mp_ddG Namespace Reference

Functions
def	main (args)
	Main - Add Membrane to Pose, Compute ddG. More...
def	compute_ddG (pose, sfxn, resnum, aa, repack_radius, sc_file)
	Compute ddG of mutation in a protein at specified residue and AA position. More...
def	mutate_residue (pose, mutant_position, mutant_aa, pack_radius, pack_scorefxn)
def	print_ddG_breakdown (native_pose, mutated_pose, sfxn, resnum, aa, fn)
	Print ddG breakdown from the pose Extract weighted energies from the native and mutated pose. More...
def	print_score_labels_to_file (native_pose, sfxn, fn)
	Get header for ddG breakdown output Save the score labels, to be printed at the top of the output breakdown file. More...
def	convert_array_to_str (array)
	Convert an array to a space deliminted string Save the score labels, to be printed at the top of the output breakdown file. More...

Variables
	_script_path_ = os.path.dirname( os.path.realpath(__file__) )

Function Documentation

compute_ddG()

def mp_ddG.compute_ddG	(		pose,
			sfxn,
			resnum,
			aa,
			repack_radius,
			sc_file
	)

Compute ddG of mutation in a protein at specified residue and AA position.

References mutate_residue(), print_ddG_breakdown(), round(), and test.T120_core.sfxn.

Referenced by main().

convert_array_to_str()

def mp_ddG.convert_array_to_str

(

array

)

Convert an array to a space deliminted string Save the score labels, to be printed at the top of the output breakdown file.

References main(), and str().

Referenced by print_ddG_breakdown(), and print_score_labels_to_file().

main()

def mp_ddG.main

(

args

)

Main - Add Membrane to Pose, Compute ddG.

References compute_ddG(), pyrosetta.create_score_function, evaluate_beta_mutants.file, run_backbone.float, enumerate_junctions.int, mutate_residue(), pyrosetta.distributed.io.pose_from_file, print_score_labels_to_file(), and str().

Referenced by convert_array_to_str().

mutate_residue()

def mp_ddG.mutate_residue	(		pose,
			mutant_position,
			mutant_aa,
			pack_radius,
			pack_scorefxn
	)

References run_backbone.float, ObjexxFCL.pow(), basic::options::OptionKeys::packing.prevent_repacking, and range.

Referenced by compute_ddG(), and main().

print_ddG_breakdown()

def mp_ddG.print_ddG_breakdown	(		native_pose,
			mutated_pose,
			sfxn,
			resnum,
			aa,
			fn
	)

Print ddG breakdown from the pose Extract weighted energies from the native and mutated pose.

Calculate the ddG of each and print the component-wise ddG vlaues

References convert_array_to_str(), evaluate_beta_mutants.file, filter, run_backbone.float, enumerate_junctions.int, ObjexxFCL.len(), range, round(), and str().

Referenced by compute_ddG().

print_score_labels_to_file()

def mp_ddG.print_score_labels_to_file	(		native_pose,
			sfxn,
			fn
	)

Get header for ddG breakdown output Save the score labels, to be printed at the top of the output breakdown file.

References convert_array_to_str(), evaluate_beta_mutants.file, filter, ObjexxFCL.len(), range, and beta_nonlocal.translate.

Referenced by main().

Variable Documentation

_script_path_

mp_ddG._script_path_ = os.path.dirname( os.path.realpath(__file__) )

private