DRRAFTER Namespace Reference

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()

Function Documentation

def DRRAFTER.estimate_error

(

args

)

References utility::options::OptionKeys::options.exit, DRRAFTER_util.get_sequences(), ObjexxFCL.len(), and fmt.print().

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().

Variable Documentation

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'

Referenced by utility::options::OptionCollection.add_built_in_options(), and utility::options::OptionCollection.load().

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

Initial value:

= ['A', 'R', 'N', 'D', 'C', 
  'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M', 
  'F', 'P','S', 'T', 'W', 'Y', 'V']

string DRRAFTER.type = ""

Referenced by pyrosetta.distributed.utility.pickle.__cereal_setstate__(), 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(), 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.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().