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/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 <sstream>
#include <algorithm>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <core/pack/task/ResidueLevelTask.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