	pdb
	pose_from_sfr
	pose_to_sfr
	PositionDdGInfo
	raw_data
	rcsb
	rna
	sequence_comparation
	serialization
	silent

Classes
struct	AtomInformation
class	CrystInfo
class	HeaderInformation
	Information stored in the Title Section records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z. More...
class	NomenclatureManager
class	RemarkInfo
class	Remarks
class	ResidueInformation
class	StructFileReaderOptions
struct	ModifiedResidueInformation
struct	LinkInformation
struct	SSBondInformation
struct	CisPeptideInformation
struct	HELIXInformation
struct	SHEETInformation
class	StructFileRep
class	StructFileRepOptions

Typedefs
typedef std::map< std::string, std::tuple< std::string, std::string, char, utility::vector1< std::string > > >	AltCodeMap
typedef utility::pointer::shared_ptr< HeaderInformation >	HeaderInformationOP
typedef utility::pointer::shared_ptr< HeaderInformation const >	HeaderInformationCOP
typedef utility::pointer::shared_ptr< Remarks >	RemarksOP
typedef utility::pointer::shared_ptr< Remarks const >	RemarksCOP
typedef std::string	String
typedef utility::pointer::shared_ptr< StructFileReaderOptions >	StructFileReaderOptionsOP
typedef utility::pointer::shared_ptr< StructFileReaderOptions const >	StructFileReaderOptionsCOP
typedef utility::pointer::shared_ptr< StructFileRep >	StructFileRepOP
typedef utility::pointer::shared_ptr< StructFileRep const >	StructFileRepCOP
typedef utility::vector0< AtomInformation >	ChainAtoms
typedef utility::pointer::shared_ptr< StructFileRepOptions >	StructFileRepOptionsOP
typedef utility::pointer::shared_ptr< StructFileRepOptions const >	StructFileRepOptionsCOP

Functions
AltCodeMap	read_alternative_3_letter_codes_from_database_file (std::string const &filename)
	Return a mapping of alternative PDB 3-letter codes to a paired set including the Rosetta 3-letter code and, optionally, any HETNAM information for the residue desired. More...
std::ostream &	operator<< (std::ostream &os, CrystInfo const &ci)
static basic::Tracer	TR ("core.io.pdb.HeaderInformation")
std::ostream &	operator<< (std::ostream &os, RemarkInfo const &ri)
bool	same_link (LinkInformation const &l1, LinkInformation const &l2)
	Do these link information correspond to the same connection (ignoring order) More...
bool	link_in_vector (utility::vector1< LinkInformation > const &link_vector, LinkInformation const &link1)
	Is the LinkInformation in the given vector? More...
std::ostream &	operator<< (std::ostream &os, AtomInformation const &ai)
	Debug printing, serializing to Tracer like object. More...
std::ostream &	operator<< (std::ostream &os, StructFileRep const &sfr)
	Output StructFileRep object to TR-like stream in human-readable format. More...
std::ostream &	operator<< (std::ostream &os, LinkInformation const &li)
	Debugging output for LinkInformation. More...
std::ostream &	operator<< (std::ostream &os, SSBondInformation const &ssb)
	Debugging output for LinkInformation. More...
static basic::Tracer	TR ("core.io.util")
std::string	pose_energies_from_sfr (StructFileRep const &sfr)
	Write Pose energies information into a string and return it. More...
void	pose_energies_from_sfr (StructFileRep const &sfr, std::stringstream &out)
	Extract the pose energies table from an SFR as a string representation for PDB output. More...
std::string	pose_data_cache_from_sfr (StructFileRep const &sfr)
	Write Pose energies information into a string and return it. More...
void	pose_data_cache_from_sfr (StructFileRep const &sfr, std::stringstream &out)
	@breif Extract the pose data cache from the SFR as a string representation for PDB output. More...
void	pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices)
void	pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices, StructFileRepOptions const &options)
void	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	pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices, StructFileRepOptions const &options)
utility::vector1< core::Size >	fix_glycan_order (utility::vector1< core::io::ResidueInformation > &rinfos, utility::vector1< core::Size > const &glycan_positions, StructFileRepOptions const &options, std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &known_links)
	Glycan IO. More...
utility::vector1< core::Size >	find_carbohydrate_order (utility::vector1< core::io::ResidueInformation > const &rinfos, utility::vector1< core::Size > const &glycan_positions, utility::vector1< core::Size > &chain_ends, std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &link_map, std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &known_links)
	Find the order of glycan residues for all glycan positions. More...
utility::vector1< core::Size >	find_carbohydrate_subbranch_order (core::Size current_res, utility::vector1< core::Size > &chain_ends, std::map< core::Size, std::map< std::string, std::pair< core::Size, std::string > > > const &connectivity, std::set< core::Size > &addressed)
	Find the order of all the glycans connected to current_res, as indicated by the connectivity map. More...
void	reorder_glycan_residues (utility::vector1< core::io::ResidueInformation > &rinfos, utility::vector1< core::Size > const &correct_order, utility::vector1< core::Size > const &glycan_positions)
	Bring glycans into the correct order, which corresponds to connectivity of ech glycan tree This requires reordering rinfos. More...
std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > >	determine_glycan_links (utility::vector1< core::io::ResidueInformation > const &rinfos, StructFileRepOptions const &options)
	Determine links between glycan residues based on coordinates Returns a map keyed on anomeric positions to the atom it's nominally attached to. More...
std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > >	explicit_links_from_sfr_linkage (std::map< std::string, utility::vector1< LinkInformation > > const &link_map, utility::vector1< core::io::ResidueInformation > const &rinfos)
void	add_glycan_links_to_map (std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > &known_links, std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &link_map, utility::vector1< core::io::ResidueInformation > const &rinfos)

Typedef Documentation

AltCodeMap

typedef std::map< std::string, std::tuple< std::string, std::string, char, utility::vector1< std::string> > > core::io::AltCodeMap

ChainAtoms

typedef utility::vector0< AtomInformation > core::io::ChainAtoms

HeaderInformationCOP

typedef utility::pointer::shared_ptr< HeaderInformation const > core::io::HeaderInformationCOP

HeaderInformationOP

typedef utility::pointer::shared_ptr< HeaderInformation > core::io::HeaderInformationOP

RemarksCOP

typedef utility::pointer::shared_ptr< Remarks const > core::io::RemarksCOP

RemarksOP

typedef utility::pointer::shared_ptr< Remarks > core::io::RemarksOP

String

typedef std::string core::io::String

StructFileReaderOptionsCOP

typedef utility::pointer::shared_ptr< StructFileReaderOptions const > core::io::StructFileReaderOptionsCOP

StructFileReaderOptionsOP

typedef utility::pointer::shared_ptr< StructFileReaderOptions > core::io::StructFileReaderOptionsOP

StructFileRepCOP

typedef utility::pointer::shared_ptr< StructFileRep const > core::io::StructFileRepCOP

StructFileRepOP

typedef utility::pointer::shared_ptr< StructFileRep > core::io::StructFileRepOP

StructFileRepOptionsCOP

typedef utility::pointer::shared_ptr< StructFileRepOptions const > core::io::StructFileRepOptionsCOP

StructFileRepOptionsOP

typedef utility::pointer::shared_ptr< StructFileRepOptions > core::io::StructFileRepOptionsOP

Function Documentation

add_glycan_links_to_map()

void core::io::add_glycan_links_to_map	(	std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > &	known_links,
		std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &	link_map,
		utility::vector1< core::io::ResidueInformation > const &	rinfos
	)

References core::scoring::pair.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

determine_glycan_links()

std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > core::io::determine_glycan_links	(	utility::vector1< core::io::ResidueInformation > const &	rinfos,
		StructFileRepOptions const &	options
	)

Determine links between glycan residues based on coordinates Returns a map keyed on anomeric positions to the atom it's nominally attached to.

References core::chemical::carbohydrates::CarbohydrateInfoManager::anomeric_position_from_code(), protocols::mpi_refinement::distance(), core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(), core::io::StructFileRepOptions::max_bond_length(), core::io::StructFileRepOptions::min_bond_length(), core::scoring::pair, TR(), and protocols::kinmatch::xyz().

Referenced by fix_glycan_order(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

explicit_links_from_sfr_linkage()

std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > core::io::explicit_links_from_sfr_linkage	(	std::map< std::string, utility::vector1< LinkInformation > > const &	link_map,
		utility::vector1< core::io::ResidueInformation > const &	rinfos
	)

References core::io::LinkInformation::name1, core::io::LinkInformation::name2, core::io::LinkInformation::resID1, core::io::LinkInformation::resID2, and TR().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

find_carbohydrate_order()

utility::vector1< core::Size > core::io::find_carbohydrate_order	(	utility::vector1< core::io::ResidueInformation > const &	rinfos,
		utility::vector1< core::Size > const &	glycan_positions,
		utility::vector1< core::Size > &	chain_ends,
		std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &	link_map,
		std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &	known_links
	)

Find the order of glycan residues for all glycan positions.

References find_carbohydrate_subbranch_order(), and core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code().

Referenced by fix_glycan_order().

find_carbohydrate_subbranch_order()

utility::vector1< core::Size > core::io::find_carbohydrate_subbranch_order	(	core::Size	current_res,
		utility::vector1< core::Size > &	chain_ends,
		std::map< core::Size, std::map< std::string, std::pair< core::Size, std::string > > > const &	connectivity,
		std::set< core::Size > &	addressed
	)

Find the order of all the glycans connected to current_res, as indicated by the connectivity map.

Referenced by find_carbohydrate_order().

fix_glycan_order()

utility::vector1< core::Size > core::io::fix_glycan_order	(	utility::vector1< core::io::ResidueInformation > &	rinfos,
		utility::vector1< core::Size > const &	glycan_positions,
		StructFileRepOptions const &	options,
		std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &	known_links
	)

Glycan IO.

Reorganize the given glycan residues such that they're in tree order.

Not 100% great, as it won't move any non-glycan residue, which may result in a funky order if there are non-glycans interspersed with the glycan residues Return the positions (in the rinfos) of the known (non-reducing) ends of the glycan chains

References determine_glycan_links(), find_carbohydrate_order(), and reorder_glycan_residues().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

link_in_vector()

bool core::io::link_in_vector	(	utility::vector1< LinkInformation > const &	link_vector,
		LinkInformation const &	link
	)

Is the LinkInformation in the given vector?

References same_link().

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info().

operator<<() [1/6]

std::ostream & core::io::operator<<	(	std::ostream &	os,
		AtomInformation const &	ai
	)

Debug printing, serializing to Tracer like object.

References core::io::AtomInformation::altLoc, core::io::AtomInformation::chainID, core::io::AtomInformation::chem_comp_type, core::io::AtomInformation::element, core::io::AtomInformation::formalcharge, core::io::AtomInformation::iCode, core::io::AtomInformation::isHet, core::io::AtomInformation::name, core::io::AtomInformation::occupancy, core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::io::AtomInformation::segmentID, core::io::AtomInformation::serial, core::io::AtomInformation::temperature, core::io::AtomInformation::terCount, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

operator<<() [2/6]

std::ostream& core::io::operator<<	(	std::ostream &	os,
		CrystInfo const &	ci
	)

operator<<() [3/6]

std::ostream & core::io::operator<<	(	std::ostream &	os,
		LinkInformation const &	li
	)

Debugging output for LinkInformation.

References core::io::LinkInformation::chainID1, core::io::LinkInformation::chainID2, core::io::LinkInformation::iCode1, core::io::LinkInformation::iCode2, core::io::LinkInformation::length, core::io::LinkInformation::name1, core::io::LinkInformation::name2, core::io::LinkInformation::resName1, core::io::LinkInformation::resName2, core::io::LinkInformation::resSeq1, and core::io::LinkInformation::resSeq2.

operator<<() [4/6]

std::ostream& core::io::operator<<	(	std::ostream &	os,
		RemarkInfo const &	ri
	)

operator<<() [5/6]

std::ostream & core::io::operator<<	(	std::ostream &	os,
		SSBondInformation const &	ssb
	)

Debugging output for LinkInformation.

Debugging output for SSBondInformation.

References core::io::SSBondInformation::chainID1, core::io::SSBondInformation::chainID2, core::io::SSBondInformation::iCode1, core::io::SSBondInformation::iCode2, core::io::SSBondInformation::length, core::io::SSBondInformation::name1, core::io::SSBondInformation::name2, core::io::SSBondInformation::resName1, core::io::SSBondInformation::resName2, core::io::SSBondInformation::resSeq1, core::io::SSBondInformation::resSeq2, core::io::SSBondInformation::sym1, and core::io::SSBondInformation::sym2.

operator<<() [6/6]

std::ostream & core::io::operator<<	(	std::ostream &	os,
		StructFileRep const &	sfr
	)

Output StructFileRep object to TR-like stream in human-readable format.

Debug printing.

pose_data_cache_from_sfr() [1/2]

std::string core::io::pose_data_cache_from_sfr

(

StructFileRep const &

sfr

)

Write Pose energies information into a string and return it.

@breif Extract the pose data cache from the SFR as a string representation for PDB output.

Added during the 2016 Chemical XRW.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) + Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::conformation::membrane::out.

Referenced by core::io::pdb::create_records_from_sfr(), protocols::jd2::mmCIFJobOutputter::dump_energies_file(), and protocols::jd2::mmtfJobOutputter::dump_energies_file().

pose_data_cache_from_sfr() [2/2]

void core::io::pose_data_cache_from_sfr	(	StructFileRep const &	sfr,
		std::stringstream &	out
	)

@breif Extract the pose data cache from the SFR as a string representation for PDB output.

References core::conformation::membrane::out, core::io::StructFileRep::pose_cache_real_data(), and core::io::StructFileRep::pose_cache_string_data().

pose_energies_from_sfr() [1/2]

std::string core::io::pose_energies_from_sfr

(

StructFileRep const &

sfr

)

Write Pose energies information into a string and return it.

Extract the pose energies table from an SFR as a string representation for PDB output.

Added during the 2016 Chemical XRW.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::conformation::membrane::out.

Referenced by core::io::pdb::create_records_from_sfr(), protocols::jd2::mmCIFJobOutputter::dump_energies_file(), and protocols::jd2::mmtfJobOutputter::dump_energies_file().

pose_energies_from_sfr() [2/2]

void core::io::pose_energies_from_sfr	(	StructFileRep const &	sfr,
		std::stringstream &	out
	)

Extract the pose energies table from an SFR as a string representation for PDB output.

References core::conformation::membrane::out, core::io::StructFileRep::score_table_filename(), core::io::StructFileRep::score_table_labels(), core::io::StructFileRep::score_table_lines(), and core::io::StructFileRep::score_table_weights().

pose_from_pose() [1/4]

void core::io::pose_from_pose	(	pose::Pose &	new_pose,
		pose::Pose const &	old_pose,
		chemical::ResidueTypeSet const &	residue_set,
		utility::vector1< core::Size > const &	residue_indices
	)

References pose_from_pose().

pose_from_pose() [2/4]

void core::io::pose_from_pose	(	pose::Pose &	new_pose,
		pose::Pose const &	old_pose,
		chemical::ResidueTypeSet const &	residue_set,
		utility::vector1< core::Size > const &	residue_indices,
		StructFileRepOptions const &	options
	)

Creates a subpose from a pose, to include only certain residues, using StructFileRep::init_from_pose() to construct the pose, and build_pose_as_is1() to construct the pose with the given options.

References core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), core::chemical::ResidueTypeSet::get_self_ptr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

pose_from_pose() [3/4]

void core::io::pose_from_pose	(	pose::Pose &	new_pose,
		pose::Pose const &	old_pose,
		utility::vector1< core::Size > const &	residue_indices
	)

Referenced by protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::InterfacePackingFilter::compute(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::constel::get_chain_terms(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), core::pose::Pose::Pose(), pose_from_pose(), protocols::features::PoseConformationFeatures::report_features(), and protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint().

pose_from_pose() [4/4]

void core::io::pose_from_pose	(	pose::Pose &	new_pose,
		pose::Pose const &	old_pose,
		utility::vector1< core::Size > const &	residue_indices,
		StructFileRepOptions const &	options
	)

References core::chemical::FA_STANDARD, and pose_from_pose().

read_alternative_3_letter_codes_from_database_file()

AltCodeMap core::io::read_alternative_3_letter_codes_from_database_file

(

std::string const &

filename

)

Return a mapping of alternative PDB 3-letter codes to a paired set including the Rosetta 3-letter code and, optionally, any HETNAM information for the residue desired.

References protocols::abinitio::filename(), and TR().

Referenced by core::io::NomenclatureManager::NomenclatureManager().

reorder_glycan_residues()

void core::io::reorder_glycan_residues	(	utility::vector1< core::io::ResidueInformation > &	rinfos,
		utility::vector1< core::Size > const &	correct_order,
		utility::vector1< core::Size > const &	glycan_positions
	)

Bring glycans into the correct order, which corresponds to connectivity of ech glycan tree This requires reordering rinfos.

Bring glycans into the correct order, which corresponds to connectivity of each glycan tree This requires reordering rinfos and rosetta_residue_name3s.

References core::io::ResidueInformation::resSeq(), and TR().

Referenced by fix_glycan_order().

same_link()

bool core::io::same_link	(	LinkInformation const &	l1,
		LinkInformation const &	l2
	)

Do these link information correspond to the same connection (ignoring order)

References protocols::antibody::l1, and protocols::antibody::l2.

Referenced by link_in_vector().

TR() [1/2]

static basic::Tracer core::io::TR ( "core.io.pdb.HeaderInformation"  )

static

Referenced by core::io::mmtf::add_extra_data(), core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence(), core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence(), core::io::carbohydrates::chain_gws_string(), core::io::external::PsiPredInterface::cleanup_after_psipred(), core::io::HeaderInformation::compound_token_to_string(), core::io::external::PsiPredInterface::create_fasta_file(), core::io::mmtf::create_sfrs_from_mmtf_filename(), determine_glycan_links(), core::io::carbohydrates::dump_gws(), core::io::carbohydrates::dump_gws_chain(), core::io::mmtf::dump_mmtf(), explicit_links_from_sfr_linkage(), core::io::HeaderInformation::fill_experimental_technique_records(), core::io::HeaderInformation::fill_wrapped_records(), core::io::HeaderInformation::finalize_compound_records(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::initialize_from_directory(), core::io::external::PsiPredInterface::parse_psipred_horiz_output(), core::io::external::PsiPredInterface::parse_psipred_output(), core::io::NomenclatureManager::pdb_code_from_rosetta_name(), read_alternative_3_letter_codes_from_database_file(), reorder_glycan_residues(), core::io::NomenclatureManager::rosetta_names_from_pdb_code(), core::io::external::PsiPredInterface::run_psipred(), core::io::external::PsiPredInterface::run_psipred_prob(), core::io::external::runpsipred_name_mangle_check(), core::io::HeaderInformation::set_line_continuation(), core::io::HeaderInformation::store_authors(), core::io::HeaderInformation::store_deposition_date(), core::io::HeaderInformation::store_experimental_techniques(), core::io::HeaderInformation::store_keywords(), core::io::HeaderInformation::store_title(), core::io::HeaderInformation::string_to_compound_token(), and core::io::carbohydrates::sugar_modifications_from_suffix().

TR() [2/2]

static basic::Tracer core::io::TR ( "core.io.util"  )

static