pyrosetta.io Namespace Reference

Namespaces
	silent_file_map

Functions
def	pose_from_pdb (filename)
def	pose_from_sequence (seq, res_type="fa_standard", auto_termini=True)
def	poses_from_files (objs, *args, **kwargs)
def	poses_from_sequences (objs, *args, **kwargs)
def	poses_from_silent (silent_filename)
def	poses_to_silent (poses, output_filename)

Function Documentation

pose_from_pdb()

def pyrosetta.io.pose_from_pdb

(

filename

)

References pyrosetta.distributed.io.pose_from_file.

Referenced by graphics_main(), HemeReplace.HemeReplace(), main(), sequence_tolerance_mf_main(), and test_protein_rna().

pose_from_sequence()

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 range.

Referenced by pyrosetta.io.poses_from_sequences(), pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent.test_poses_to_silent(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTest.test_smoke(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti.test_smoke_multi(), and pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti.test_smoke_multi_from_instance().

poses_from_files()

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(), InterfaceStrandFinderMover.apply(), MPDomainAssembly.apply(), doit(), and main().

poses_from_sequences()

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().

poses_from_silent()

def pyrosetta.io.poses_from_silent

(

silent_filename

)

Returns an Iterator object which is composed of Pose objects from a silent file.

@atom-moyer

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

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 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().