demo.D090_Ala_scan Namespace Reference

Functions
def	scanning
	Methods. More...
def	interface_ddG
def	mutate_residue
def	calc_binding_energy
def	scanning_analysis

Variables
tuple	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
string	default = '../test/data/test_dock.pdb'
string	help = 'the PDB file containing the protein to refine'
	pdb_filename = options.pdb_filename
	partners = options.partners
	mutant_aa = options.mutant_aa
tuple	interface_cutoff = float(options.interface_cutoff)
tuple	output = bool(options.output)
tuple	trials = int(options.trials)
	trial_output = options.trial_output

Function Documentation

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

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

Referenced by demo.D090_Ala_scan.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(), name, basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, and basic::options::OptionKeys::DisulfideInsertion.scorefxn.

Referenced by demo.D090_Ala_scan.scanning().

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 basic::options::OptionKeys::packing.prevent_repacking, basic::options::OptionKeys::relax::range.range, and pyrosetta.standard_packer_task().

Referenced by demo.D090_Ala_scan.interface_ddG().

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(), fmt.join(), basic::options::OptionKeys::in::file.list, name, basic::database.open(), pyrosetta.distributed.io.pose_from_file, fmt.print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, demo.D090_Ala_scan.scanning_analysis(), basic::options::OptionKeys::DisulfideInsertion.scorefxn, and pyrosetta.Vector1().

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(), ObjexxFCL.len(), basic::database.open(), basic::options::OptionKeys::relax::range.range, binder.split(), and sum().

Referenced by demo.D090_Ala_scan.scanning().

Variable Documentation

string demo.D090_Ala_scan.default = '../test/data/test_dock.pdb'

string demo.D090_Ala_scan.help = 'the PDB file containing the protein to refine'

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

Referenced by add_rosetta_options_11(), add_rosetta_options_4(), and AnchorFinderMover.apply().

demo.D090_Ala_scan.mutant_aa = options.mutant_aa

Referenced by main().

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

tuple demo.D090_Ala_scan.parser = optparse.OptionParser()

INTERPRETING RESULTS.

Interaction Energy vs. Binding Energy COMMANDLINE COMPATIBILITY

demo.D090_Ala_scan.partners = options.partners

demo.D090_Ala_scan.pdb_filename = options.pdb_filename

demo.D090_Ala_scan.trial_output = options.trial_output

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