Rosetta  2020.50
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Functions
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
 
struct  CisPeptideInformation
 
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...
 
struct  HELIXInformation
 
struct  LinkInformation
 
struct  ModifiedResidueInformation
 
class  NomenclatureManager
 
class  RemarkInfo
 
class  Remarks
 
class  ResidueInformation
 
struct  SHEETInformation
 
struct  SSBondInformation
 
class  StructFileReaderOptions
 
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)
 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::Sizefix_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::Sizefind_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::Sizefind_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

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

Function Documentation

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 
)
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 
)
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 
)
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().

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().

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::pass_2_resolve_residue_types().

bool core::io::link_in_vector ( utility::vector1< LinkInformation > const &  link_vector,
LinkInformation const &  link 
)
std::ostream& core::io::operator<< ( std::ostream &  os,
RemarkInfo const &  ri 
)
std::ostream& core::io::operator<< ( std::ostream &  os,
CrystInfo const &  ci 
)
std::ostream & core::io::operator<< ( std::ostream &  os,
AtomInformation const &  ai 
)
std::ostream & core::io::operator<< ( std::ostream &  os,
StructFileRep const &  sfr 
)

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

Debug printing.

References core::io::StructFileRep::chains().

std::ostream & core::io::operator<< ( std::ostream &  os,
LinkInformation const &  li 
)
std::ostream & core::io::operator<< ( std::ostream &  os,
SSBondInformation const &  ssb 
)
std::string core::io::pose_data_cache_from_sfr ( StructFileRep const &  sfr)

Write Pose energies information into a string and return it.

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::mmtfJobOutputter::dump_energies_file(), and protocols::jd2::mmCIFJobOutputter::dump_energies_file().

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

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

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

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::mmtfJobOutputter::dump_energies_file(), and protocols::jd2::mmCIFJobOutputter::dump_energies_file().

void core::io::pose_energies_from_sfr ( StructFileRep const &  sfr,
std::stringstream &  out 
)
void core::io::pose_from_pose ( pose::Pose new_pose,
pose::Pose const &  old_pose,
utility::vector1< core::Size > const &  residue_indices 
)
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 
)
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().

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().

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 TR().

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

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().

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

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