Rosetta 3.4
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core::io::pdb Namespace Reference

Classes

class  AtomInformation
 Atom_information contain information for individual atom. only fields that predent in file will be initialazed, other will have default value. That class basicaly reflect structure of 'ATOM' line in PDB file format. More...
class  ResidueInformation
 Intermediate format for easy construction of core::conformation::Residue objects. Subset of data from "ATOM" lines that is shared by all atoms in a residue. More...
class  FileData
 FileData class. Hold data created from PDB file. More...
class  Field
 Data type Class to represent one field in PDB file. More...
class  PDB_DReader
 PDB Reader it self, D - for dynamic approch of type handling. More...

Typedefs

typedef std::string String
 Record type, represent one line in pdb file.
typedef std::vector
< AtomInformation
AtomChain
typedef std::map< String, FieldRecord

Functions

static basic::Tracer TR ("core.io.pdb.file_data")
 Tracer instance for this file.
static
numeric::random::RandomGenerator 
RG (231411)
 random number generator for randomizing missing density coordinates
static std::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.
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.
void build_pose_from_pdb_as_is (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
void build_pose_as_is1 (io::pdb::FileData &fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing)
bool is_residue_type_recognized (Size const pdb_residue_index, std::string const &pdb_name, core::chemical::ResidueTypeCAPs 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)
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, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices)
std::ostream & operator<< (std::ostream &os, Record const &R)
std::vector< Stringsplit (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
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.
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.
void dump_pdb_residue (conformation::Residue const &rsd, Size &atom_number, std::ostream &out)
 Writes pdb data.
void dump_pdb (pose::Pose const &pose, std::ostream &out, std::string const &tag="1")
 Writes <pose> data.
void dump_pdb (pose::Pose const &pose, std::string const &filename, std::string const &tag="1")
 Writes the <pose> data to <filename>
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
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
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)
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.

Variables

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

Typedef Documentation

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

Record type, represent one line in pdb file.


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 
)

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::io::pdb::ResidueInformation::chainID, 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::FileData::filename, core::conformation::Conformation::fill_missing_atoms(), core::chemical::ResidueType::has(), core::chemical::ResidueType::has_variant_type(), core::pose::initialize_atomid_map(), core::pose::initialize_disulfide_bonds(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_polymer(), is_residue_type_recognized(), core::chemical::ResidueType::is_upper_terminus(), 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::chemical::PROTONATED, core::io::pdb::FileData::remarks, core::io::pdb::ResidueInformation::resid, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::io::pdb::ResidueInformation::resName, core::io::pdb::ResidueInformation::temps, core::io::pdb::ResidueInformation::terCount, core::pose::Pose::total_residue(), core::conformation::Residue::type(), core::chemical::UPPER_TERMINUS, core::io::pdb::ResidueInformation::xyz, and protocols::kinmatch::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,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename 
)
static std::string const core::io::pdb::chr_chains ( "ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz"  ) [static]
std::string core::io::pdb::convert_atom_name ( std::string const &  res_name,
std::string  atom_name 
)
std::string core::io::pdb::convert_res_name ( std::string const &  name)

Temporary hacky hack Need better mechanism for this

References make_table_of_pilot_apps::name.

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 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 
)
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 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 
)
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::extract_scores ( core::pose::Pose const &  pose,
utility::io::ozstream &  out 
)
bool core::io::pdb::is_residue_type_recognized ( Size const  pdb_residue_index,
std::string const &  pdb_name,
core::chemical::ResidueTypeCAPs 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 local_strip_whitespace().

Referenced by build_pose_as_is1().

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

Remove spaces from given string.

Referenced by build_pose_as_is1(), and is_residue_type_recognized().

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.

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

Debug printing, serialazing to Tracer like object.

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 
)
void core::io::pdb::pose_from_pose ( pose::Pose new_pose,
pose::Pose const &  old_pose,
utility::vector1< core::Size > const &  residue_indices 
)
std::string core::io::pdb::print_d ( const char *  format,
double  d 
)

print double with format to string

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

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

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

random number generator for randomizing missing density coordinates

std::vector<String> core::io::pdb::split ( const String s)

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

Referenced by core::conformation::symmetry::VirtualCoordinates::add_coordinate_from_string(), core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), protocols::jd2::JobOutputter::affixed_numbered_name(), protocols::loophash::LoopHashSampler::build_structures(), core::kinematics::MoveMap::init_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(), 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::CstResInteractions::read_data(), protocols::toolbox::match_enzdes_util::ResInteractions::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), protocols::loophash::BackboneDB::read_homologs(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::conformation::symmetry::SymmData::read_symmetry_info_from_pdb(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), and protocols::moves::StructureRestrictor::setup_relevant_chains().

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

Tracer instance for this file.

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

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]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

special Tracer instance acting as special param for all traced_dump_pdb functions

Referenced by traced_dump_pdb().

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