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