setup_for_complex_scoring_general Namespace Reference

Functions
def	main ()
def	get_mut_string (seq)
	Some helper functions #######. More...
def	check_nostruct_matches (sequence)
def	list_NC_BPs (bps, seq)
def	list_mutated_BPs (bps, seq)
def	list_NC_BPs_noGU (bps, seq)
def	find_offset (ss)
def	find_pairs (secstruct)
def	get_ss (seq)

Variables
string	wt_ss = '(((((.((....)))))))'
string	wt_seq = 'acaugaggaucacccaugu'
	parser = argparse.ArgumentParser(description="Set up ddg calculations for list of RNP mutants")
	action
	default
	False
	help
	dest
	rebuild_surrounding
	type
	str
	int
	args = parser.parse_args()

Function Documentation

check_nostruct_matches()

def setup_for_complex_scoring_general.check_nostruct_matches

(

sequence

)

find_offset()

def setup_for_complex_scoring_general.find_offset

(

ss

)

References ObjexxFCL.len(), and range.

find_pairs()

def setup_for_complex_scoring_general.find_pairs

(

secstruct

)

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

Referenced by main().

get_mut_string()

def setup_for_complex_scoring_general.get_mut_string

(

seq

)

Some helper functions #######.

References ObjexxFCL.len(), range, and str.

Referenced by main().

get_ss()

def setup_for_complex_scoring_general.get_ss

(

seq

)

References basic::database.open().

Referenced by main().

list_mutated_BPs()

def setup_for_complex_scoring_general.list_mutated_BPs	(		bps,
			seq
	)

References ObjexxFCL.len(), and range.

Referenced by main().

list_NC_BPs()

def setup_for_complex_scoring_general.list_NC_BPs	(		bps,
			seq
	)

References ObjexxFCL.len(), and range.

Referenced by main().

list_NC_BPs_noGU()

def setup_for_complex_scoring_general.list_NC_BPs_noGU	(		bps,
			seq
	)

References ObjexxFCL.len(), and range.

Referenced by main().

main()

def setup_for_complex_scoring_general.main

(

)

References utility::options::OptionKeys::options.exit, find_pairs(), run_backbone.float, get_mut_string(), get_ss(), int, join(), ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, list_mutated_BPs(), list_NC_BPs(), list_NC_BPs_noGU(), test_terpenes.lower, basic::database.open(), print(), range, binder.replace(), str, and test.T040_Types.values.

Variable Documentation

action

setup_for_complex_scoring_general.action

args

setup_for_complex_scoring_general.args = parser.parse_args()

default

setup_for_complex_scoring_general.default

dest

setup_for_complex_scoring_general.dest

False

setup_for_complex_scoring_general.False

help

setup_for_complex_scoring_general.help

int

setup_for_complex_scoring_general.int

Referenced by main().

parser

setup_for_complex_scoring_general.parser = argparse.ArgumentParser(description="Set up ddg calculations for list of RNP mutants")

rebuild_surrounding

setup_for_complex_scoring_general.rebuild_surrounding

str

setup_for_complex_scoring_general.str

Referenced by get_mut_string(), and main().

type

setup_for_complex_scoring_general.type

wt_seq

string setup_for_complex_scoring_general.wt_seq = 'acaugaggaucacccaugu'

wt_ss

string setup_for_complex_scoring_general.wt_ss = '(((((.((....)))))))'