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 utility::vector1< Record >	RecordDef
	Definitions of all possible records (line types), that can exist in a PDB file. (Indexed by RecordType enum.) 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< Record >	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. More...
utility::vector1< Record >	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. 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< Record >	create_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

Record

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.

RecordDef

typedef utility::vector1< Record > core::io::pdb::RecordDef

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

String

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

Enumeration Type Documentation

RecordType

enum core::io::pdb::RecordType

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

add_to_multimodel_pdb() [1/4]

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

add_to_multimodel_pdb() [2/4]

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

add_to_multimodel_pdb() [3/4]

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
	)

Adds a pose to a multimodel pdb file (or creates the file) Use default StructFileRepOptions.

Referenced by add_to_multimodel_pdb(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::do_a_simulated_annealing_round(), dump_multimodel_pdb(), and core::energy_methods::DumpTrajectoryEnergy::dump_pose().

add_to_multimodel_pdb() [4/4]

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.

build_pose_from_pdb_as_is() [1/5]

void core::io::pdb::build_pose_from_pdb_as_is	(	pose::Pose &	pose,
		chemical::ResidueTypeSet const &	residue_set,
		std::string const &	filename
	)

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

build_pose_from_pdb_as_is() [2/5]

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
	)

References core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), create_sfr_from_pdb_file_contents(), core::io::StructFileRep::filename(), protocols::abinitio::filename(), and core::chemical::ResidueTypeSet::get_self_ptr().

build_pose_from_pdb_as_is() [3/5]

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
	)

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

build_pose_from_pdb_as_is() [4/5]

void core::io::pdb::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.

References protocols::abinitio::filename().

Referenced by protocols::splice::RotLibOut::apply(), core::import_pose::RNA_HelixAssembler::build_init_pose(), build_pose_from_pdb_as_is(), protocols::constraint_generator::get_native_pose(), core::pose::rna::RNA_IdealCoord::init(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), core::pack::dunbrack::load_unboundrot(), protocols::relax::AtomCoordinateCstMover::parse_my_tag(), core::energy_methods::RMS_Energy::RMS_Energy(), core::energy_methods::SAXSEnergy::SAXSEnergy(), and protocols::relax::RelaxProtocolBase::set_up_constraints().

build_pose_from_pdb_as_is() [5/5]

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(), protocols::abinitio::filename(), core::chemical::FULL_ATOM_t, and core::pose::Pose::residue_type_set_for_pose().

create_pdb_contents_from_sfr()

std::string core::io::pdb::create_pdb_contents_from_sfr	(	StructFileRep const &	sfr,
		core::io::StructFileRepOptionsCOP	options
	)

create a full pdb as a string given a StructFileRep object

Create a full .pdb as a string given a StructFileRep object.

References create_pdb_line_from_record(), and create_records_from_sfr().

Referenced by dump_pdb(), dump_pdb_residue(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), and core::import_pose::PDBSilentStruct::print_conformation().

create_pdb_info_for_single_residue_pose()

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::conformation::Residue::chain(), core::pose::Pose::residue(), and core::conformation::Residue::seqpos().

Referenced by dump_pdb_residue().

create_pdb_line_from_record()

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().

create_record_from_pdb_line()

Record core::io::pdb::create_record_from_pdb_line

(

std::string const &

line

)

Convert a .pdb file line into a Record data structure.

References core::io::pdb::RecordCollection::record_from_record_type().

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

create_records_from_pdb_file_contents()

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().

create_records_from_pdb_lines()

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().

create_records_from_sfr()

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

Create vector of records from given StructFileRep object.

Create vector of Record from given StructFileRep object. Used in PDB writing support.

References core::io::CrystInfo::A(), core::io::StructFileRep::additional_string_output(), core::io::CrystInfo::alpha(), core::io::CrystInfo::B(), protocols::vip::base_name(), core::io::CrystInfo::beta(), core::io::CrystInfo::C(), core::io::AtomInformation::chainID, protocols::loops::chainID, core::io::StructFileRep::chains(), CONECT, core::io::AtomInformation::connected_indices, CRYST1, core::io::StructFileRep::crystinfo(), core::io::AtomInformation::element, core::io::StructFileRep::foldtree_string(), core::io::CrystInfo::gamma(), core::io::StructFileRep::header(), HELIX, core::io::StructFileRep::HELIXInformations(), core::io::StructFileRep::heterogen_names(), HETNAM, core::io::AtomInformation::iCode, protocols::loops::iCode, core::io::AtomInformation::isHet, LINK, core::io::StructFileRep::link_map(), core::io::AtomInformation::name, core::io::RemarkInfo::num, core::io::AtomInformation::occupancy, core::conformation::membrane::out, core::io::StructFileRep::pdb_comments(), core::io::StructFileRep::pose_cache_real_data(), core::io::StructFileRep::pose_cache_string_data(), core::io::pose_data_cache_from_sfr(), core::io::pose_energies_from_sfr(), core::io::pdb::RecordCollection::record_from_record_type(), REMARK, core::io::StructFileRep::remarks(), core::io::StructFileRep::residue_type_base_names(), core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, protocols::loops::resSeq, core::io::StructFileRep::score_table_labels(), core::io::StructFileRep::score_table_lines(), core::io::AtomInformation::segmentID, SEQRES, core::io::AtomInformation::serial, SHEET, core::io::StructFileRep::SHEETInformations(), core::io::CrystInfo::spacegroup(), SSBOND, core::io::StructFileRep::ssbond_map(), core::io::AtomInformation::temperature, core::io::AtomInformation::terCount, core::id::to_string(), UNKNOW, core::io::RemarkInfo::value, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

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

create_sfr_from_pdb_file_contents() [1/2]

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().

create_sfr_from_pdb_file_contents() [2/2]

StructFileRep core::io::pdb::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.

References create_records_from_pdb_file_contents(), and create_sfr_from_pdb_records().

Referenced by build_pose_from_pdb_as_is(), create_sfr_from_pdb_file_contents(), core::import_pose::PDBSilentStruct::init_from_lines(), protocols::chromophore::ReadResidueCoordinatesFromPDB::parse_pdb(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::import_pose::pose_from_file(), and core::import_pose::pose_from_pdbstring().

create_sfr_from_pdb_records() [1/2]

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().

create_sfr_from_pdb_records() [2/2]

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::StructFileRep::chains(), core::io::AtomInformation::element, core::io::StructFileRep::header(), core::io::AtomInformation::iCode, core::io::AtomInformation::isHet, core::io::StructFileRep::modeltag(), 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::StructFileRep::remarks(), 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().

dump_multimodel_pdb() [1/4]

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

dump_multimodel_pdb() [2/4]

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

dump_multimodel_pdb() [3/4]

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().

dump_multimodel_pdb() [4/4]

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.

dump_pdb() [1/8]

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(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_pdb() [2/8]

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

dump_pdb() [3/8]

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(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_pdb() [4/8]

bool core::io::pdb::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.

Referenced by add_to_multimodel_pdb(), protocols::moves::PDBDumpMover::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::apply(), LigandDiscoverySearch::discover(), core::pose::Pose::dump_file(), protocols::motifs::MotifHit::dump_motif_hit(), dump_pdb(), core::pose::Pose::dump_pdb(), core::scoring::motif::ResPairMotif::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(), protocols::nonlocal::emit_intermediate(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::recces::options::RECCES_Options::initialize_from_command_line(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_random_chunks(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::output_pose(), IdentifyLigandMotifs::output_single_motif_to_pdb(), core::scoring::packstat::pose_to_pack_data(), protocols::pack_daemon::DaemonSet::process_pose_request_for_entity(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::write_output(), and protocols::jd3::pose_outputters::PDBPoseOutputter::write_output().

dump_pdb() [5/8]

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().

dump_pdb() [6/8]

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]	pose	The pose to turn into a PDB.
[in]	jd2_job_data	Additional data to append to the PDB file data from the Job.
[out]	out	The 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(), protocols::abinitio::filename(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_pdb() [7/8]

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]	pose	The pose to turn into a PDB.
[in]	jd2_job_data	Additional data to append to the PDB file data (from the job).
[out]	out	The 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(), protocols::abinitio::filename(), and core::conformation::membrane::out.

dump_pdb() [8/8]

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(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_pdb_residue() [1/4]

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

PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), core::fragment::dump_frames_as_pdb(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), core::pack::rotamers::dump_library(), core::pack::rotamer_set::RotamerSets::dump_pdb(), dump_pdb_residue(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::match::downstream::ScoringSecMatchRPE::evaluate_residues(), core::scoring::motif::HACK_dump_helix(), core::scoring::lkball::setup_water_builders_for_residue_type(), protocols::match::output::CloudPDBWriter::write_match_groups(), and protocols::hotspot_hashing::HotspotStubSet::write_stub().

dump_pdb_residue() [2/4]

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

PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter.

References core::pose::Pose::append_residue_by_jump(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(), core::conformation::Residue::clone(), create_pdb_contents_from_sfr(), create_pdb_info_for_single_residue_pose(), core::pose::Pose::pdb_info(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

dump_pdb_residue() [3/4]

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

dump_pdb_residue() [4/4]

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

operator<<() [1/2]

std::ostream & core::io::pdb::operator<<	(	std::ostream &	os,
		Field const &	field
	)

References core::io::pdb::Field::end, core::io::pdb::Field::start, and core::io::pdb::Field::value.

operator<<() [2/2]

std::ostream & core::io::pdb::operator<<	(	std::ostream &	os,
		Record const &	record
	)

read_record_definitions_from_file()

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

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

store_base_residue_type_name_in_sfr()

void core::io::pdb::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.

Remarks

Called by store_heterogen_name_record_in_sfr().

References protocols::loops::chainID, protocols::loops::iCode, core::io::StructFileRep::residue_type_base_names(), and protocols::loops::resSeq.

Referenced by core::io::mmcif::create_sfr_from_cif_file_op(), and store_heterogen_name_record_in_sfr().

store_chain_sequence_record_in_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().

store_cis_peptide_record_in_sfr()

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::CisPeptideInformation::chainID1, core::io::CisPeptideInformation::chainID2, core::io::StructFileRep::cispep_map(), core::io::CisPeptideInformation::icode1, core::io::CisPeptideInformation::icode2, core::io::CisPeptideInformation::measure, core::io::CisPeptideInformation::pep1, core::io::CisPeptideInformation::pep2, core::io::CisPeptideInformation::seqNum1, core::io::CisPeptideInformation::seqNum2, and TR().

Referenced by create_sfr_from_pdb_records().

store_crystallographic_parameter_record_in_sfr()

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

Convert .pdb CRYST1 record into SFR data.

References core::io::CrystInfo::A(), core::io::CrystInfo::alpha(), core::io::CrystInfo::B(), core::io::CrystInfo::beta(), core::io::CrystInfo::C(), core::io::StructFileRep::crystinfo(), core::io::CrystInfo::gamma(), core::io::CrystInfo::spacegroup(), and TR().

Referenced by create_sfr_from_pdb_records().

store_formula_record_in_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().

store_heterogen_name_record_in_sfr()

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().

store_heterogen_synonym_record_in_sfr()

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().

store_link_record_in_sfr()

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

Convert .pdb LINK record into SFR data.

References core::io::LinkInformation::chainID1, core::io::LinkInformation::chainID2, core::io::LinkInformation::iCode1, core::io::LinkInformation::iCode2, core::io::LinkInformation::length, core::io::StructFileRep::link_map(), core::io::LinkInformation::name1, core::io::LinkInformation::name2, core::io::LinkInformation::resID1, core::io::LinkInformation::resID2, core::io::LinkInformation::resName1, core::io::LinkInformation::resName2, core::io::LinkInformation::resSeq1, core::io::LinkInformation::resSeq2, and TR().

Referenced by create_sfr_from_pdb_records().

store_mod_res_record_in_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::ModifiedResidueInformation::chainID, core::io::ModifiedResidueInformation::comment, core::io::ModifiedResidueInformation::iCode, core::io::StructFileRep::modres_map(), core::io::ModifiedResidueInformation::resName, core::io::ModifiedResidueInformation::seqNum, core::io::ModifiedResidueInformation::stdRes, and TR().

Referenced by create_sfr_from_pdb_records().

store_ssbond_record_in_sfr()

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::SSBondInformation::chainID1, core::io::SSBondInformation::chainID2, core::io::SSBondInformation::iCode1, core::io::SSBondInformation::iCode2, core::io::SSBondInformation::length, core::io::SSBondInformation::resID1, core::io::SSBondInformation::resID2, core::io::SSBondInformation::resName1, core::io::SSBondInformation::resName2, core::io::SSBondInformation::resSeq1, core::io::SSBondInformation::resSeq2, core::io::StructFileRep::ssbond_map(), and TR().

Referenced by create_sfr_from_pdb_records().

store_unknown_records_in_sfr()

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().

TR()

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

static

Referenced by build_pose_from_pdb_as_is(), create_sfr_from_pdb_records(), dump_pdb(), read_record_definitions_from_file(), 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(), and store_unknown_records_in_sfr().