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pdb_writer.hh File Reference

Function(s) for pdb writing. More...

#include <core/io/pdb/Record.hh>
#include <core/io/StructFileRep.fwd.hh>
#include <core/io/StructFileRepOptions.hh>
#include <core/io/StructFileReaderOptions.fwd.hh>
#include <core/id/AtomID_Mask.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/io/ozstream.fwd.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::io
 
 core::io::pdb
 

Functions

bool core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::string const &file_name)
 Writes <pose> to a PDB file, returns false if an error occurs Use default StructFileRepOptions. More...
 
bool core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::string const &file_name, core::io::StructFileRepOptionsCOP options)
 Writes <pose> to a PDB file, returns false if an error occurs. More...
 
void core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &out_fname)
 Writes <pose> to a given stream in PDB file format Use default StructFileRepOptions. More...
 
void core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::ostream &out, core::io::StructFileRepOptionsCOP options, std::string const &out_fname="")
 Writes <pose> to a given stream in PDB file format If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string. More...
 
void core::io::pdb::dump_pdb (pose::Pose const &pose, std::ostream &out, id::AtomID_Mask const &mask, core::io::StructFileRepOptionsCOP options)
 This version takes an AtomID mask. More...
 
void core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::ostream &out, utility::vector1< core::Size > const &residue_indices, core::io::StructFileRepOptionsCOP options)
 
bool core::io::pdb::dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::string const &file_name)
 Writes poses to a single PDB file, returns false if an error occurs Use default StructFileRepOptions. More...
 
bool core::io::pdb::dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, String const &file_name, core::io::StructFileRepOptionsCOP options)
 Writes poses to a single PDB file, returns false if an error occurs. More...
 
void core::io::pdb::dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::ostream &out)
 Writes poses to a given stream in PDB file format Use default StructFileRepOptions. More...
 
void core::io::pdb::dump_multimodel_pdb (utility::vector1< core::pose::PoseCOP > const &poses, std::ostream &out, core::io::StructFileRepOptionsCOP options)
 Writes poses to a given stream in PDB file format. More...
 
bool core::io::pdb::add_to_multimodel_pdb (core::pose::Pose const &pose, std::string const &file_name, std::string const &model_tag, bool clear_existing_structures)
 Adds a pose to a multimodel pdb file (or creates the file) Use default StructFileRepOptions. More...
 
bool core::io::pdb::add_to_multimodel_pdb (core::pose::Pose const &pose, std::string const &file_name, std::string const &model_tag, core::io::StructFileRepOptionsCOP options, bool clear_existing_structures)
 Adds a pose to a multimodel pdb file (or creates the file) More...
 
void core::io::pdb::add_to_multimodel_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &model_tag)
 Adds a pose to a multimodel pdb file Use default StructFileRepOptions. More...
 
void core::io::pdb::add_to_multimodel_pdb (core::pose::Pose const &pose, std::ostream &out, std::string const &model_tag, core::io::StructFileRepOptionsCOP options)
 Adds a pose to a multimodel pdb file. More...
 
std::string core::io::pdb::dump_pdb_residue (conformation::Residue const &rsd, core::io::StructFileRepOptionsCOP options=nullptr, core::Size start_atom_number=1)
 PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number. More...
 
std::string core::io::pdb::dump_pdb_residue (conformation::Residue const &rsd, core::Size &atom_number, core::io::StructFileRepOptionsCOP options=nullptr)
 PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter. More...
 
void core::io::pdb::dump_pdb_residue (conformation::Residue const &rsd, core::Size &atom_number, std::ostream &out, core::io::StructFileRepOptionsCOP options=nullptr)
 Writes pdb data for the given residue, incrementing atom_number counter. More...
 
void core::io::pdb::dump_pdb_residue (conformation::Residue const &rsd, std::ostream &out, core::Size start_atom_number=1, core::io::StructFileRepOptionsCOP options=nullptr)
 Writes pdb data for the given residue, beginning from the given atom number. More...
 
std::string core::io::pdb::create_pdb_contents_from_sfr (StructFileRep const &sfr, core::io::StructFileRepOptionsCOP options)
 create a full pdb as a string given a StructFileRep object More...
 
std::string core::io::pdb::create_pdb_line_from_record (Record const &record)
 Create a formatted line for .pdb output. More...
 
std::vector< Record > core::io::pdb::create_records_from_sfr (StructFileRep const &sfr, core::io::StructFileRepOptionsCOP options=nullptr)
 Create vector of records from given StructFileRep object. More...
 
void core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::string const &jd2_job_data, utility::io::ozstream &out, std::string const &filename="")
 Writes a pose to a given stream in PDB file format, optionally appending a given string and optionally extracting scores from the pose. More...
 
void core::io::pdb::dump_pdb (core::pose::Pose const &pose, std::string const &jd2_job_data, std::string &out, std::string const &filename="")
 Writes a pose to a given string in PDB file format, optionally appending a given string and optionally extracting scores from the pose. More...
 

Detailed Description

Function(s) for pdb writing.

Author
Sergey Lyskov (Serge.nosp@m.y.Ly.nosp@m.skov@.nosp@m.jhu..nosp@m.edu)
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com), XRW 2016 Team Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org) to remove make_shared from header, 17 Oct. 2019.