Rosetta 3.3
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src Namespace Reference

Namespaces

namespace  protocols

Classes

class  PyJobDistributor
class  PySocketClient
class  PyMOL_Mover
class  PyMOL_Observer

Functions

def add_extend
def new_vector1_init
def replace_init
def Vector1
def generate_nonstandard_residue_set
def standard_task_factory
def standard_packer_task
def add_extra_options
def generate_resfile_from_pose
 TOOLBOX these methods are useful in PyRosetta and intended to demonstrate proper syntax for various common activities for those interested, Rosetta hag a Surface Area calculator and a Radius of Gyration calculator, they are EnergyMethods sa and rg respectively, create an empty ScoreFunction and use ScoreFunction.set_weight to use these calculations other common geometry calculators are CA_rmsd and all_atom_rmsd.
def generate_resfile_from_pdb
def mutate_residue
def cleanATOM
def cleanCRYS
def pose_from_sequence
def load_from_rcsb
def pose_from_rcsb
def get_secstruct
def get_hbonds
def init
def version

Variables

tuple PlatformBits = platform.architecture()
dictionary X11Colors

Function Documentation

def src::add_extend (   vectype)
def src::add_extra_options ( )
def src::cleanATOM (   pdb_file,
  edit = -4 
)
Writes a PDB file from  <pdb_file> with all lines not beginning with
ATOM removed tp  <pdb_file>.clean.pdb
note: the second argument, <edit>, if for PDB files not ending in .pdb

example:
    cleanATOM('1YY9.pdb')
See also:
    Pose
    Pose.dump_pdb
    pose_from_pdb
    pose_from_rcsb
    cleanCRYS
def src::cleanCRYS (   pdb_file,
  olig = 2 
)
Writes a PDB file for a monomer of  <pdb_file>  if it is a  <olig>-mer
to  <pdb_file>.mono
note: this is a simple sequence comparison

example:
    cleanCRYS('1YY8.pdb',2)
See also:
    Pose
    Pose.dump_pdb
    pose_from_pdb
    pose_from_rcsb
    cleanATOM
def src::generate_nonstandard_residue_set (   params_list)
def src::generate_resfile_from_pdb (   pdbfilename,
  resfilename,
  input_sc = True 
)
Writes a resfile for PDB file  <pdbfilename>  named  <resfilename> ,
optionally allowing input side chains to be used in packing

example:
    generate_resfile_from_pdb('1YY8.pdb','1YY8.resfile')
See also:
    Pose
    PackRotamersMover
    TaskFactory
def src::generate_resfile_from_pose (   pose,
  resfilename,
  input_sc = True 
)

TOOLBOX these methods are useful in PyRosetta and intended to demonstrate proper syntax for various common activities for those interested, Rosetta hag a Surface Area calculator and a Radius of Gyration calculator, they are EnergyMethods sa and rg respectively, create an empty ScoreFunction and use ScoreFunction.set_weight to use these calculations other common geometry calculators are CA_rmsd and all_atom_rmsd.

Writes a resfile for  <pose>  named  <resfilename> , optionally allowing
input side chains to be used in packing

example:
    generate_resfile_from_pose(pose,'1YY8.resfile')
See also:
    Pose
    PackRotamersMover
    TaskFactory
def src::get_hbonds (   pose)
Returns a HBondSet of the hydrogen bonding in  <pose>
note: more info in rosetta.core.scoring.hbonds

example:
    hbset=get_hbonds(pose)
    hbset.hbond(1).acc_res()
See also:
    Pose
    Energies
    HBondSet
    ScoreFunction
    create_score_function
def src::get_secstruct (   pose,
  space = 8,
  page = 80 
)
Predicts the secondary structure of  <pose> , loading this data into
the pose's secstruct information and printing the prediction to screen

example:
    get_secstruct(pose)
See also:
    Pose
    Pose.secstruct
    Pose.sequence
    pose_from_pdb
    pose_from_sequence
    pose_from_rcsb
def src::init (   args)
def src::load_from_rcsb (   pdb_code)
Writes PDB data for RCSB data for  <pdb_code>  into the file  <pdb_code>.pdb

example:
    load_from_rcsb('1YY8')
See also:
    Pose
    pose_from_pdb
    pose_from_rcsb
    pose_from_sequence
    cleanATOM
    cleanCRYS
def src::mutate_residue (   pose,
  resid,
  new_res 
)
Replaces the residue at  <resid>  in  <pose>  with  <new_res>
note: <new_res>  is the single letter name for the desired ResidueType

example:
    mutate_residue(pose,30,A)
See also:
    Pose
    PackRotamersMover
def src::new_vector1_init (   self,
  arg1 = None,
  arg2 = False 
)
def src::pose_from_rcsb (   pdb_code,
  ATOM = True,
  CRYS = True 
)
Returns a pose for RCSB PDB  <pdb_code> , also writes this data to
<pdb_code>.pdb, optionally calls cleanATOM and cleanCYRS

example:
    pose=pose_from_rcsb('1YY8')
See also:
    Pose
    pose_from_pdb
    pose_from_sequence
    load_from_rcsb
    cleanATOM
    cleanCRYS
def src::pose_from_sequence (   seq,
  res_type = 'fa_standard' 
)
Returns a pose generated from amino acid single letters in  <seq>  using
the  <res_type>  ResidueType

example:
    pose=pose_from_sequence('THANKSEVAN')
See also:
    Pose
    make_pose_from_sequence
    pose_from_pdb
    pose_from_rcsb
def src::replace_init (   cls,
  init 
)
def src::standard_packer_task (   pose)
def src::standard_task_factory ( )
def src::Vector1 (   l)
Create Vector1 object deducing type from the given list
def src::version ( )

Variable Documentation

tuple src::PlatformBits = platform.architecture()
dictionary src::X11Colors
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