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Rosetta
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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/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) |
header of classes for resfile options
this class chooses a random conformer for every residue in a specified chain
1.9.1