surface_docking.py File Reference

Namespaces
	app.surface_docking.surface_docking

Functions
def	app.surface_docking.surface_docking.input_checker
def	app.surface_docking.surface_docking.run
def	app.surface_docking.surface_docking.append_data

Variables
tuple	app.surface_docking.surface_docking.parser = argparse.ArgumentParser(description='Surface Docking Script',fromfile_prefix_chars='@')
tuple	app.surface_docking.surface_docking.args = parser.parse_args(['@flags'])
	app.surface_docking.surface_docking.input = args.s
	app.surface_docking.surface_docking.path = args.database
	app.surface_docking.surface_docking.constraints = args.constraints
tuple	app.surface_docking.surface_docking.decoy_num = int(args.n)
	app.surface_docking.surface_docking.frag3 = args.f3
	app.surface_docking.surface_docking.frag9 = args.f9
	app.surface_docking.surface_docking.disulf_file = args.d
	app.surface_docking.surface_docking.nosmallshear_ref = args.nosmallshear
tuple	app.surface_docking.surface_docking.newpath = os.path.expandvars(path)
list	app.surface_docking.surface_docking.opts
tuple	app.surface_docking.surface_docking.Rargs = rosetta.utility.vector1_string()
tuple	app.surface_docking.surface_docking.sol_cycles = randint(1,5)
int	app.surface_docking.surface_docking.sol_outer_cycles = 5
int	app.surface_docking.surface_docking.sol_inner_cycles = 5
int	app.surface_docking.surface_docking.ads_cycles = 5
int	app.surface_docking.surface_docking.ads_outer_cycles = 5
int	app.surface_docking.surface_docking.ads_inner_cycles = 5
tuple	app.surface_docking.surface_docking.start_pose = Pose()
list	app.surface_docking.surface_docking.PDB = input[:-4]
float	app.surface_docking.surface_docking.elec = 1.0
tuple	app.surface_docking.surface_docking.score_high = create_score_function("score12")
tuple	app.surface_docking.surface_docking.score_pack = create_score_function("score12")
tuple	app.surface_docking.surface_docking.std_scorefxn = create_score_function("score12")
tuple	app.surface_docking.surface_docking.switch_low = SwitchResidueTypeSetMover('centroid')
tuple	app.surface_docking.surface_docking.switch_high = SwitchResidueTypeSetMover('fa_standard')
tuple	app.surface_docking.surface_docking.cwd1 = os.getcwd()
tuple	app.surface_docking.surface_docking.cwd2 = cwd1.split('/')
tuple	app.surface_docking.surface_docking.cwdn = len(cwd2)
list	app.surface_docking.surface_docking.dir = cwd2[cwdn - 1]
tuple	app.surface_docking.surface_docking.jd = PyJobDistributor("AdsState_" + PDB + "_" + dir, decoy_num, score_high)
tuple	app.surface_docking.surface_docking.jd1 = PyJobDistributor("SolState_" + PDB + "_" + dir, decoy_num, score_high)
	app.surface_docking.surface_docking.x = jd1.current_name
	app.surface_docking.surface_docking.y = jd.current_name
tuple	app.surface_docking.surface_docking.time_start = datetime.datetime.now()
tuple	app.surface_docking.surface_docking.pose = Pose()
tuple	app.surface_docking.surface_docking.combined_pose = Pose()
tuple	app.surface_docking.surface_docking.abinitio = Abinitio(PDB, frag3, frag9)
tuple	app.surface_docking.surface_docking.cen_relax = CentroidRelax()
tuple	app.surface_docking.surface_docking.fa_relax = FullAtomRelax(score_high, score_pack, std_scorefxn, nosmallshear_ref)
tuple	app.surface_docking.surface_docking.sol_pose = Pose()
tuple	app.surface_docking.surface_docking.curr_sol = str(x)
tuple	app.surface_docking.surface_docking.curr_ads = str(y)
string	app.surface_docking.surface_docking.append_surf_sol = "grep SURFA "
string	app.surface_docking.surface_docking.append_surf_ads = "grep SURFA "
tuple	app.surface_docking.surface_docking.time_end = datetime.datetime.now()
	app.surface_docking.surface_docking.time_diff = time_end-time_start