Rosetta Core  2014.35
Classes | Typedefs | Functions | Variables
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< Stringsplit (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 boost::bimap< std::string, std::string > core::io::pdb::NameBimap
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.

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 
)
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 
)
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 
)
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 
)
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 
)
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)
void core::io::pdb::convert_nucleic_acid_atom_names_to_standard ( ResidueInformation &  rinfo,
bool  const 
)
void core::io::pdb::convert_nucleic_acid_residue_info_to_standard ( utility::vector1< ResidueInformation > &  all_rinfo,
bool const  force_RNA 
)
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 
)
void core::io::pdb::dump_connect_info ( pose::Pose const &  pose,
std::ostream &  out,
std::map< id::AtomID, Size > &  atom_id_output 
)
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 
)
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 
)
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 
)
void core::io::pdb::fill_name_map ( core::io::pdb::NameBimap name_map,
ResidueInformation const &  rinfo,
chemical::ResidueType const &  rsd_type,
FileDataOptions const &  options 
)
void core::io::pdb::fixup_rinfo_based_on_residue_type_set ( utility::vector1< ResidueInformation > &  rinfos,
chemical::ResidueTypeSet const &  residue_set 
)
void core::io::pdb::flip_atom_xyz ( core::conformation::ResidueOP rsd,
std::string const &  sister1_name,
std::string const &  sister2_name 
)
int core::io::pdb::get_chirality_sign ( Vector const &  xyz_sister1,
Vector const &  xyz_sister2,
Vector const &  xyz_parent,
Vector const &  xyz_cousin 
)
int core::io::pdb::get_closest_sister ( Vector const &  xyz_sister1,
Vector const &  xyz_sister2,
Vector const &  xyz_outgroup 
)
bool core::io::pdb::is_NA ( std::string const &  res_name)
bool core::io::pdb::is_old_RNA ( std::string const &  res_name)
bool core::io::pdb::is_potential_old_DNA ( std::string const &  res_name)
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)
std::ostream& core::io::pdb::operator<< ( std::ostream &  os,
Field const &  F 
)
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 
)
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 
)
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 
)
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 
)
int core::io::pdb::sgn ( Real const &  x)
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]troutput 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]troutput 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 
)

Variable Documentation

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