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Rosetta
2020.50
|
Functions | |
def | get_coord_csts |
def | find_pairs |
def | find_pairs_dict |
def | parse_fasta |
def | parse_secstruct |
def | get_near_residues |
def | setup_job |
def | get_n_cycles |
def | write_flags_file |
def | estimate_error |
Variables | |
list | protein_one_letter |
tuple | parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" ) |
string | help = 'fasta file for the full structure' |
string | type = "" |
string | default = "" |
string | nargs = '+' |
string | action = 'store_true' |
tuple | args = parser.parse_args() |
def DRRAFTER.estimate_error | ( | args | ) |
def DRRAFTER.find_pairs | ( | secstruct, | |
helix_chars = ['(',' , |
|||
a, | |||
b | |||
) |
References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and basic::options::OptionKeys::relax::range.range.
Referenced by find_pairs_dict().
def DRRAFTER.find_pairs_dict | ( | secstruct, | |
helix_chars = ['(',' , |
|||
a, | |||
b | |||
) |
References find_pairs().
Referenced by setup_job().
def DRRAFTER.get_coord_csts | ( | ref_pdb, | |
dist, | |||
exclude_resi = [] |
|||
) |
References utility::options::OptionKeys::options.exit, basic::database.open(), fmt.print(), basic::options::OptionKeys::relax::range.range, and binder.replace().
Referenced by setup_job().
def DRRAFTER.get_n_cycles | ( | remodel_residues | ) |
References ObjexxFCL.len(), min(), and DRRAFTER_util.parse_tag().
Referenced by write_flags_file().
def DRRAFTER.get_near_residues | ( | struct, | |
resnums, | |||
chains, | |||
dist_cutoff | |||
) |
References ObjexxFCL.len(), basic::options::OptionKeys::relax::range.range, and DRRAFTER_util.read_pdb().
Referenced by setup_job().
def DRRAFTER.parse_fasta | ( | fasta | ) |
References utility::options::OptionKeys::options.exit, ObjexxFCL.len(), basic::database.open(), DRRAFTER_util.parse_tag(), and fmt.print().
Referenced by setup_job().
def DRRAFTER.parse_secstruct | ( | secstruct_file | ) |
References basic::database.open().
Referenced by setup_job().
def DRRAFTER.setup_job | ( | args | ) |
References basic::options::OptionKeys::stepwise.enumerate, utility::options::OptionKeys::options.exit, find_pairs_dict(), get_coord_csts(), get_near_residues(), DRRAFTER_util.get_sequences(), fmt.join(), ObjexxFCL.len(), DRRAFTER_util.make_tag_with_dashes(), basic::database.open(), parse_fasta(), parse_secstruct(), DRRAFTER_util.parse_tag(), DRRAFTER_util.pdbslice(), fmt.print(), basic::options::OptionKeys::relax::range.range, and write_flags_file().
def DRRAFTER.write_flags_file | ( | args, | |
helix_chunks, | |||
use_init_structs, | |||
input_structs_for_dash_s | |||
) |
References get_n_cycles(), ObjexxFCL.len(), and basic::database.open().
Referenced by setup_job().
string DRRAFTER.action = 'store_true' |
Referenced by add_rosetta_options_15().
tuple DRRAFTER.args = parser.parse_args() |
string DRRAFTER.default = "" |
string DRRAFTER.help = 'fasta file for the full structure' |
string DRRAFTER.nargs = '+' |
tuple DRRAFTER.parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" ) |
list DRRAFTER.protein_one_letter |
string DRRAFTER.type = "" |
Referenced by pyrosetta.distributed.utility.pickle.__cereal_setstate__(), pyrosetta.distributed.cluster.exceptions.InputFileError.__init__(), pyrosetta.distributed.cluster.exceptions.OutputError.__init__(), pyrosetta.distributed.cluster.converter_tasks._is_packed(), pyrosetta.distributed.cluster.converter_tasks._parse_dict(), pyrosetta.distributed.cluster.converters._parse_environment(), pyrosetta.distributed.cluster.converter_tasks._parse_iterable(), pyrosetta.distributed.cluster.converters._parse_protocols(), pyrosetta.distributed.cluster.converters._parse_pyrosetta_build(), pyrosetta.distributed.cluster.converters._parse_scratch_dir(), pyrosetta.distributed.cluster.converters._parse_sha1(), pyrosetta.distributed.cluster.converters._parse_system_info(), pyrosetta.distributed.cluster.converters._parse_tasks(), basic::datacache::DataMap.add(), basic::datacache::ConstDataMap.add(), binder.add_relevant_include_for_decl(), add_rosetta_options_9(), test.T850_SubClassing.My_New_Mover.apply(), utility::json_spirit::Value_impl< Config >.check_type(), pyrosetta.defineEnergyMethodCreator(), utility.from_string(), basic::datacache::HierarchicalDataMap.get(), GlycanClashCheckMover.get_name(), DockGlycansProtocol.get_name(), basic::datacache::HierarchicalDataMap.get_or_null(), utility::json_spirit::Value_impl< Config >.get_real(), basic::datacache.get_set_from_datamap(), options_class.Option.getDoxygenRow(), options_class.Option.getMarkdownRow(), options_class.Option.getOptionCC(), options_class.Option.getWikiTableRow(), harvest_scores(), pyrosetta.distributed.viewer.core.init(), GlycanClashCheckMover.init(), DockGlycansProtocol.init(), utility::json_spirit::Value_impl< Config >.is_null(), LigandRepackMinimizeProtocol.LigandRepackMinimizeProtocol(), main(), fmt::internal.make_type(), fmt::internal::MakeArg< Formatter >.MakeArg(), name2elt(), pyrosetta.bindings.energies.nonzero_weights_dtype(), utility::json_spirit::Value_impl< Config >.operator==(), basic::datacache::DataMap.operator[](), basic::datacache::ConstDataMap.operator[](), fmt::ArgList.operator[](), options_class.Option_Group(), utility::xsd_util.output_all_tag_options(), pyrosetta.distributed.cluster.converter_tasks.parse_client(), pyrosetta.distributed.cluster.converter_tasks.parse_decoy_name(), pyrosetta.distributed.cluster.converter_tasks.parse_input_packed_pose(), pyrosetta.distributed.cluster.converter_tasks.parse_instance_kwargs(), pyrosetta.distributed.cluster.converter_tasks.parse_scorefile(), numeric.read_tensor_from_file(), binder::Context.request_bindings(), ScoreFragmentSetMover.run(), FragmentAssemblyMover.run(), basic::datacache::HierarchicalDataMap.set(), binder.simplify_std_class_name(), utility.string_split(), rosetta_binders.stringstream_add_on_binder(), erraser_util.subprocess_call(), erraser_util.subprocess_out(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_packer_nstruct(), pyrosetta.distributed.packed_pose.core.to_dict(), pyrosetta.distributed.packed_pose.core.to_packed(), pyrosetta.distributed.packed_pose.core.to_pose(), fmt::ArgList.type(), options_class.wrapCStrig(), fmt::BasicWriter< Char >.write_double(), and numeric.write_tensor_to_file().