demo.D050_Packer_task Namespace Reference

Functions
def	packer_task (pose, PDB_out=False)
def	generate_resfile_from_pose (pose, resfilename, pack=True, design=False, input_sc=True, freeze=[], specific={})
	PERIPHERAL METHODS. More...
def	generate_resfile_from_pdb (pdbfilename, resfilename, pack=True, design=False, input_sc=True, freeze=[], specific={})

Variables
	extra_options
	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
	dest
	default
	help
	options
	args
	pdb_filename = options.pdb_filename
	pose = Pose()
	PDB_out = bool(options.PDB_out)

Function Documentation

generate_resfile_from_pdb()

def demo.D050_Packer_task.generate_resfile_from_pdb	(		pdbfilename,
			resfilename,
			pack = True,
			design = False,
			input_sc = True,
			freeze = [],
			specific = {}
	)

  Writes a resfile for the PDB file <pdbfilename>  named  <resfilename>
     <pack> = True allows packing by default
     <design> = True allows design using all amino acids by default
     <input_sc> = True allows usage of the original side chain conformation
     <freeze> is an optional list of (pose) residue numbers to exclude
          (preserve the side chain conformations of these residues)
     <specific> is an optional dictionary with (pose) residue numbers as keys
          and resfile keywords as corresponding values
          (for setting individual residue options, it may be easier to add
          these numbers to freeze and edit the resfile manually)

  example:
      generate_resfile_from_pdb('1YY8.pdb','1YY8.resfile')
  See also:
      generate_resfile_from_pose
      Pose
      PackRotamersMover
      TaskFactory

References demo.D050_Packer_task.generate_resfile_from_pose(), and pyrosetta.distributed.io.pose_from_file().

generate_resfile_from_pose()

def demo.D050_Packer_task.generate_resfile_from_pose	(		pose,
			resfilename,
			pack = True,
			design = False,
			input_sc = True,
			freeze = [],
			specific = {}
	)

PERIPHERAL METHODS.

Writes a resfile for  <pose>  named  <resfilename>
   <pack> = True allows packing by default
   <design> = True allows design using all amino acids by default
   <input_sc> = True allows usage of the original side chain conformation
   <freeze> is an optional list of (pose) residue numbers to exclude
        (preserve the side chain conformations of these residues)
   <specific> is an optional dictionary with (pose) residue numbers as keys
        and resfile keywords as corresponding values
        (for setting individual residue options, it may be easier to add
        these numbers to freeze and edit the resfile manually)

example:
    generate_resfile_from_pose(pose,'1YY8.resfile')
See also:
    Pose
    PackRotamersMover
    TaskFactory

References predPRE.chain, basic::database.open(), ObjexxFCL.rjust(), and str().

Referenced by demo.D050_Packer_task.generate_resfile_from_pdb(), and demo.D050_Packer_task.packer_task().

packer_task()

def demo.D050_Packer_task.packer_task	(		pose,
			PDB_out = False
	)

Demonstrates the syntax necessary for basic usage of the PackerTask object
    performs demonstrative sidechain packing and selected design
    using  <pose>  and writes structures to PDB files if  <PDB_out>
    is True

References demo.D050_Packer_task.generate_resfile_from_pose(), pyrosetta.distributed.io.get_fa_scorefxn(), print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, range, oop_conformations.scorefxn, and pyrosetta.standard_packer_task().

Referenced by ElecDensMinPackMinMover.apply(), HotspotPlacementMover.apply(), byres_analysis(), protocols::jd2::RECONMPIJobDistributor.design_this_nodes_pose(), do_rtmin(), main(), RotamerAnalysis(), rottrial_residue(), rottrialmin_residue(), scmove_residue(), and single_res_task().

Variable Documentation

args

demo.D050_Packer_task.args

default

demo.D050_Packer_task.default

dest

demo.D050_Packer_task.dest

extra_options

demo.D050_Packer_task.extra_options

help

demo.D050_Packer_task.help

options

demo.D050_Packer_task.options

parser

demo.D050_Packer_task.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

pdb_filename

demo.D050_Packer_task.pdb_filename = options.pdb_filename

PDB_out

demo.D050_Packer_task.PDB_out = bool(options.PDB_out)

pose

demo.D050_Packer_task.pose = Pose()