predict_ddG Namespace Reference

Functions
def	main
	Main - Add Membrane to Pose, Compute ddG. More...
def	compute_ddG
	Compute ddG of mutation in a protein at specified residue and AA position. More...
def	mutate_residue
def	print_ddG_breakdown
	Print ddG breakdown from the pose Extract weighted energies from the native and mutated pose. More...
def	print_score_labels_to_file
	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
	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
tuple	_script_path_ = os.path.dirname( os.path.realpath(__file__) )

Function Documentation

def predict_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.T220_AtomAtomPairEnergies.sfxn.

Referenced by main().

def predict_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().

Referenced by print_ddG_breakdown(), and print_score_labels_to_file().

def predict_ddG.main

(

args

)

Main - Add Membrane to Pose, Compute ddG.

References compute_ddG(), pyrosetta.create_score_function, basic::options::OptionKeys::in::file.file, mutate_residue(), and print_score_labels_to_file().

Referenced by convert_array_to_str().

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

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

Referenced by compute_ddG(), and main().

def predict_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(), basic::options::OptionKeys::in::file.file, basic::options::OptionKeys::mh::filter.filter, ObjexxFCL.len(), basic::options::OptionKeys::relax::range.range, and round().

Referenced by compute_ddG().

def predict_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(), basic::options::OptionKeys::in::file.file, basic::options::OptionKeys::mh::filter.filter, ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.

Referenced by main().

Variable Documentation

tuple predict_ddG._script_path_ = os.path.dirname( os.path.realpath(__file__) )