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core::io::pdb Namespace Reference

Classes

struct  Field
 
class  RecordCollection
 

Typedefs

typedef std::string String
 
typedef std::map< std::string,
Field
Record
 A type for storing a .pdb file record as a map of field names to Fields. More...
 
typedef std::map< RecordType,
Record
RecordDef
 Definitions of all possible records (line types), that can exist in a PDB file. More...
 

Enumerations

enum  RecordType {
  HEADER = 1, OBSLTE, TITLE, SPLIT,
  CAVEAT, COMPND, SOURCE, KEYWDS,
  EXPDTA, NUMMD, MDLTYP, AUTHOR,
  REVDAT, SPRSDE, JRNL, REMARK,
  DBREF, DBREF1, DBREF2, SEQADV,
  SEQRES, MODRES, HET, HETNAM,
  HETSYN, FORMUL, HELIX, SHEET,
  SSBOND, LINK, CISPEP, SITE,
  CRYST1, ORIGX1, ORIGX2, ORIGX3,
  SCALE1, SCALE2, SCALE3, MTRIX1,
  MTRIX2, MTRIX3, MODEL, ATOM,
  ANISOU, TER, HETATM, ENDMDL,
  CONECT, MASTER, END, UNKNOW,
  N_RECORD_TYPES = UNKNOW
}
 Enumerators for all of the record types used in PDB files, according to: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html. More...
 

Functions

static basic::Tracer TR ("core.io.pdb.file_data")
 
void build_pose_from_pdb_as_is (pose::Pose &pose, std::string const &filename)
 Builds a pose into <pose>, without repacking or optimizing hydrogens; using the full-atom ResidueTypeSet. More...
 
void build_pose_from_pdb_as_is (pose::Pose &pose, std::string const &filename, StructFileReaderOptions const &pdr_options)
 Builds a pose into <pose>, without repacking or optimizing hydrogens; using the full-atom ResidueTypeSet and a set of options. More...
 
void build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
 
void build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, StructFileReaderOptions const &pdr_options)
 
void build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, std::istream &file_contents, StructFileReaderOptions const &pdr_options)
 
std::ostream & operator<< (std::ostream &os, Field const &field)
 
Record create_record_from_pdb_line (std::string const &line)
 Convert a .pdb file line into a Record data structure. More...
 
utility::vector1< Recordcreate_records_from_pdb_lines (utility::vector1< std::string > const &lines)
 Create a list of .pdb format records from the lines from a .pdb file. More...
 
utility::vector1< Recordcreate_records_from_pdb_file_contents (std::string const &pdb_contents)
 Create a list of .pdb format records from the entire contents of a .pdb file. More...
 
StructFileRep create_sfr_from_pdb_records (utility::vector1< Record > &records, StructFileReaderOptions const &options)
 Create a representation of structural file data from a list of .pdb format records with options. More...
 
StructFileRep create_sfr_from_pdb_records (utility::vector1< Record > &records)
 Create a representation of structural file data from a list of .pdb format records. More...
 
StructFileRep create_sfr_from_pdb_file_contents (std::string const &pdb_contents, StructFileReaderOptions const &options)
 Create a representation of structural file data from .pdb file contents with options. More...
 
StructFileRep create_sfr_from_pdb_file_contents (std::string const &pdb_contents)
 Create a representation of structural file data from .pdb file contents. More...
 
void store_chain_sequence_record_in_sfr (Record seqres_record, StructFileRep &sfr)
 Create a representation of structural file data from a .pdb file by file. More...
 
void store_mod_res_record_in_sfr (Record modres_record, StructFileRep &sfr)
 Convert .pdb MODRES record into SFR data. More...
 
void store_base_residue_type_name_in_sfr (std::string const &hetID, std::string const &text_field, StructFileRep &sfr)
 Parse .pdb HETNAM text field to extract full resID and convert into SFR data. More...
 
void store_heterogen_name_record_in_sfr (Record hetnam_record, StructFileRep &sfr)
 Convert .pdb HETNAM record into SFR data. More...
 
void store_heterogen_synonym_record_in_sfr (Record hetsyn_record, StructFileRep &sfr)
 Convert .pdb HETSYN record into SFR data. More...
 
void store_formula_record_in_sfr (Record formul_record, StructFileRep &sfr)
 Convert .pdb FORMUL record into SFR data. More...
 
void store_ssbond_record_in_sfr (Record ssbond_record, StructFileRep &sfr)
 Convert .pdb SSBOND record into SFR data. More...
 
void store_link_record_in_sfr (Record link_record, StructFileRep &sfr)
 Convert .pdb LINK record into SFR data. More...
 
void store_cis_peptide_record_in_sfr (Record cispep_record, StructFileRep &sfr)
 Convert .pdb CISPEP record into SFR data. More...
 
void store_crystallographic_parameter_record_in_sfr (Record crystal_record, StructFileRep &sfr)
 Convert .pdb CRYST1 record into SFR data. More...
 
void store_unknown_records_in_sfr (utility::vector1< Record > unknown_records, StructFileRep &sfr)
 Parse and store unknown record types into SFR data. More...
 
bool dump_pdb (core::pose::Pose const &pose, std::string const &file_name)
 Writes <pose> to a PDB file, returns false if an error occurs Use default StructFileRepOptions. More...
 
bool dump_pdb (core::pose::Pose const &pose, std::string const &file_name, core::io::StructFileRepOptionsCOP options)
 Writes <pose> to a PDB file, returns false if an error occurs. More...
 
void dump_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &out_fname)
 Writes <pose> to a given stream in PDB file format Use default StructFileRepOptions. More...
 
void dump_pdb (core::pose::Pose const &pose, std::ostream &out, core::io::StructFileRepOptionsCOP options, std::string const &out_fname="")
 Writes <pose> to a given stream in PDB file format If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string. More...
 
void dump_pdb (pose::Pose const &pose, std::ostream &out, id::AtomID_Mask const &mask, core::io::StructFileRepOptionsCOP options)
 This version takes an AtomID mask. More...
 
void dump_pdb (core::pose::Pose const &pose, std::ostream &out, utility::vector1< core::Size > const &residue_indices, core::io::StructFileRepOptionsCOP options)
 
bool dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::string const &file_name)
 Writes poses to a single PDB file, returns false if an error occurs Use default StructFileRepOptions. More...
 
bool dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, String const &file_name, core::io::StructFileRepOptionsCOP options)
 Writes poses to a single PDB file, returns false if an error occurs. More...
 
void dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::ostream &out)
 Writes poses to a given stream in PDB file format Use default StructFileRepOptions. More...
 
void dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::ostream &out, core::io::StructFileRepOptionsCOP options)
 Writes poses to a given stream in PDB file format. More...
 
bool add_to_multimodel_pdb (core::pose::Pose const &pose, std::string const &file_name, std::string const &model_tag, bool clear_existing_structures)
 Adds a pose to a multimodel pdb file (or creates the file) Use default StructFileRepOptions. More...
 
bool add_to_multimodel_pdb (core::pose::Pose const &pose, std::string const &file_name, std::string const &model_tag, core::io::StructFileRepOptionsCOP options, bool clear_existing_structures)
 Adds a pose to a multimodel pdb file (or creates the file) More...
 
void add_to_multimodel_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &model_tag)
 Adds a pose to a multimodel pdb file Use default StructFileRepOptions. More...
 
void add_to_multimodel_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &model_tag, core::io::StructFileRepOptionsCOP options)
 Adds a pose to a multimodel pdb file. More...
 
std::string create_pdb_contents_from_sfr (StructFileRep const &sfr, core::io::StructFileRepOptionsCOP options)
 create a full pdb as a string given a StructFileRep object More...
 
std::string create_pdb_line_from_record (Record const &record)
 Create a formatted line for .pdb output. More...
 
std::vector< Recordcreate_records_from_sfr (StructFileRep const &sfr, core::io::StructFileRepOptionsCOP options=nullptr)
 Create vector of records from given StructFileRep object. More...
 
pose::PDBInfoOP create_pdb_info_for_single_residue_pose (pose::Pose const &pose, core::io::StructFileRepOptionsCOP)
 
std::string dump_pdb_residue (conformation::Residue const &rsd, core::io::StructFileRepOptionsCOP options=nullptr, core::Size start_atom_number=1)
 PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number. More...
 
std::string dump_pdb_residue (conformation::Residue const &rsd, core::Size &atom_number, core::io::StructFileRepOptionsCOP options=nullptr)
 PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter. More...
 
void dump_pdb_residue (conformation::Residue const &rsd, std::ostream &out, core::Size start_atom_number=1, core::io::StructFileRepOptionsCOP options=nullptr)
 Writes pdb data for the given residue, beginning from the given atom number. More...
 
void dump_pdb_residue (conformation::Residue const &rsd, core::Size &atom_number, std::ostream &out, core::io::StructFileRepOptionsCOP options=nullptr)
 Writes pdb data for the given residue, incrementing atom_number counter. More...
 
void dump_pdb (core::pose::Pose const &pose, std::string const &jd2_job_data, utility::io::ozstream &out, std::string const &filename="")
 Writes a pose to a given stream in PDB file format, optionally appending a given string and optionally extracting scores from the pose. More...
 
void dump_pdb (core::pose::Pose const &pose, std::string const &jd2_job_data, std::string &out, std::string const &filename="")
 Writes a pose to a given string in PDB file format, optionally appending a given string and optionally extracting scores from the pose. More...
 
std::ostream & operator<< (std::ostream &os, Record const &record)
 
RecordDef read_record_definitions_from_file (std::string const &filename, std::map< std::string, RecordType > const &record_type_map)
 Return a mapping of PDB record types to record definitions. More...
 

Typedef Documentation

typedef std::map< std::string, Field > core::io::pdb::Record

A type for storing a .pdb file record as a map of field names to Fields.

Definitions of all possible records (line types), that can exist in a PDB file.

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

Enumeration Type Documentation

Enumerators for all of the record types used in PDB files, according to: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html.

Enumerator
HEADER 
OBSLTE 
TITLE 
SPLIT 
CAVEAT 
COMPND 
SOURCE 
KEYWDS 
EXPDTA 
NUMMD 
MDLTYP 
AUTHOR 
REVDAT 
SPRSDE 
JRNL 
REMARK 
DBREF 
DBREF1 
DBREF2 
SEQADV 
SEQRES 
MODRES 
HET 
HETNAM 
HETSYN 
FORMUL 
HELIX 
SHEET 
SSBOND 
LINK 
CISPEP 
SITE 
CRYST1 
ORIGX1 
ORIGX2 
ORIGX3 
SCALE1 
SCALE2 
SCALE3 
MTRIX1 
MTRIX2 
MTRIX3 
MODEL 
ATOM 
ANISOU 
TER 
HETATM 
ENDMDL 
CONECT 
MASTER 
END 
UNKNOW 
N_RECORD_TYPES 

Function Documentation

bool core::io::pdb::add_to_multimodel_pdb ( core::pose::Pose const &  pose,
std::string const &  file_name,
std::string const &  model_tag,
bool  clear_existing_structures 
)
bool core::io::pdb::add_to_multimodel_pdb ( core::pose::Pose const &  pose,
std::string const &  file_name,
std::string const &  model_tag,
core::io::StructFileRepOptionsCOP  options,
bool  clear_existing_structures 
)

Adds a pose to a multimodel pdb file (or creates the file)

References add_to_multimodel_pdb(), and core::conformation::membrane::out.

void core::io::pdb::add_to_multimodel_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
std::string const &  model_tag 
)

Adds a pose to a multimodel pdb file Use default StructFileRepOptions.

References add_to_multimodel_pdb().

void core::io::pdb::add_to_multimodel_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
std::string const &  model_tag,
core::io::StructFileRepOptionsCOP  options 
)

Adds a pose to a multimodel pdb file.

References dump_pdb().

void core::io::pdb::build_pose_from_pdb_as_is ( pose::Pose pose,
std::string const &  filename 
)
void core::io::pdb::build_pose_from_pdb_as_is ( pose::Pose pose,
std::string const &  filename,
StructFileReaderOptions const &  pdr_options 
)

Builds a pose into <pose>, without repacking or optimizing hydrogens; using the full-atom ResidueTypeSet and a set of options.

References build_pose_from_pdb_as_is(), core::chemical::FULL_ATOM_t, and core::pose::Pose::residue_type_set_for_pose().

void core::io::pdb::build_pose_from_pdb_as_is ( pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename 
)
void core::io::pdb::build_pose_from_pdb_as_is ( pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
StructFileReaderOptions const &  pdr_options 
)
void core::io::pdb::build_pose_from_pdb_as_is ( pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
std::istream &  file_contents,
StructFileReaderOptions const &  pdr_options 
)
std::string core::io::pdb::create_pdb_contents_from_sfr ( StructFileRep const &  sfr,
core::io::StructFileRepOptionsCOP  options 
)
pose::PDBInfoOP core::io::pdb::create_pdb_info_for_single_residue_pose ( pose::Pose const &  pose,
core::io::StructFileRepOptionsCOP   
)

Create a faux PDBInfo object from a Residue

References core::pose::Pose::residue().

Referenced by dump_pdb_residue().

std::string core::io::pdb::create_pdb_line_from_record ( Record const &  record)

Create a formatted line for .pdb output.

create PDB string from Record data. Thank you, Frank! ~Labonte

Referenced by protocols::constel::create_constel_records_from_sfr(), create_pdb_contents_from_sfr(), and store_unknown_records_in_sfr().

Record core::io::pdb::create_record_from_pdb_line ( std::string const &  line)
utility::vector1< Record > core::io::pdb::create_records_from_pdb_file_contents ( std::string const &  pdb_contents)

Create a list of .pdb format records from the entire contents of a .pdb file.

References create_records_from_pdb_lines().

Referenced by create_sfr_from_pdb_file_contents().

utility::vector1< Record > core::io::pdb::create_records_from_pdb_lines ( utility::vector1< std::string > const &  lines)

Create a list of .pdb format records from the lines from a .pdb file.

References create_record_from_pdb_line().

Referenced by create_records_from_pdb_file_contents(), and core::import_pose::determine_file_type().

std::vector< Record > core::io::pdb::create_records_from_sfr ( StructFileRep const &  sfr,
core::io::StructFileRepOptionsCOP  options 
)
StructFileRep core::io::pdb::create_sfr_from_pdb_file_contents ( std::string const &  pdb_contents,
StructFileReaderOptions const &  options 
)
StructFileRep core::io::pdb::create_sfr_from_pdb_file_contents ( std::string const &  pdb_contents)

Create a representation of structural file data from .pdb file contents.

References create_sfr_from_pdb_file_contents().

StructFileRep core::io::pdb::create_sfr_from_pdb_records ( utility::vector1< Record > &  records,
StructFileReaderOptions const &  options 
)

Create a representation of structural file data from a list of .pdb format records with options.

Remarks
The bulk of SFR generation occurs within this function.

References core::io::AtomInformation::altLoc, core::io::AtomInformation::chainID, core::io::AtomInformation::element, core::io::AtomInformation::iCode, core::io::AtomInformation::isHet, core::io::AtomInformation::name, core::io::StructFileReaderOptions::new_chain_order(), core::io::RemarkInfo::num, core::io::StructFileReaderOptions::obey_ENDMDL(), core::io::AtomInformation::occupancy, core::io::StructFileRepOptions::pdb_comments(), core::io::StructFileRepOptions::read_only_ATOM_entries(), core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::io::AtomInformation::segmentID, core::io::AtomInformation::serial, store_chain_sequence_record_in_sfr(), store_cis_peptide_record_in_sfr(), store_crystallographic_parameter_record_in_sfr(), store_formula_record_in_sfr(), store_heterogen_name_record_in_sfr(), store_heterogen_synonym_record_in_sfr(), store_link_record_in_sfr(), store_mod_res_record_in_sfr(), store_ssbond_record_in_sfr(), store_unknown_records_in_sfr(), core::chemical::orbitals::strip_whitespace(), core::io::AtomInformation::temperature, core::io::AtomInformation::terCount, TR(), core::io::RemarkInfo::value, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by create_sfr_from_pdb_file_contents(), create_sfr_from_pdb_records(), and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

StructFileRep core::io::pdb::create_sfr_from_pdb_records ( utility::vector1< Record > &  records)

Create a representation of structural file data from a list of .pdb format records.

References create_sfr_from_pdb_records().

bool core::io::pdb::dump_multimodel_pdb ( utility::vector1< core::pose::PoseCOP > const &  poses,
std::string const &  file_name 
)

Writes poses to a single PDB file, returns false if an error occurs Use default StructFileRepOptions.

Referenced by dump_multimodel_pdb().

bool core::io::pdb::dump_multimodel_pdb ( utility::vector1< core::pose::PoseCOP > const &  poses,
String const &  file_name,
core::io::StructFileRepOptionsCOP  options 
)

Writes poses to a single PDB file, returns false if an error occurs.

References dump_multimodel_pdb(), and core::conformation::membrane::out.

void core::io::pdb::dump_multimodel_pdb ( utility::vector1< core::pose::PoseCOP > const &  poses,
std::ostream &  out 
)

Writes poses to a given stream in PDB file format Use default StructFileRepOptions.

References dump_multimodel_pdb().

void core::io::pdb::dump_multimodel_pdb ( utility::vector1< core::pose::PoseCOP > const &  poses,
std::ostream &  out,
core::io::StructFileRepOptionsCOP  options 
)

Writes poses to a given stream in PDB file format.

References add_to_multimodel_pdb().

bool core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::string const &  file_name 
)
bool core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
String const &  file_name,
core::io::StructFileRepOptionsCOP  options 
)

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(), core::conformation::membrane::out, and TR().

void core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
std::string const &  out_fname 
)

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

Writes <pose> to a given stream in PDB file format Use default StructFileRepOptions If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

References dump_pdb().

void core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
core::io::StructFileRepOptionsCOP  options,
std::string const &  out_fname 
)

Writes <pose> to a given stream in PDB file format If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

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

References create_pdb_contents_from_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

void core::io::pdb::dump_pdb ( pose::Pose const &  pose,
std::ostream &  out,
id::AtomID_Mask const &  mask,
core::io::StructFileRepOptionsCOP  options 
)

This version takes an AtomID mask.

Used by Will's motif hash stuff, I think.

References create_pdb_contents_from_sfr().

void core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::ostream &  out,
utility::vector1< core::Size > const &  residue_indices,
core::io::StructFileRepOptionsCOP  options 
)

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 create_pdb_contents_from_sfr().

void core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::string const &  jd2_job_data,
utility::io::ozstream &  out,
std::string const &  filename = "" 
)

Writes a pose to a given stream in PDB file format, optionally appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It's an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

Parameters
[in]poseThe pose to turn into a PDB.
[in]jd2_job_dataAdditional data to append to the PDB file data (from the job).
[out]outThe output stream that the PDB file data will be written to.
[in]filename(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

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 dump_pdb().

void core::io::pdb::dump_pdb ( core::pose::Pose const &  pose,
std::string const &  jd2_job_data,
std::string &  out,
std::string const &  filename = "" 
)

Writes a pose to a given string in PDB file format, optionally appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It's an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

Parameters
[in]poseThe pose to turn into a PDB.
[in]jd2_job_dataAdditional data to append to the PDB file data from the Job.
[out]outThe output string that the PDB file data will be written to.
[in]filename(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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

std::string core::io::pdb::dump_pdb_residue ( conformation::Residue const &  rsd,
core::io::StructFileRepOptionsCOP  options,
core::Size  start_atom_number 
)
std::string core::io::pdb::dump_pdb_residue ( conformation::Residue const &  rsd,
core::Size atom_number,
core::io::StructFileRepOptionsCOP  options 
)
void core::io::pdb::dump_pdb_residue ( conformation::Residue const &  rsd,
std::ostream &  out,
core::Size  start_atom_number,
core::io::StructFileRepOptionsCOP  options 
)

Writes pdb data for the given residue, beginning from the given atom number.

Note
Python compatible wrapper avoiding reference parameter

References dump_pdb_residue().

void core::io::pdb::dump_pdb_residue ( conformation::Residue const &  rsd,
core::Size atom_number,
std::ostream &  out,
core::io::StructFileRepOptionsCOP  options 
)

Writes pdb data for the given residue, incrementing atom_number counter.

References dump_pdb_residue().

std::ostream & core::io::pdb::operator<< ( std::ostream &  os,
Record const &  record 
)
std::ostream & core::io::pdb::operator<< ( std::ostream &  os,
Field const &  field 
)
RecordDef core::io::pdb::read_record_definitions_from_file ( std::string const &  filename,
std::map< std::string, RecordType > const &  record_type_map 
)

Return a mapping of PDB record types to record definitions.

Note
A mapping of strings to RecordType enums must be passed, because the RecordCollection singleton does not exist or is in the process of being instantiated when this function is called.

References TR().

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

void core::io::pdb::store_base_residue_type_name_in_sfr ( std::string const &  hetID,
std::string const &  text_field,
StructFileRep &  sfr 
)
void core::io::pdb::store_chain_sequence_record_in_sfr ( Record  seqres_record,
StructFileRep &  sfr 
)

Create a representation of structural file data from a .pdb file by file.

Create a representation of structural file data from a .pdb file by filename. Convert .pdb SEQRES record into SFR data.

References core::io::StructFileRep::chain_sequences(), and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_cis_peptide_record_in_sfr ( Record  cispep_record,
StructFileRep &  sfr 
)

Convert .pdb CISPEP record into SFR data.

References core::io::StructFileRep::cispep_map(), core::io::CisPeptideInformation::pep1, and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_crystallographic_parameter_record_in_sfr ( Record  crystal_record,
StructFileRep &  sfr 
)
void core::io::pdb::store_formula_record_in_sfr ( Record  formul_record,
StructFileRep &  sfr 
)

Convert .pdb FORMUL record into SFR data.

References core::io::StructFileRep::heterogen_formulae(), and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_heterogen_name_record_in_sfr ( Record  hetnam_record,
StructFileRep &  sfr 
)

Convert .pdb HETNAM record into SFR data.

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

References core::io::StructFileRep::heterogen_names(), store_base_residue_type_name_in_sfr(), and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_heterogen_synonym_record_in_sfr ( Record  hetsyn_record,
StructFileRep &  sfr 
)

Convert .pdb HETSYN record into SFR data.

References core::io::StructFileRep::heterogen_synonyms(), and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_link_record_in_sfr ( Record  link_record,
StructFileRep &  sfr 
)
void core::io::pdb::store_mod_res_record_in_sfr ( Record  modres_record,
StructFileRep &  sfr 
)

Convert .pdb MODRES record into SFR data.

References core::io::StructFileRep::modres_map(), core::io::ModifiedResidueInformation::resName, and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_ssbond_record_in_sfr ( Record  ssbond_record,
StructFileRep &  sfr 
)

Convert .pdb SSBOND record into SFR data.

Author
Watkins

References core::io::StructFileRep::ssbond_map(), and TR().

Referenced by create_sfr_from_pdb_records().

void core::io::pdb::store_unknown_records_in_sfr ( utility::vector1< Record >  unknown_records,
StructFileRep &  sfr 
)

Parse and store unknown record types into SFR data.

When a .pdb file is converted into a vector1 of records, unrecognized record types are labeled and stored as UNKNOW records. This function parses out Rosetta-specific information and stores it in the SFR.

References create_pdb_line_from_record(), core::io::StructFileRep::pdb_comments(), and TR().

Referenced by create_sfr_from_pdb_records().

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