core::io::pdb Namespace Reference

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

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 a PDB file. More...
typedef std::string	String
typedef std::vector < AtomInformation >	AtomChain
typedef boost::undirected_graph < AtomInformation >	AtomInfoGraph
typedef AtomInfoGraph::vertex_descriptor	AIVD
typedef boost::bimap < std::string, std::string >	NameBimap
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...
std::ostream &	operator<< (std::ostream &os, FileData const &fd)
void	fill_name_map (core::io::pdb::NameBimap &name_map, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type, FileDataOptions const &options)
void	write_additional_pdb_data (std::ostream &out, pose::Pose const &pose, io::pdb::FileData const &fd, bool write_fold_tree=false)
	Adds data to the end of a pdb that are not a standard part of the pdb format. 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 full-atom 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 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, 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)
void	fixup_rinfo_based_on_residue_type_set (utility::vector1< ResidueInformation > &rinfos, chemical::ResidueTypeSet const &residue_set)
std::string	convert_res_name (std::string const &name)
std::string	convert_atom_name (std::string const &res_name, std::string atom_name)
	for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard) More...
void	convert_nucleic_acid_residue_info_to_standard (utility::vector1< ResidueInformation > &all_rinfo, bool const force_RNA)
bool	is_potential_old_DNA (std::string const &res_name)
bool	is_old_RNA (std::string const &res_name)
bool	is_NA (std::string const &res_name)
bool	missing_O2prime (utility::vector1< AtomInformation > const &atoms)
void	convert_nucleic_acid_atom_names_to_standard (ResidueInformation &rinfo, bool const force_RNA=false)
	This is a pretty good framework and could allow for other crazy nucleic acid atom name schemes. More...
void	convert_nucleic_acid_atom_name_to_standard (AtomInformation &atom_info)
void	check_and_correct_sister_atoms (core::conformation::ResidueOP &rsd)
	due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms (like OP1 <–> OP2, or H41 <–> H42) in PDBs is totally wacky. This is an attempt to regularize... and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize. More...
void	check_and_correct_sister_atom_based_on_chirality (core::conformation::ResidueOP &rsd, std::string const sister1_name, std::string const sister2_name, std::string const parent_name, std::string const cousin_name)
void	check_and_correct_sister_atom_based_on_outgroup (core::conformation::ResidueOP &rsd, std::string const sister1_name, std::string const sister2_name, std::string const outgroup_name)
void	flip_atom_xyz (core::conformation::ResidueOP &rsd, std::string const &sister1_name, std::string const &sister2_name)
int	sgn (Real const &x)
int	get_chirality_sign (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_parent, Vector const &xyz_cousin)
int	get_closest_sister (Vector const &xyz_sister1, Vector const &xyz_sister2, Vector const &xyz_outgroup)
core::Real	bonding_distance_threshold (std::string element1, std::string element2)
	Get theshold distance below which two atoms are considered bonded. (1.2*covalent) More...
core::Real	score_mapping (NameBimap const &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type)
	Scoring scheme for the heuristic PDB renaming. More...
void	remap_names_on_geometry (NameBimap &mapping, ResidueInformation const &rinfo, chemical::ResidueType const &rsd_type)
	Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names. More...
std::vector< String >	split (const String &s)
std::string	print_i (const char *format, int I)
	print int with format to string More...
std::string	print_d (const char *format, double d)
	print double with format to string 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 for the given residue, incrementing atom_number counter. More...
void	dump_pdb_residue (conformation::Residue const &rsd, std::ostream &out, Size start_atom_number=1)
	Writes pdb data for the given residue, beginning from the given atom number. 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="1")
	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="1")
	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	extract_scores (core::pose::Pose const &pose, std::string const &filename, std::ostream &out)
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
static basic::Tracer	TR ("core.io.pdb.file_data")
static numeric::random::RandomGenerator	RG (231411)
static basic::Tracer	TR ("core.io.pdb.HeaderInformation")
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...

Typedef Documentation

typedef AtomInfoGraph::vertex_descriptor core::io::pdb::AIVD

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

typedef boost::undirected_graph<AtomInformation > core::io::pdb::AtomInfoGraph

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

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

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

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

typedef boost::bimap< std::string, std::string > core::io::pdb::NameBimap

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

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

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

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

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

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

Function Documentation

core::Real core::io::pdb::bonding_distance_threshold	(	std::string	element1,
		std::string	element2
	)

Get theshold distance below which two atoms are considered bonded. (1.2*covalent)

The closest distance of a non-bonded contact is likely to be something like the opposite atoms cyclobutane. This would be sqrt(2)*covalent bond distance. We thus set the contact distance threshold to 1.2*covalent bond distance to allow bond length flexibility. In initial tests this looks to give a clean decision.

Pass-by-value is deliberate, as we want to strip the elements of whitespace

References core::chemical::Element::CovalentRadius, core::chemical::ChemicalManager::element_set(), core::chemical::ChemicalManager::get_instance(), strip_whitespace(), and utility_exit_with_message.

Referenced by remap_names_on_geometry(), and score_mapping().

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
	)

References core::chemical::aa_cys, core::pose::add_comment(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::PDBInfo::add_unrecognized_atom(), 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(), basic::options::OptionKeys::in::auto_setup_metals, core::chemical::BRANCH_LOWER_TERMINUS_VARIANT, core::chemical::BRANCH_POINT_VARIANT, core::io::pdb::FileData::carbohydrate_residue_type_base_names, core::io::pdb::ResidueInformation::chainID, core::io::pdb::FileDataOptions::chains_whose_residues_are_separate_chemical_entities(), check_and_correct_sister_atoms(), core::io::pdb::FileDataOptions::check_if_residues_are_Ctermini(), core::io::pdb::FileDataOptions::check_if_residues_are_Ntermini(), chemical, core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::io::pdb::FileData::create_working_data(), core::io::pdb::FileData::crystinfo, core::chemical::DEPROTONATED, core::conformation::Conformation::detect_bonds(), basic::options::OptionKeys::in::detect_oops, core::conformation::Conformation::detect_pseudobonds(), numeric::xyzVector< class >::distance_squared(), core::chemical::DISULFIDE, core::io::pdb::FileDataOptions::exit_if_missing_heavy_atoms(), core::io::pdb::FileData::filename, core::conformation::Conformation::fill_missing_atoms(), fill_name_map(), core::scoring::cryst::fix_bfactorsH(), core::scoring::cryst::fix_bfactorsMissing(), fixup_rinfo_based_on_residue_type_set(), getline(), core::chemical::ResidueType::has(), core::conformation::Residue::has(), core::chemical::ResidueType::has_variant_type(), core::io::pdb::FileData::header_information(), core::pose::PDBInfo::header_information(), core::io::pdb::ResidueInformation::iCode, core::pose::initialize_atomid_map(), core::pose::initialize_disulfide_bonds(), core::pose::ncbb::initialize_oops(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueType::is_lower_terminus(), core::conformation::Residue::is_metalbinding(), core::chemical::ResidueType::is_polymer(), core::conformation::Residue::is_protein(), is_residue_type_recognized(), core::chemical::ResidueType::is_upper_terminus(), core::io::pdb::FileDataOptions::keep_input_protonation_state(), key, core::sequence::left, length, core::io::pdb::FileData::link_map, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::io::pdb::FileDataOptions::missing_dens_as_jump(), core::io::pdb::FileData::modeltag, core::pose::PDBInfo::modeltag(), core::pose::Pose::n_residue(), core::pose::PDBInfo::name(), core::chemical::ResidueTypeSet::name3_map(), core::chemical::ResidueType::natoms(), nres, core::pose::PDBInfo::obsolete(), basic::options::option, basic::options::OptionKeys::out::file::pdb_comments, core::pose::Pose::pdb_info(), core::io::pdb::FileDataOptions::preserve_crystinfo(), core::io::pdb::FileDataOptions::preserve_header(), core::chemical::PROTONATED, core::io::pdb::FileData::remarks, core::pose::PDBInfo::remarks(), core::io::pdb::ResidueInformation::resid(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::pose::PDBInfo::resize_atom_records(), core::io::pdb::ResidueInformation::resName, core::io::pdb::ResidueInformation::resSeq, right, runtime_assert, core::id::NamedAtomID_Map< T >::set(), core::pose::PDBInfo::set_chains(), core::pose::PDBInfo::set_crystinfo(), core::pose::PDBInfo::set_icodes(), core::pose::PDBInfo::set_numbering(), core::pose::Pose::set_xyz(), utility::string_split(), core::pose::PDBInfo::temperature(), core::io::pdb::ResidueInformation::temps, core::io::pdb::ResidueInformation::terCount, core::pose::Pose::total_residue(), TR, core::conformation::Residue::type(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, user, utility_exit_with_message, xyz, core::io::pdb::ResidueInformation::xyz, and core::conformation::Residue::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 full-atom ResidueTypeSet.

References options.

Referenced by build_pose_from_pdb_as_is(), core::pose::rna::RNA_IdealCoord::init(), 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 full-atom ResidueTypeSet and a set of options.

References build_pose_from_pdb_as_is(), chemical, core::chemical::FA_STANDARD, and residue_type_set.

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 options.

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
	)

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

void core::io::pdb::check_and_correct_sister_atom_based_on_chirality	(	core::conformation::ResidueOP &	rsd,
		std::string const	sister1_name,
		std::string const	sister2_name,
		std::string const	parent_name,
		std::string const	cousin_name
	)

References core::chemical::ResidueType::atom(), flip_atom_xyz(), get_chirality_sign(), core::conformation::Residue::has(), core::chemical::Atom::ideal_xyz(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by check_and_correct_sister_atoms().

void core::io::pdb::check_and_correct_sister_atom_based_on_outgroup	(	core::conformation::ResidueOP &	rsd,
		std::string const	sister1_name,
		std::string const	sister2_name,
		std::string const	outgroup_name
	)

References core::chemical::ResidueType::atom(), flip_atom_xyz(), get_closest_sister(), core::conformation::Residue::has(), core::chemical::Atom::ideal_xyz(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by check_and_correct_sister_atoms().

void core::io::pdb::check_and_correct_sister_atoms

(

core::conformation::ResidueOP &

rsd

)

due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms (like OP1 <–> OP2, or H41 <–> H42) in PDBs is totally wacky. This is an attempt to regularize... and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize.

References check_and_correct_sister_atom_based_on_chirality(), and check_and_correct_sister_atom_based_on_outgroup().

Referenced by build_pose_as_is1().

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

for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard)

References basic::options::TR, and utility_exit_with_message.

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

void core::io::pdb::convert_nucleic_acid_atom_name_to_standard

(

AtomInformation &

atom_info

)

References basic::init(), and core::io::pdb::AtomInformation::name.

Referenced by convert_nucleic_acid_atom_names_to_standard().

void core::io::pdb::convert_nucleic_acid_atom_names_to_standard	(	ResidueInformation &	rinfo,
		bool	const
	)

This is a pretty good framework and could allow for other crazy nucleic acid atom name schemes.

References core::io::pdb::ResidueInformation::atoms, convert_nucleic_acid_atom_name_to_standard(), core::io::pdb::AtomInformation::name, basic::options::option, basic::options::OptionKeys::in::show_all_fixes, core::io::pdb::ResidueInformation::temps, basic::options::TR, and core::io::pdb::ResidueInformation::xyz.

Referenced by convert_nucleic_acid_residue_info_to_standard().

void core::io::pdb::convert_nucleic_acid_residue_info_to_standard	(	utility::vector1< ResidueInformation > &	all_rinfo,
		bool const	force_RNA
	)

References core::io::pdb::ResidueInformation::atoms, convert_nucleic_acid_atom_names_to_standard(), is_NA(), is_old_RNA(), is_potential_old_DNA(), missing_O2prime(), basic::options::option, core::io::pdb::ResidueInformation::resName, basic::options::OptionKeys::in::show_all_fixes, and basic::options::TR.

Referenced by fixup_rinfo_based_on_residue_type_set().

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

(

std::string const &

name

)

Temporary hacky hack Need better mechanism for this for nucleic acids, slightly better mechanism is below (convert_nucleic_acid_residue_info_to_standard)

References basic::options::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.

References chain, core::chemical::element::F, core::chemical::element::I, nres, basic::options::option, basic::options::OptionKeys::out::file::output_orbitals, core::pose::Pose::residue(), runtime_assert, 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
	)

References core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), basic::options::OptionKeys::inout::connect_info_cutoff, CUTOFF, core::chemical::element::I, basic::options::option, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by 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.

References basic::options::option, basic::options::OptionKeys::out::file::output_virtual, 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.

References chain, core::chemical::element::F, core::chemical::element::I, nres, basic::options::option, basic::options::OptionKeys::out::file::output_orbitals, basic::options::OptionKeys::out::file::output_virtual, core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by core::scoring::packstat::pose_to_pack_data().

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

Writes <pose> data.

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

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 for the given residue, incrementing atom_number counter.

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(), chain, core::conformation::Residue::chain(), core::chemical::element::F, core::chemical::element::I, core::conformation::Residue::name3(), core::conformation::Residue::natoms(), basic::options::option, core::conformation::Residue::orbital_name(), core::conformation::Residue::orbital_xyz(), basic::options::OptionKeys::out::file::output_orbitals, runtime_assert, and core::conformation::Residue::seqpos().

Referenced by core::fragment::dump_frames_as_pdb(), core::pack::dunbrack::dump_library(), core::pack::rotamer_set::RotamerSets::dump_pdb(), and core::scoring::methods::setup_water_builders_for_residue_type().

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

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

Note

Python compatible wrapper avoiding reference parameter

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)

References extract_scores(), and utility::io::ozstream::filename().

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

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(), score, score_type, core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), weights, and core::scoring::Energies::weights().

Referenced by extract_scores().

void core::io::pdb::fill_name_map	(	core::io::pdb::NameBimap &	name_map,
		ResidueInformation const &	rinfo,
		chemical::ResidueType const &	rsd_type,
		FileDataOptions const &	options
	)

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::io::pdb::ResidueInformation::atoms, core::chemical::ResidueType::has(), core::chemical::ResidueType::name3(), remap_names_on_geometry(), core::chemical::ResidueType::remap_pdb_atom_names(), rename, core::io::pdb::FileDataOptions::residues_for_atom_name_remapping(), and core::io::pdb::ResidueInformation::xyz.

Referenced by build_pose_as_is1().

void core::io::pdb::fixup_rinfo_based_on_residue_type_set	(	utility::vector1< ResidueInformation > &	rinfos,
		chemical::ResidueTypeSet const &	residue_set
	)

References convert_nucleic_acid_residue_info_to_standard(), core::chemical::FA_RNA, and core::chemical::ResidueTypeSet::name().

Referenced by build_pose_as_is1().

void core::io::pdb::flip_atom_xyz	(	core::conformation::ResidueOP &	rsd,
		std::string const &	sister1_name,
		std::string const &	sister2_name
	)

References core::conformation::Residue::name3(), basic::options::option, core::conformation::Residue::set_xyz(), basic::options::OptionKeys::in::show_all_fixes, basic::options::TR, and core::conformation::Residue::xyz().

Referenced by check_and_correct_sister_atom_based_on_chirality(), and check_and_correct_sister_atom_based_on_outgroup().

int core::io::pdb::get_chirality_sign	(	Vector const &	xyz_sister1,
		Vector const &	xyz_sister2,
		Vector const &	xyz_parent,
		Vector const &	xyz_cousin
	)

References cross(), dot(), sgn(), sign(), and utility_exit_with_message.

Referenced by check_and_correct_sister_atom_based_on_chirality().

int core::io::pdb::get_closest_sister	(	Vector const &	xyz_sister1,
		Vector const &	xyz_sister2,
		Vector const &	xyz_outgroup
	)

References numeric::xyzVector< class >::distance().

Referenced by check_and_correct_sister_atom_based_on_outgroup().

bool core::io::pdb::is_NA

(

std::string const &

res_name

)

Referenced by core::pose::Pose::alpha(), core::pose::Pose::beta(), core::pose::Pose::chi(), convert_nucleic_acid_residue_info_to_standard(), core::pose::Pose::delta(), core::pose::Pose::epsilon(), core::pose::Pose::gamma(), core::pose::Pose::set_alpha(), core::pose::Pose::set_beta(), core::pose::Pose::set_chi(), core::pose::Pose::set_delta(), core::pose::Pose::set_epsilon(), core::pose::Pose::set_gamma(), core::pose::Pose::set_zeta(), core::scoring::loop_graph::LoopGraph::update(), and core::pose::Pose::zeta().

bool core::io::pdb::is_old_RNA

(

std::string const &

res_name

)

Referenced by convert_nucleic_acid_residue_info_to_standard().

bool core::io::pdb::is_potential_old_DNA

(

std::string const &

res_name

)

Referenced by convert_nucleic_acid_residue_info_to_standard().

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

References options.

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

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

bool core::io::pdb::missing_O2prime

(

utility::vector1< AtomInformation > const &

atoms

)

Referenced by convert_nucleic_acid_residue_info_to_standard().

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

Debug output.

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.

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.

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
	)

References options.

Referenced by core::pose::Pose::Pose(), and pose_from_pose().

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
	)

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

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
	)

References options, 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,
		FileDataOptions const &	options
	)

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

Note

This function returns a string sized to 1024 characters! You will likely want to resize the returned string. ~Labonte

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

Note

This function returns a string sized to 1024 characters! You will likely want to resize the returned string. ~Labonte

Referenced by core::io::pdb::FileData::append_residue(), and core::io::pdb::PDB_DReader::createRecords().

void core::io::pdb::remap_names_on_geometry	(	NameBimap &	mapping,
		ResidueInformation const &	rinfo,
		chemical::ResidueType const &	rsd_type
	)

Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names.

References core::io::pdb::ResidueInformation::atoms, bonding_distance_threshold(), core::io::pdb::ResidueInformation::chainID, core::chemical::ResidueType::graph(), core::io::pdb::ResidueInformation::iCode, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::io::pdb::ResidueInformation::resName, core::io::pdb::ResidueInformation::resSeq, basic::options::TR, utility_exit_with_message, and core::io::pdb::ResidueInformation::xyz.

Referenced by fill_name_map().

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.)

Referenced by extract_scores().

core::Real core::io::pdb::score_mapping	(	NameBimap const &	mapping,
		ResidueInformation const &	rinfo,
		chemical::ResidueType const &	rsd_type
	)

Scoring scheme for the heuristic PDB renaming.

References numeric::abs_difference(), core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::bond_iterators(), core::chemical::ResidueType::bonded_neighbor(), bonding_distance_threshold(), numeric::dihedral_degrees(), numeric::xyzVector< class >::distance_squared(), core::chemical::Atom::element_type(), core::chemical::ResidueType::graph(), core::chemical::Atom::ideal_xyz(), inverse(), core::chemical::ResidueType::natoms(), score, numeric::sign(), target, and core::io::pdb::ResidueInformation::xyz.

Referenced by core::io::pdb::GeometricRenameIsomorphismCallback::operator()().

int core::io::pdb::sgn

(

Real const &

x

)

Referenced by core::scoring::func::GaussianChainQuadrupleFunc::dfunc(), core::scoring::func::GaussianChainQuadrupleFunc::func(), and get_chirality_sign().

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

(

const String &

s

)

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

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

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

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

(

"core.io.pose_io"

)

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

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

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
	)

Adds data to the end of a pdb that are not a standard part of the pdb format.

References chain, core::io::pdb::FileData::chains, core::scoring::dssp::Dssp::dssp_reduced(), dump_connect_info(), core::chemical::element::F, core::pose::Pose::fold_tree(), core::pose::get_all_comments(), core::pose::get_comment(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::pose::is_ideal_pose(), core::pose::Pose::n_residue(), core::conformation::Residue::name1(), core::pose::Pose::omega(), basic::options::option, option, basic::options::OptionKeys::out::file::output_orbitals, basic::options::OptionKeys::out::file::output_torsions, core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), spacing, core::conformation::membrane::thickness, core::pose::Pose::total_atoms(), core::pose::Pose::total_residue(), TR, user, and width.

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

Variable Documentation

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

static

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

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

static

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

static

Referenced by build_pose_as_is1(), build_pose_from_pdb_as_is(), core::io::pdb::HeaderInformation::compound_token_to_string(), 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(), core::io::pdb::FileData::get_residue_information(), 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(), core::io::pdb::FileData::update_atom_information_based_on_occupancy(), and write_additional_pdb_data().

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().