fusion

Auxiliary functions for combining PDB structures with disordered tails/linkers.

Functions

apply_basic_idealize(pose, start_res, end_res, sfxn[, ...])	Idealize bond geometry of a range of residues in a Pose object.
pack_sidechains(score_function, pose)	Add side-chains to a Pose using a PackRotamersMover with the given score function.
create_fusion_pose(sequences, pdb_structures, output_name)	Create a full-length fused Pose object from provided sequences and PDB structures.
check_is_pdb(input_pdbs)	Check provided filepaths: if they are not PDB files and are instead mmCIF, convert to PDB.
fuse_structures(input_fastas, input_pdbs, output_name)	Fuse sequences and PDB structures into a full-length PDB structure.

Module Contents

ensemblify.modelling.fusion.apply_basic_idealize(pose, start_res, end_res, sfxn, fast=False)

Idealize bond geometry of a range of residues in a Pose object.

Uses the basic_idealize protocol from PyRosetta. The provided Pose object is modified in place. In short, the Mover stochastically picks a move-able position (between the provived start and end points), forces that position into ideal bond geometry, and tries to use minimization to bring the coordinates back to very near their starting points.

Parameters:

• pose (pyrosetta.rosetta.core.pose.Pose) – The Pose object to be idealized.

• start_res (int) – The starting residue index (1-indexed) for the idealization range.

• end_res (int) – The ending residue index (1-indexed) for the idealization range.

• sfxn (pyrosetta.rosetta.scoring.ScoreFunction) – The ScoreFunction to be used for the idealization.

• fast (bool) – If True, uses a faster version of the idealization protocol. Defaults to False, which uses the standard idealization protocol.

ensemblify.modelling.fusion.pack_sidechains(score_function, pose)

Add side-chains to a Pose using a PackRotamersMover with the given score function.

Changes provided Pose object in place.

Parameters:

• score_function (pyrosetta.rosetta.core.scoring.ScoreFunction) – The score function to use for packing.

• pose (pyrosetta.rosetta.core.pose.Pose) – The Pose object to pack side-chains into.

ensemblify.modelling.fusion.create_fusion_pose(sequences, pdb_structures, output_name, output_dir=None, fusion_verbose=True, pyrosetta_verbose=False)

Create a full-length fused Pose object from provided sequences and PDB structures.

Parameters:

• sequences (list[str]) – List of sequences to be fused, where each sequence corresponds to a segment of the full-length structure.

• pdb_structures (list[str]) – List of .pdb file paths corresponding to the folded domains in the full length structure.

• output_name (str) – Name for the output fused .pdb file (without extension).

• output_dir (str | None) – Directory where the output .pdb file will be saved. Defaults to current working directory.

• fusion_verbose (bool) – Whether to print verbose output during the fusion process. Defaults to True.

• pyrosetta_verbose (bool) – Whether to initialize PyRosetta with verbose output. Defaults to False.

Returns:

The final fused Pose object containing all sequences and PDB structures. list[tuple[str, tuple[int, int]]]]:

The list of fusion objects used in Pose fusion, reporting on their sequence or PDB filepath and their residue ranges in the full length sequence.

Return type:

pyrosetta.rosetta.core.pose.Pose

ensemblify.modelling.fusion.check_is_pdb(input_pdbs)

Check provided filepaths: if they are not PDB files and are instead mmCIF, convert to PDB.

Parameters:

input_pdbs (list[str]) – Path(s) to file(s) to check.

Returns:

Same as input if all files are in PDB format. If inputs are in mmCIF format, they are converted to PDB and the new filepaths are returned.

Return type:

list[str]

ensemblify.modelling.fusion.fuse_structures(input_fastas, input_pdbs, output_name, output_dir=None)

Fuse sequences and PDB structures into a full-length PDB structure.

Parameters:

• input_fastas (list[str]) – Path(s) to FASTA file(s) containing the sequences of all protein domains (folded + disordered) to be fused, in order from N- to C-terminal.

• input_pdbs (list[str]) – Path(s) to PDB or mmCIF file(s) containing the structures of folded protein domains to be fused, in order from N- to C-terminal.

• output_name (str) – Name for the output fused PDB file (without extension).

• output_dir (str) – Directory where the output .pdb file will be saved. Defaults to current working directory.

Returns:

str:

Path to the steric clash report from applying Pulchra to the fused PDB structure.

str:

Path to the fused PDB structure.

Return type:

tuple[str,str]