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util.cc File Reference

Util functions for Input and Output. Very general IO should go to utility/io. These should be related to core in a deep way or not able to be called from utility. More...

#include <core/io/util.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/StructFileRepOptions.hh>
#include <core/io/pose_to_sfr/PoseToStructFileRepConverter.hh>
#include <core/io/pose_from_sfr/PoseFromSFRBuilder.hh>
#include <core/io/ResidueInformation.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>
#include <core/scoring/Energies.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/datacache/CacheableStringFloatMap.hh>
#include <basic/datacache/CacheableStringMap.hh>
#include <utility/exit.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <utility/string_util.hh>
#include <ObjexxFCL/format.hh>
#include <map>

Namespaces

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

Functions

static basic::Tracer core::io::TR ("core.io.util")
 
std::string core::io::pose_energies_from_sfr (StructFileRep const &sfr)
 Write Pose energies information into a string and return it. More...
 
void core::io::pose_energies_from_sfr (StructFileRep const &sfr, std::stringstream &out)
 Extract the pose energies table from an SFR as a string representation for PDB output. More...
 
std::string core::io::pose_data_cache_from_sfr (StructFileRep const &sfr)
 Write Pose energies information into a string and return it. More...
 
void core::io::pose_data_cache_from_sfr (StructFileRep const &sfr, std::stringstream &out)
 Extract the pose data cache from the SFR as a string representation for PDB output. More...
 
void core::io::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices)
 
void core::io::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, utility::vector1< core::Size > const &residue_indices, StructFileRepOptions const &options)
 
void core::io::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::pose_from_pose (pose::Pose &new_pose, pose::Pose const &old_pose, chemical::ResidueTypeSet const &residue_set, utility::vector1< core::Size > const &residue_indices, StructFileRepOptions const &options)
 
utility::vector1< core::Sizecore::io::fix_glycan_order (utility::vector1< core::io::ResidueInformation > &rinfos, utility::vector1< core::Size > const &glycan_positions, StructFileRepOptions const &options, std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &known_links)
 Glycan IO. More...
 
utility::vector1< core::Sizecore::io::find_carbohydrate_order (utility::vector1< core::io::ResidueInformation > const &rinfos, utility::vector1< core::Size > const &glycan_positions, utility::vector1< core::Size > &chain_ends,std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &link_map, std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &known_links)
 Find the order of glycan residues for all glycan positions. More...
 
utility::vector1< core::Sizecore::io::find_carbohydrate_subbranch_order (core::Size current_res, utility::vector1< core::Size > &chain_ends,std::map< core::Size, std::map< std::string, std::pair< core::Size, std::string > > > const &connectivity, std::set< core::Size > &addressed)
 Find the order of all the glycans connected to current_res, as indicated by the connectivity map. More...
 
void core::io::reorder_glycan_residues (utility::vector1< core::io::ResidueInformation > &rinfos, utility::vector1< core::Size > const &correct_order, utility::vector1< core::Size > const &glycan_positions)
 Bring glycans into the correct order, which corresponds to connectivity of ech glycan tree This requires reordering rinfos. More...
 
std::map< std::pair
< core::Size, std::string >
, std::pair< core::Size,
std::string > > 
core::io::determine_glycan_links (utility::vector1< core::io::ResidueInformation > const &rinfos, StructFileRepOptions const &options)
 Determine links between glycan residues based on coordinates Returns a map keyed on anomeric positions to the atom it's nominally attached to. More...
 
std::map< std::string,
std::map< std::string,
std::pair< std::string,
std::string > > > 
core::io::explicit_links_from_sfr_linkage (std::map< std::string, utility::vector1< LinkInformation > > const &link_map, utility::vector1< core::io::ResidueInformation > const &rinfos)
 
void core::io::add_glycan_links_to_map (std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > &known_links, std::map< std::pair< core::Size, std::string >, std::pair< core::Size, std::string > > const &link_map, utility::vector1< core::io::ResidueInformation > const &rinfos)
 

Detailed Description

Util functions for Input and Output. Very general IO should go to utility/io. These should be related to core in a deep way or not able to be called from utility.

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com), XRW 2016 Team