pyrosetta_help.threading package

Module contents

pyrosetta_help.threading.get_alignment(target: str, template: str) → Dict[str, str]

Returns alignments using PairwiseAligner, formerly was using pairwise2.align.globalxs

pyrosetta_help.threading.get_nonprotein_pose(pose)

pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover requires some weird things. This does the same, makes a ligand only pose.

Parameters:

pose –

Returns:

pyrosetta_help.threading.make_fragment_sets(*poses: Iterable[Pose], lengths: Iterable[int] = (3,)) → vector1_std_shared_ptr_core_fragment_FragSet_t

pyrosetta_help.threading.oligomer_thread(pose, sequence)

pyrosetta_help.threading.rangify(values)

Given a list of integers, returns a list of tuples of ranges (interger pairs).

Parameters:

values –

Returns:

pyrosetta_help.threading.steal_ligands(donor_pose, acceptor_pose) → None

Steals non-Protein residues from donor_pose and adds them to acceptor_pose

Do not use with nucleic acid polymers.

Parameters:

• donor_pose –

• acceptor_pose –

Returns:

pyrosetta_help.threading.thread(target_sequence: str, template_pose: Pose, target_pose: Pose | None = None, target_name: str = 'target', template_name: str = 'template', fragment_sets: vector1_std_shared_ptr_core_fragment_FragSet_t | None = None, align: SequenceAlignment | None = None) → Tuple[Pose, ThreadingMover, vector1_bool]

Given the target sequence and the optional blank target pose (in case there’s some reason for it), thread the sequence against the template pose — which is assumed to be a single chain. Optionally using fragments from fragment_sets. The three outputs are the target_pose, the threader instance and a vector of the residues threaded.

>>> print(threader.frag_libs()[1].nr_frames())

>>> qt = threader.get_qt_mapping(threaded)
>>> print(f'Template residue {21} is residue {q[21]} in target')

Parameters:

• target_sequence –

• template_pose –

• target_pose –

• target_name –

• template_name –

• fragment_sets –

• align –

Returns:

pyrosetta_help.threading.write_grishin(target_name, target_sequence, template_name, template_sequence, outfile)