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 = ""

Functions

Variables

Function Documentation

Variable Documentation