core::io::pdb Namespace Reference

Classes
class	Field
	Data type Class to represent one field in PDB file. More...
class	AtomInformation
	A class that contains information for individual atoms. More...
class	ResidueInformation
	Intermediate format for easy construction of core::conformation::Residue objects. More...
struct	LinkInformation
	A structure for storing information from PDB LINK records. More...
class	FileData
	FileData class. Hold data created from PDB file. More...
class	FileDataOptions
class	HeaderInformation
	Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z. More...
class	PDB_DReader
	PDB Reader it self, D - for dynamic approch of type handling. More...
class	PDB_DReaderOptions

Typedefs
typedef std::map< std::string, Field >	Record
typedef std::map< std::string, Record >	RecordRef
	collection of all possible records (line types), that can exist in PDB file. More...
typedef std::string	String
	Record type, represent one line in pdb file. More...
typedef std::vector < AtomInformation >	AtomChain
typedef utility::pointer::owning_ptr < FileDataOptions >	FileDataOptionsOP
typedef utility::pointer::owning_ptr < FileDataOptions const >	FileDataOptionsCOP
typedef utility::pointer::owning_ptr < HeaderInformation >	HeaderInformationOP
typedef utility::pointer::owning_ptr < HeaderInformation const >	HeaderInformationCOP
typedef utility::pointer::owning_ptr < PDB_DReaderOptions >	PDB_DReaderOptionsOP
typedef utility::pointer::owning_ptr < PDB_DReaderOptions const >	PDB_DReaderOptionsCOP

Functions
std::ostream &	operator<< (std::ostream &os, Field const &F)
	Debug output. More...
std::ostream &	operator<< (std::ostream &os, Record const &R)
	Debug printing, serialazing to Tracer like object. More...
static basic::Tracer	TR ("core.io.pdb.file_data")
static numeric::random::RandomGenerator	RG (231411)
static string const	chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz")
std::ostream &	operator<< (std::ostream &os, FileData const &fd)
std::string	convert_res_name (std::string const &name)
std::string	convert_atom_name (std::string const &res_name, std::string atom_name)
std::string	local_strip_whitespace (std::string const &name)
void	write_additional_pdb_data (std::ostream &out, pose::Pose const &pose, io::pdb::FileData const &, bool write_fold_tree)
	Writes. More...
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 fullatom ResidueTypeSet. More...
void	build_pose_from_pdb_as_is (pose::Pose &pose, std::string const &filename, PDB_DReaderOptions const &pdr_options)
	Builds a pose into <pose>, without repacking or optimizing hydrogens; using the fullatom 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, PDB_DReaderOptions const &pdr_options)
void	build_pose_as_is1 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, FileDataOptions const &options)
bool	is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCOPs const &rsd_type_list, std::map< std::string, Vector > const &xyz, std::map< std::string, double > const &rtemp, utility::vector1< Size > &UA_res_nums, utility::vector1< std::string > &UA_res_names, utility::vector1< std::string > &UA_atom_names, utility::vector1< numeric::xyzVector< Real > > &UA_coords, utility::vector1< core::Real > &UA_temps)
bool	is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCOPs const &rsd_type_list, std::map< std::string, Vector > const &xyz, std::map< std::string, double > const &rtemp, utility::vector1< Size > &UA_res_nums, utility::vector1< std::string > &UA_res_names, utility::vector1< std::string > &UA_atom_names, utility::vector1< numeric::xyzVector< Real > > &UA_coords, utility::vector1< core::Real > &UA_temps, FileDataOptions const &options)
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, FileDataOptions 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, FileDataOptions const &options)
static basic::Tracer	TR ("core.io.pdb.HeaderInformation")
std::vector< String >	split (const String &s)
std::string	print_i (const char *format, int I)
std::string	print_d (const char *format, double d)
basic::Tracer	TR_dump_pdb_dummy ("core.io.pdb.pose_io.dump_pdb_dummy")
	special Tracer instance acting as special param for all traced_dump_pdb functions More...
basic::Tracer	TR ("core.io.pose_io")
void	dump_pdb (pose::Pose const &pose, std::ostream &out, id::AtomID_Mask const &mask, std::string const &tag="1")
	Writes <pose> data. More...
void	dump_bfactor_pdb (pose::Pose const &pose, id::AtomID_Map< Real > const &bfactor, std::ostream &out, std::string const &tag="1")
	Writes <pose> bfactor data. More...
void	dump_pdb_residue (conformation::Residue const &rsd, Size &atom_number, std::ostream &out)
	Writes pdb data. More...
void	dump_pdb (pose::Pose const &pose, std::ostream &out, std::string const &tag="1")
	Writes <pose> data. More...
void	dump_pdb (pose::Pose const &pose, std::string const &filename, std::string const &tag="1")
	Writes the <pose> data to <filename> More...
void	traced_dump_pdb (basic::Tracer const &tr, pose::Pose const &pose, std::ostream &out, std::string const &tag)
	dump_pdb depending on visibility of tracer More...
void	traced_dump_pdb (basic::Tracer const &tr, pose::Pose const &pose, std::string const &filename, std::string const &tag)
	dump_pdb depending on visibility of tracer More...
core::Real	restrict_prec (core::Real inval)
	Utility function to round a real value to the given precisions (number of digits after the decimal place) for output. For use solely by extract_scores() More...
void	extract_scores (pose::Pose const &pose, utility::io::ozstream &out)
	Write <pose> Energies information into an output stream (e.g. the tail of a pdb file) More...
void	dump_connect_info (pose::Pose const &pose, std::ostream &out, std::map< id::AtomID, Size > &atom_id_output)
void	dump_connect_info (pose::Pose const &pose, std::ostream &out)
	dump_connect_info Figure out CONECT fields for PDB output – atoms that are bonded in Rosetta but won't look that way to RASMOL or Pymol because of distance – useful for centroid poses. More...

Variables
basic::Tracer	TR_dump_pdb_dummy
	special Tracer instance acting as special param for all traced_dump_pdb functions More...

Typedef Documentation

typedef std::vector<AtomInformation> core::io::pdb::AtomChain

Definition at line 111 of file file_data.hh.

typedef utility::pointer::owning_ptr< FileDataOptions const > core::io::pdb::FileDataOptionsCOP

Definition at line 31 of file file_data_options.fwd.hh.

typedef utility::pointer::owning_ptr< FileDataOptions > core::io::pdb::FileDataOptionsOP

Definition at line 28 of file file_data_options.fwd.hh.

typedef utility::pointer::owning_ptr< HeaderInformation const > core::io::pdb::HeaderInformationCOP

Definition at line 28 of file HeaderInformation.fwd.hh.

typedef utility::pointer::owning_ptr< HeaderInformation > core::io::pdb::HeaderInformationOP

Definition at line 25 of file HeaderInformation.fwd.hh.

typedef utility::pointer::owning_ptr< PDB_DReaderOptions const > core::io::pdb::PDB_DReaderOptionsCOP

Definition at line 31 of file pdb_dynamic_reader_options.fwd.hh.

typedef utility::pointer::owning_ptr< PDB_DReaderOptions > core::io::pdb::PDB_DReaderOptionsOP

Definition at line 28 of file pdb_dynamic_reader_options.fwd.hh.

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

Definition at line 29 of file Field.fwd.hh.

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

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

Definition at line 35 of file Field.fwd.hh.

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

Record type, represent one line in pdb file.

Definition at line 57 of file file_data.hh.

Function Documentation

void core::io::pdb::build_pose_as_is1	(	io::pdb::FileData &	fd,
		pose::Pose &	pose,
		chemical::ResidueTypeSet const &	residue_set,
		id::AtomID_Mask &	missing,
		FileDataOptions const &	options
	)

Definition at line 821 of file file_data.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_cys, core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::BRANCH_LOWER_TERMINUS, core::chemical::BRANCH_POINT, core::io::pdb::FileData::carbohydrate_residue_type_base_names, core::io::pdb::ResidueInformation::chainID, protocols::loops::chainID, core::io::pdb::FileDataOptions::chains_whose_residues_are_separate_chemical_entities(), core::io::pdb::FileDataOptions::check_if_residues_are_Ctermini(), core::io::pdb::FileDataOptions::check_if_residues_are_Ntermini(), core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::io::pdb::FileData::create_working_data(), core::chemical::DEPROTONATED, core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::chemical::DISULFIDE, core::io::pdb::FileDataOptions::exit_if_missing_heavy_atoms(), core::io::pdb::FileData::filename, core::conformation::Conformation::fill_missing_atoms(), core::chemical::ResidueType::has(), core::chemical::ResidueType::has_variant_type(), core::io::pdb::FileData::header_information(), core::pose::initialize_atomid_map(), core::pose::initialize_disulfide_bonds(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_polymer(), is_residue_type_recognized(), core::chemical::ResidueType::is_upper_terminus(), core::io::pdb::FileDataOptions::keep_input_protonation_state(), core::io::pdb::FileData::links, local_strip_whitespace(), core::chemical::LOWER_TERMINUS, core::chemical::ResidueType::mainchain_atoms(), core::io::pdb::FileData::modeltag, core::pose::Pose::n_residue(), core::chemical::ResidueType::name(), core::chemical::ResidueTypeSet::name3_map(), core::chemical::ResidueType::natoms(), core::pose::Pose::pdb_info(), core::io::pdb::FileDataOptions::preserve_header(), core::chemical::PROTONATED, core::io::pdb::FileData::remarks, core::io::pdb::ResidueInformation::resid, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::residue_type_base_name(), core::io::pdb::ResidueInformation::resName, core::io::pdb::ResidueInformation::temps, core::io::pdb::ResidueInformation::terCount, core::pose::Pose::total_residue(), TR(), core::conformation::Residue::type(), core::chemical::UPPER_TERMINUS, protocols::kinmatch::xyz(), and core::io::pdb::ResidueInformation::xyz.

Referenced by core::import_pose::build_pose_as_is(), build_pose_from_pdb_as_is(), and pose_from_pose().

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 fullatom ResidueTypeSet.

Definition at line 747 of file file_data.cc.

Referenced by build_pose_from_pdb_as_is(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), core::pack::dunbrack::load_unboundrot(), core::scoring::methods::RMS_Energy::RMS_Energy(), and core::scoring::saxs::SAXSEnergy::SAXSEnergy().

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

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

Definition at line 757 of file file_data.cc.

References build_pose_from_pdb_as_is(), core::chemical::FA_STANDARD, and core::chemical::ChemicalManager::get_instance().

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

Definition at line 768 of file file_data.cc.

References build_pose_from_pdb_as_is().

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

Definition at line 779 of file file_data.cc.

References build_pose_as_is1(), core::io::pdb::PDB_DReader::createFileData(), core::io::pdb::FileData::filename, and TR().

static string const core::io::pdb::chr_chains ( "ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz"  )

static

Referenced by core::io::pdb::FileData::append_residue().

std::string core::io::pdb::convert_atom_name	(	std::string const &	res_name,
		std::string	atom_name
	)

Definition at line 547 of file file_data.cc.

References TR().

Referenced by core::io::pdb::FileData::create_working_data().

std::string core::io::pdb::convert_res_name

(

std::string const &

name)

Temporary hacky hack Need better mechanism for this

Definition at line 529 of file file_data.cc.

References TR().

Referenced by core::io::pdb::FileData::create_working_data().

void core::io::pdb::dump_bfactor_pdb	(	pose::Pose const &	pose,
		id::AtomID_Map< Real > const &	bfactor,
		std::ostream &	out,
		std::string const &	tag
	)

Writes <pose> bfactor data.

Definition at line 149 of file pose_io.cc.

References core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void core::io::pdb::dump_connect_info	(	pose::Pose const &	pose,
		std::ostream &	out,
		std::map< id::AtomID, Size > &	atom_id_output
	)

Definition at line 515 of file pose_io.cc.

References core::kinematics::AtomTree::atom_dont_do_update(), core::pose::Pose::atom_tree(), core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), CUTOFF, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by dump_connect_info(), and write_additional_pdb_data().

void core::io::pdb::dump_connect_info	(	pose::Pose const &	pose,
		std::ostream &	out
	)

dump_connect_info Figure out CONECT fields for PDB output – atoms that are bonded in Rosetta but won't look that way to RASMOL or Pymol because of distance – useful for centroid poses.

Definition at line 564 of file pose_io.cc.

References dump_connect_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

Writes <pose> data.

Definition at line 86 of file pose_io.cc.

References core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::moves::PDBDumpMover::apply(), protocols::rna::RNA_DeNovoProtocol::apply(), protocols::MakeRotLib::calc_std_dev(), protocols::motifs::MotifHit::dump_motif_hit(), protocols::nonlocal::emit_intermediate(), for(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::scoring::packstat::pose_to_pack_data(), and protocols::pack_daemon::DaemonSet::process_pose_request_for_entity().

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

Writes <pose> data.

Definition at line 249 of file pose_io.cc.

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

void core::io::pdb::dump_pdb	(	pose::Pose const &	pose,
		std::string const &	filename,
		std::string const &	tag = "1"
	)

Writes the <pose> data to <filename>

example(s): dump_pdb(pose,'my_pose.pdb') See also: Pose Pose.dump_pdb

Definition at line 259 of file pose_io.cc.

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

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

Writes pdb data.

Definition at line 205 of file pose_io.cc.

References core::conformation::Residue::atom(), core::chemical::AtomType::atom_has_orbital(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::bonded_orbitals(), core::conformation::Residue::chain(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::conformation::Residue::orbital_name(), core::conformation::Residue::orbital_xyz(), and core::conformation::Residue::seqpos().

Referenced by core::fragment::dump_frames_as_pdb(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), core::pack::dunbrack::dump_library(), core::pack::rotamer_set::RotamerSets::dump_pdb(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::match::downstream::ScoringSecMatchRPE::evaluate_residues(), core::scoring::methods::setup_water_builders_for_residue_type(), protocols::match::output::CloudPDBWriter::write_match_groups(), and protocols::hotspot_hashing::HotspotStubSet::write_stub().

void core::io::pdb::extract_scores	(	core::pose::Pose const &	pose,
		utility::io::ozstream &	out
	)

Write <pose> Energies information into an output stream (e.g. the tail of a pdb file)

Definition at line 456 of file pose_io.cc.

References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::n_score_types, core::conformation::Residue::name(), core::scoring::name_from_score_type(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), restrict_prec(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and core::scoring::Energies::weights().

Referenced by protocols::jd2::PDBJobOutputter::extract_scores().

bool core::io::pdb::is_residue_type_recognized	(	Size const	pdb_residue_index,
		std::string const &	pdb_name,
		core::chemical::ResidueTypeCOPs const &	rsd_type_list,
		std::map< std::string, Vector > const &	xyz,
		std::map< std::string, double > const &	rtemp,
		utility::vector1< Size > &	UA_res_nums,
		utility::vector1< std::string > &	UA_res_names,
		utility::vector1< std::string > &	UA_atom_names,
		utility::vector1< numeric::xyzVector< Real > > &	UA_coords,
		utility::vector1< core::Real > &	UA_temps
	)

The input rsd_type_list are all the residue types that have the same 3 letter code as pdb_name. Return true if the list is non-empty and false otherwise. If no residue types match, then either exit, ignore or remember the residue based on the following options in the option system:

-in:ignore_waters -in:ignore_unrecognized_res -in:remember_unrecognized_waters -in:remember_unrecognized_res

Definition at line 1292 of file file_data.cc.

Referenced by build_pose_as_is1().

bool core::io::pdb::is_residue_type_recognized	(	Size const	pdb_residue_index,
		std::string const &	pdb_name,
		core::chemical::ResidueTypeCOPs const &	rsd_type_list,
		std::map< std::string, Vector > const &	xyz,
		std::map< std::string, double > const &	rtemp,
		utility::vector1< Size > &	UA_res_nums,
		utility::vector1< std::string > &	UA_res_names,
		utility::vector1< std::string > &	UA_atom_names,
		utility::vector1< numeric::xyzVector< Real > > &	UA_coords,
		utility::vector1< core::Real > &	UA_temps,
		FileDataOptions const &	options
	)

The input rsd_type_list are all the residue types that have the same 3 letter code as pdb_name. Return true if the list is non-empty and false otherwise. If no residue types match, then either exit, ignore or remember the residue based on the following options in a FileDataOptions instance:

-ignore_waters -ignore_unrecognized_res -remember_unrecognized_waters -remember_unrecognized_res

Definition at line 1318 of file file_data.cc.

References core::io::pdb::FileDataOptions::ignore_unrecognized_res(), core::io::pdb::FileDataOptions::ignore_waters(), local_strip_whitespace(), core::io::pdb::FileDataOptions::remember_unrecognized_res(), core::io::pdb::FileDataOptions::remember_unrecognized_water(), and TR().

std::string core::io::pdb::local_strip_whitespace ( std::string const &  name)

inline

Remove spaces from given string.

Definition at line 649 of file file_data.cc.

Referenced by build_pose_as_is1(), and is_residue_type_recognized().

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

Debug output.

Definition at line 61 of file Field.cc.

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

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

Debug printing, serialazing to Tracer like object.

Debug printing, serializing to Tracer like object.

Definition at line 226 of file Field.cc.

std::ostream& core::io::pdb::operator<<	(	std::ostream &	os,
		FileData const &	fd
	)

Debug/Info function. Output FileData object to TR like stream in human redable format.

Definition at line 513 of file file_data.cc.

References core::io::pdb::FileData::chains.

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

Definition at line 1368 of file file_data.cc.

Referenced by protocols::forge::remodel::RemodelLoopMover::loophash_stage(), core::pose::Pose::Pose(), pose_from_pose(), and protocols::features::PoseConformationFeatures::report_features().

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

Definition at line 1378 of file file_data.cc.

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

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

Definition at line 1392 of file file_data.cc.

References pose_from_pose().

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

Definition at line 1403 of file file_data.cc.

References build_pose_as_is1(), and core::io::pdb::FileData::init_from_pose().

std::string core::io::pdb::print_d	(	const char *	format,
		double	d
	)

print double with format to string

Definition at line 326 of file pdb_dynamic_reader.cc.

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

std::string core::io::pdb::print_i	(	const char *	format,
		int	I
	)

print int with format to string

Definition at line 318 of file pdb_dynamic_reader.cc.

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

core::Real core::io::pdb::restrict_prec

(

core::Real

inval)

Utility function to round a real value to the given precisions (number of digits after the decimal place) for output. For use solely by extract_scores()

Apparently, there isn't an easy way to do this in C++, or even the general goal of limiting the precision in output streams. (setprecision() with default formatting doesn't correctly handle very small numbers, and with fixed precision outputs superfluous zeros.)

Definition at line 443 of file pose_io.cc.

Referenced by extract_scores().

static numeric::random::RandomGenerator core::io::pdb::RG ( 231411  )

static

Referenced by core::io::pdb::FileData::randomize_missing_coords().

std::vector<String> core::io::pdb::split

(

const String &

s)

split String by new line symbols, return vector of string.

Definition at line 81 of file pdb_dynamic_reader.cc.

References core::io::serialization::size(), and protocols::loops::start.

Referenced by core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), core::conformation::symmetry::VirtualCoordinates::add_coordinate_from_string(), protocols::jd2::JobOutputter::affixed_numbered_name(), protocols::features::deserialize_db_listener_data(), protocols::loophash::extract_sample_weights(), core::kinematics::MoveMap::init_from_file(), protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), main(), protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input(), protocols::jobdist::BasicJob::output_tag(), core::io::pdb::PDB_DReader::parse(), core::chemical::sdf::parse_bond_type_data(), protocols::hotspot_hashing::LSMSearchPattern::parse_lsm_spec(), core::chemical::sdf::V3Parser::ParseAtom(), core::chemical::sdf::ctabV3000Parser::ParseAtom(), core::chemical::sdf::ctabV2000Parser::ParseAtomTypeData(), core::chemical::sdf::V3Parser::ParseBond(), core::chemical::sdf::ctabV3000Parser::ParseBond(), core::chemical::sdf::V3Parser::ParseTable(), core::chemical::sdf::ctabV3000Parser::ParseTable(), core::import_pose::pose_from_pdb(), core::conformation::symmetry::SymDof::read(), protocols::jd2::parser::BluePrint::read_blueprint(), protocols::toolbox::match_enzdes_util::ResInteractions::read_data(), protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::scoring::methods::SequenceDependentRefEnergy::read_energy_weight_table(), protocols::loophash::BackboneDB::read_homologs(), protocols::loops::LoopsFileIO::read_loop_file_stream(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::relax::FastRelax::read_script_file(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::conformation::symmetry::SymmData::read_symmetry_info_from_pdb(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), and protocols::moves::StructureRestrictor::setup_relevant_chains().

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

static

basic::Tracer core::io::pdb::TR

(

"core.io.pose_io"

)

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

static

Referenced by core::io::pdb::FileData::append_residue(), build_pose_as_is1(), build_pose_from_pdb_as_is(), core::io::pdb::HeaderInformation::compound_token_to_string(), convert_atom_name(), convert_res_name(), core::io::pdb::FileData::create_working_data(), core::io::pdb::PDB_DReader::createFileData(), core::io::pdb::HeaderInformation::experimental_technique_to_string(), core::io::pdb::HeaderInformation::fill_experimental_technique_records(), core::io::pdb::HeaderInformation::fill_wrapped_records(), is_residue_type_recognized(), core::io::pdb::FileData::randomize_missing_coords(), core::io::pdb::HeaderInformation::set_line_continuation(), core::io::pdb::HeaderInformation::store_compound(), core::io::pdb::HeaderInformation::store_deposition_date(), core::io::pdb::HeaderInformation::store_experimental_techniques(), core::io::pdb::FileData::store_heterogen_names(), core::io::pdb::HeaderInformation::store_keywords(), core::io::pdb::FileData::store_link_record(), core::io::pdb::HeaderInformation::store_title(), core::io::pdb::HeaderInformation::string_to_compound_token(), core::io::pdb::HeaderInformation::string_to_experimental_technique(), and write_additional_pdb_data().

basic::Tracer core::io::pdb::TR_dump_pdb_dummy

(

"core.io.pdb.pose_io.dump_pdb_dummy"

)

special Tracer instance acting as special param for all traced_dump_pdb functions

void core::io::pdb::traced_dump_pdb	(	basic::Tracer const &	tr,
		pose::Pose const &	pose,
		std::ostream &	out,
		std::string const &	tag
	)

dump_pdb depending on visibility of tracer

Parameters

[in]

tr

output performed if tracer is visible or if passed dummy tracer core::io::pdb::TR_dump_pdb_dummy

Definition at line 277 of file pose_io.cc.

References core::pose::Pose::dump_pdb(), and TR_dump_pdb_dummy.

void core::io::pdb::traced_dump_pdb	(	basic::Tracer const &	tr,
		pose::Pose const &	pose,
		std::string const &	filename,
		std::string const &	tag
	)

dump_pdb depending on visibility of tracer

Parameters

[in]

tr

output performed if tracer is visible or if passed dummy tracer core::io::pdb::TR_dump_pdb_dummy

Definition at line 298 of file pose_io.cc.

References core::pose::Pose::dump_pdb(), and TR_dump_pdb_dummy.

void core::io::pdb::write_additional_pdb_data	(	std::ostream &	out,
		pose::Pose const &	pose,
		io::pdb::FileData const &	,
		bool	write_fold_tree
	)

Writes.

Definition at line 678 of file file_data.cc.

References core::io::pdb::FileData::chains, core::scoring::dssp::Dssp::dssp_reduced(), dump_connect_info(), core::pose::Pose::fold_tree(), core::pose::get_comment(), core::conformation::Residue::is_coarse(), core::pose::is_ideal_pose(), core::pose::Pose::n_residue(), core::conformation::Residue::name1(), core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), and TR().

Referenced by core::io::pdb::FileData::dump_pdb().

Variable Documentation

basic::Tracer core::io::pdb::TR_dump_pdb_dummy

special Tracer instance acting as special param for all traced_dump_pdb functions

Referenced by traced_dump_pdb().