DRRAFTER Namespace Reference

Functions
def	get_coord_csts (ref_pdb, dist, exclude_resi=[])
def	find_pairs (secstruct, helix_chars=['(',')', '{', '}', '<', '>', 'a', 'b'])
def	find_pairs_dict (secstruct, helix_chars=['(',')', '[', ']', '{', '}', '<', '>', 'a', 'b'])
def	parse_fasta (fasta)
def	parse_secstruct (secstruct_file)
def	get_near_residues (struct, resnums, chains, dist_cutoff)
def	setup_job (args)
def	get_n_cycles (remodel_residues)
def	write_flags_file (args, helix_chunks, use_init_structs, input_structs_for_dash_s)
def	estimate_error (args)

Variables
list	protein_one_letter
	parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" )
	type
	str
	default
	help
	nargs
	float
	action
	False
	int
	args = parser.parse_args()

Function Documentation

estimate_error()

def DRRAFTER.estimate_error

(

args

)

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

find_pairs()

def DRRAFTER.find_pairs	(		secstruct,
			helix_chars = ['(',')', '{', '}', '<', '>', 'a', 'b']
	)

References ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, and range.

Referenced by find_pairs_dict().

find_pairs_dict()

def DRRAFTER.find_pairs_dict	(		secstruct,
			helix_chars = ['(',')', '[', ']', '{', '}', '<', '>', 'a', 'b']
	)

References find_pairs().

Referenced by setup_job().

get_coord_csts()

def DRRAFTER.get_coord_csts	(		ref_pdb,
			dist,
			exclude_resi = []
	)

References utility::options::OptionKeys::options.exit, basic::database.open(), print(), range, binder.replace(), and str.

Referenced by setup_job().

get_n_cycles()

def DRRAFTER.get_n_cycles

(

remodel_residues

)

References ObjexxFCL.len(), min(), and DRRAFTER_util.parse_tag().

Referenced by write_flags_file().

get_near_residues()

def DRRAFTER.get_near_residues	(		struct,
			resnums,
			chains,
			dist_cutoff
	)

References ObjexxFCL.len(), range, and DRRAFTER_util.read_pdb().

Referenced by setup_job().

parse_fasta()

def DRRAFTER.parse_fasta

(

fasta

)

References utility::options::OptionKeys::options.exit, ObjexxFCL.len(), basic::database.open(), DRRAFTER_util.parse_tag(), and print().

Referenced by setup_job().

parse_secstruct()

def DRRAFTER.parse_secstruct

(

secstruct_file

)

References basic::database.open().

Referenced by setup_job().

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(), join(), ObjexxFCL.len(), DRRAFTER_util.make_tag_with_dashes(), basic::database.open(), parse_fasta(), parse_secstruct(), DRRAFTER_util.parse_tag(), DRRAFTER_util.pdbslice(), print(), range, set(), str, and write_flags_file().

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

action

DRRAFTER.action

args

DRRAFTER.args = parser.parse_args()

default

DRRAFTER.default

False

DRRAFTER.False

float

DRRAFTER.float

help

DRRAFTER.help

int

DRRAFTER.int

nargs

DRRAFTER.nargs

parser

DRRAFTER.parser = argparse.ArgumentParser( description="DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta" )

protein_one_letter

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']

str

DRRAFTER.str

Referenced by get_coord_csts(), and setup_job().

type

DRRAFTER.type