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ResfileReader.hh File Reference

header of classes for resfile options More...

#include <core/pack/task/ResfileReader.fwd.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/chemical/ResidueProperty.hh>
#include <core/chemical/AA.hh>
#include <utility/vector1.hh>
#include <utility/fixedsizearray1.hh>
#include <utility/VirtualBase.hh>
#include <utility/excn/Exceptions.hh>
#include <iosfwd>
#include <list>
#include <map>
#include <string>

Classes

class  core::pack::task::ResfileReaderException
 
class  core::pack::task::ResfileContents
 
class  core::pack::task::ResfileCommand
 abstract/interface class for Resfile reader command objects More...
 
class  core::pack::task::NATRO
 NATRO disables packing and designing at a position, the residue will be totally unchanged. More...
 
class  core::pack::task::NATAA
 NATAA allows repacking but no sequence changes (all rotamers are of the original residue) More...
 
class  core::pack::task::ALLAA
 ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) More...
 
class  core::pack::task::ALLAAxc
 ALLAAxc allows repacking and designing to any canonical noncysteine residue. More...
 
class  core::pack::task::ALLAAwc
 allows repacking and designing to any canonical residue (default state of PackerTask) More...
 
class  core::pack::task::PIKAA
 PIKAA allows residues specifed in a following string. More...
 
class  core::pack::task::PIKNA
 PIKNA allows nucleic acid residues specifed in a following string. More...
 
class  core::pack::task::NOTAA
 NOTAA disallows residues specified in a following string, and allows packing. More...
 
class  core::pack::task::PROPERTY
 Allows designing on ANY residue type Property. (Only currently works with Cannonical AAs) JAB. More...
 
class  core::pack::task::POLAR
 POLAR allows polar residues and packing. More...
 
class  core::pack::task::APOLAR
 APOLAR allows nonpolar residues and packing. More...
 
class  core::pack::task::APOLA
 APOLA is a deprecated version of APOLAR allows nonpolar residues and packing. More...
 
class  core::pack::task::CHARGED
 CHARGED allows charged residues and packing JAB. More...
 
class  core::pack::task::AROMATIC
 AROMATIC allows designing only aromatic residues. JAB. More...
 
class  core::pack::task::EX
 EX handles the various extrachi options. More...
 
class  core::pack::task::EX_CUTOFF
 EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) More...
 
class  core::pack::task::USE_INPUT_SC
 USE_INPUT_SC turns on inclusion of the current rotamer for the packer. More...
 
class  core::pack::task::AUTO
 AUTO suggests that a packer can/should reconsider the design setting at a/each residue. More...
 
class  core::pack::task::SCAN
 SCAN suggests to some packing routines that if there are multiple type choices for this residue, then each of them should be considered explicitly in one way or another. More...
 
class  core::pack::task::TARGET
 TARGET flags the position as "targeted", and can optionally specify a "targeted" type. More...
 
class  core::pack::task::NO_ADDUCTS
 NO_ADDUCTS will disable adducts, assuming they exist. More...
 
class  core::pack::task::FIX_HIS_TAUTOMER
 FIX_HIS_TAUTOMER: when a histidine is present when the PackerTask is initialized, this flag will fix its tautomer (whether its hydrogen is on ND1 or NE2. Does nothing if not histidine at initialization (meaning if it mutates to histidine later this flag will have no effect). More...
 

Namespaces

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

Functions

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...
 
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...
 
void core::pack::task::onError (std::string message)
 

Detailed Description

header of classes for resfile options

this class chooses a random conformer for every residue in a specified chain

Author
Steven Lewis
Andrew Leaver-Fay
Gordon Lemmon