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Rosetta
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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/ResidueTypeSet.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>#include <core/pose/Pose.fwd.hh>#include <basic/Tracer.hh>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <utility/exit.hh>#include <utility/vector1.hh>#include <utility/string_util.hh>#include <map>#include <utility/stream_util.hh>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) |
| @breif 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::Size > | core::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::Size > | core::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::Size > | core::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) |
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.
1.9.1