Rosetta  2021.16
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ResfileReader.cc File Reference

implementation of resfile reader and its command classes More...

#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/ResidueIndexDescription.hh>
#include <core/chemical/types.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueProperties.hh>
#include <utility>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <utility/assert.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <string>
#include <fstream>
#include <sstream>
#include <algorithm>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <utility/vector1.hh>

Namespaces

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

Functions

static basic::Tracer core::pack::task::TR ("core.pack.task.ResfileReader")
 
std::map< std::string,
ResfileCommandOP > 
core::pack::task::create_command_map ()
 utility for resfile reader, commands MUST be entered into this hard-coded map More...
 
bool core::pack::task::comment_begin (utility::vector1< std::string > const &tokens, Size which_token)
 utility function for resfile reader (checks for a leading # signaling a comment) More...
 
void core::pack::task::parse_resfile (pose::Pose const &pose, PackerTask &the_task)
 changes the state of the given PackerTask according to the commands in the resfile at read in from the -pack:resfile option system. More...
 
void core::pack::task::parse_resfile (pose::Pose const &pose, PackerTask &the_task, std::string const &filename)
 changes the state of the given PackerTask according to the commands in the resfile at filename More...
 
void core::pack::task::parse_resfile_string (pose::Pose const &pose, PackerTask &the_task, std::string const &resfile_fname, std::string const &resfile_string)
 changes the state of the given PackerTask according to the commands in the resfile. More...
 
void core::pack::task::parse_resfile_string (pose::Pose const &pose, PackerTask &the_task, std::string const &resfile_fname, std::string const &resfile_string, core::select::residue_selector::ResidueSubset const &mask)
 changes the state of the given PackerTask according to the commands in the resfile. More...
 
std::string core::pack::task::get_token (const Size which_token, const utility::vector1< std::string > &tokens, const bool make_upper_case=true)
 utility function to increment next token to be parsed More...
 
utility::vector1< std::string > core::pack::task::tokenize_line (std::istream &inputstream)
 Split the line into vector of strings. Each separated string is a 'token'. More...
 
utility::vector1< std::string > core::pack::task::tokenize_line (std::string const &line)
 Split the line into vector of strings. Each separated string is a 'token'. More...
 
void core::pack::task::onError (std::string message)
 

Detailed Description

implementation of resfile reader and its command classes

Author
Steven Lewis (smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om)
Andrew Leaver-Fay
Gordon Lemmon , adapted from the ResfileReader code by Steven Lewis (smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om) and Andrew Leaver-Fay
Gordon Lemmon , adapted from the ResfileReader code
Steven Lewis (smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om)
Andrew Leaver-Fay
Reworked a bit by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org) during the 2019 PackerPalette mini-XRW to use PackerPalettes.
Gordon Lemmon (glemm.nosp@m.on@g.nosp@m.mail..nosp@m.com), adapted from the ResfileReader code by Steven Lewis (smlew.nosp@m.i@un.nosp@m.c.edu) and Andrew Leaver-Fay
Gordon Lemmon (glemm.nosp@m.on@g.nosp@m.mail..nosp@m.com)
Gordon Lemmon (glemm.nosp@m.on@g.nosp@m.mail..nosp@m.com), adapted from the ResfileReader code by Steven Lewis (smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om) and Andrew Leaver-Fay