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demo.D050_Packer_task Namespace Reference

Functions

def packer_task
 
def generate_resfile_from_pose
 PERIPHERAL METHODS. More...
 
def generate_resfile_from_pdb
 

Variables

tuple parser = optparse.OptionParser()
 INTERPRETING RESULTS. More...
 
string default = '../test/data/test_in.pdb'
 
string help = 'the PDB file containing the loop to remodel'
 
 pdb_filename = options.pdb_filename
 
tuple pose = Pose()
 
tuple PDB_out = bool(options.PDB_out)
 

Function Documentation

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.

Referenced by demo.D050_Packer_task.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 basic::options::OptionKeys::run.chain, demo.D050_Packer_task.generate_resfile_from_pdb(), basic::database.open(), and ObjexxFCL.rjust().

Referenced by demo.D050_Packer_task.generate_resfile_from_pdb(), and demo.D050_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(), name, fmt.print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, basic::options::OptionKeys::DisulfideInsertion.scorefxn, and pyrosetta.standard_packer_task().

Referenced by main().

Variable Documentation

string demo.D050_Packer_task.default = '../test/data/test_in.pdb'
string demo.D050_Packer_task.help = 'the PDB file containing the loop to remodel'
tuple demo.D050_Packer_task.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

demo.D050_Packer_task.pdb_filename = options.pdb_filename
tuple demo.D050_Packer_task.PDB_out = bool(options.PDB_out)
tuple demo.D050_Packer_task.pose = Pose()