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pyrosetta.io Namespace Reference

Namespaces

 silent_file_map
 

Functions

def pose_from_pdb
 
def pose_from_sequence
 
def poses_from_files
 
def poses_from_sequences
 
def poses_from_silent
 
def poses_to_silent
 

Function Documentation

def pyrosetta.io.pose_from_pdb (   filename)
def pyrosetta.io.pose_from_sequence (   seq,
  res_type = "fa_standard",
  auto_termini = True 
)
Returns a Pose object generated from a single-letter sequence of amino acid
residues in <seq> using the <res_type> ResidueType and creates N- and C-
termini if <auto_termini> is set to True.

Unlike make_pose_from_sequence(), this method generates a default PDBInfo
and sets all torsion angles to 180 degrees.

Example:
    pose = pose_from_sequence("THANKSEVAN")
See also:
    Pose
    make_pose_from_sequence()
    pose_from_file()
    pose_from_rcsb()

References name, and basic::options::OptionKeys::relax::range.range.

Referenced by pyrosetta.io.poses_from_sequences(), and pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent().

def pyrosetta.io.poses_from_files (   objs,
  args,
  kwargs 
)
Returns an iterator object which is composed of Pose objects from input files.

Example:
import glob
poses = pyrosetta.io.poses_from_files(glob.glob("path/to/pdbs/*.pdb"))

References pyrosetta.distributed.io.pose_from_file.

Referenced by apps::public1::scenarios::chemically_conjugated_docking.add_extra_bodies(), and MPDomainAssembly.apply().

def pyrosetta.io.poses_from_sequences (   objs,
  args,
  kwargs 
)
Returns an iterator object which is composed of Pose objects with input sequences.

Example:
poses = pyrosetta.io.poses_from_sequences(["TEST", "TESTING [ATP]", "ACDEFGHIKLMNPQRSTVWY"])

References pyrosetta.io.pose_from_sequence().

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPoseIO.test_pose_io().

def pyrosetta.io.poses_from_silent (   silent_filename)
Returns an Iterator object which is composed of Pose objects from a silent file.

@atom-moyer

References name.

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent().

def pyrosetta.io.poses_to_silent (   poses,
  output_filename 
)
Takes a Pose or list of poses and outputs them as a binary silent file.
This method requires a Pose object.
If you are using a PackedPose, use pyrosetta.distributed.io.to_silent()

Inputs:
poses: Pose or list of poses. This function automatically detects which one.
output_filename: The desired name of the output silent file.

Example:
poses_to_silent(poses, "mydesigns.silent")

The decoy name written to your silent file is take from pose.pdb_info().name()
To set a different decoy name, change it in your pose before calling this function.
Example:
pose.pdb_info().name("my_tag.pdb")

@srgerb

References name, and basic::options::OptionKeys::ddg.output_silent.

Referenced by pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent(), and pyrosetta.distributed.io.to_silent().