demo.D090_Ala_scan Namespace Reference

Functions
def	scanning (pdb_filename, partners, mutant_aa='A', interface_cutoff=8.0, output=False, trials=1, trial_output='')
	Methods. More...
def	interface_ddG (pose, mutant_position, mutant_aa, movable_jumps, scorefxn='', cutoff=8.0, out_filename='')
def	mutate_residue (pose, mutant_position, mutant_aa, pack_radius=0.0, pack_scorefxn='')
def	calc_binding_energy (pose, scorefxn, center, cutoff=8.0)
def	scanning_analysis (trial_output)

Variables
	extra_options
	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
	dest
	default
	help
	options
	args
	pdb_filename = options.pdb_filename
	partners = options.partners
	mutant_aa = options.mutant_aa
	interface_cutoff = float(options.interface_cutoff)
	output = bool(options.output)
	trials = int(options.trials)
	trial_output = options.trial_output

Function Documentation

calc_binding_energy()

def demo.D090_Ala_scan.calc_binding_energy	(		pose,
			scorefxn,
			center,
			cutoff = 8.0
	)

References ObjexxFCL.len(), natoms(), range, oop_conformations.scorefxn, pyrosetta.standard_task_factory(), and basic::options::OptionKeys::in::file.xyz.

Referenced by demo.D090_Ala_scan.interface_ddG().

interface_ddG()

def demo.D090_Ala_scan.interface_ddG	(		pose,
			mutant_position,
			mutant_aa,
			movable_jumps,
			scorefxn = '',
			cutoff = 8.0,
			out_filename = ''
	)

References demo.D090_Ala_scan.calc_binding_energy(), demo.D090_Ala_scan.mutate_residue(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, oop_conformations.scorefxn, and str().

Referenced by demo.D090_Ala_scan.scanning().

mutate_residue()

def demo.D090_Ala_scan.mutate_residue	(		pose,
			mutant_position,
			mutant_aa,
			pack_radius = 0.0,
			pack_scorefxn = ''
	)

Replaces the residue at  <mutant_position>  in  <pose>  with  <mutant_aa>
    and repack any residues within  <pack_radius>  Angstroms of the mutating
    residue's center (nbr_atom) using  <pack_scorefxn>
note: <mutant_aa>  is the single letter name for the desired ResidueType

example:
    mutate_residue(pose, 30, A)
See also:
    Pose
    PackRotamersMover
    MutateResidue
    pose_from_sequence

References enumerate_junctions.int, basic::options::OptionKeys::packing.prevent_repacking, range, and pyrosetta.standard_packer_task().

Referenced by demo.D090_Ala_scan.interface_ddG().

scanning()

def demo.D090_Ala_scan.scanning	(		pdb_filename,
			partners,
			mutant_aa = 'A',
			interface_cutoff = 8.0,
			output = False,
			trials = 1,
			trial_output = ''
	)

Methods.

Performs "scanning" at an interface within  <pdb_filename>  between
    <partners>  by mutating relevant residues to  <mutant_aa>  and repacking
    residues within  <pack_radius>  Angstroms, further repacking all
    residues within  <interface_cutoff>  of the interface residue, scoring
    the complex and subtracting the score of a pose with the partners
    separated by 500 Angstroms.
    <trials>  scans are performed (to average results) with summaries written
    to  <trial_output>_(trial#).txt.
    Structures are exported to a PyMOL instance.

References demo.D090_Ala_scan.interface_ddG(), join(), basic::options::OptionKeys::in::file.list, basic::database.open(), pyrosetta.distributed.io.pose_from_file, print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, range, demo.D090_Ala_scan.scanning_analysis(), oop_conformations.scorefxn, str(), and pyrosetta.Vector1().

scanning_analysis()

def demo.D090_Ala_scan.scanning_analysis

(

trial_output

)

Average the values of all files in this directory with  <trial_output>  in
    their title and return the mutations (rows) that are 1 or more standard
    deviations from the mean score change

References ObjexxFCL.abs(), run_backbone.float, ObjexxFCL.len(), basic::database.open(), range, binder.split(), and sum().

Referenced by demo.D090_Ala_scan.scanning().

Variable Documentation

args

demo.D090_Ala_scan.args

default

demo.D090_Ala_scan.default

dest

demo.D090_Ala_scan.dest

extra_options

demo.D090_Ala_scan.extra_options

help

demo.D090_Ala_scan.help

interface_cutoff

demo.D090_Ala_scan.interface_cutoff = float(options.interface_cutoff)

mutant_aa

demo.D090_Ala_scan.mutant_aa = options.mutant_aa

Referenced by main().

options

demo.D090_Ala_scan.options

output

demo.D090_Ala_scan.output = bool(options.output)

parser

demo.D090_Ala_scan.parser = optparse.OptionParser()

INTERPRETING RESULTS.

Interaction Energy vs. Binding Energy

COMMANDLINE COMPATIBILITY

partners

demo.D090_Ala_scan.partners = options.partners

pdb_filename

demo.D090_Ala_scan.pdb_filename = options.pdb_filename

trial_output

demo.D090_Ala_scan.trial_output = options.trial_output

trials

demo.D090_Ala_scan.trials = int(options.trials)