modelling

Author(s):

Nuno P. Fernandes

Year:

2026

Copyright:

GNU Public License v3

Added in version 1.0.0.

This module contains functions for creating and manipulating PyRosetta Pose objects and associated PDB files.

If desired, these can then be used as starting structures for conformational ensemble generation.

Example applications

Create a PyRosetta Pose object from a PDB file or sequence

The ensemblify.modelling.setup_pose function can be used to initialize a Pose object from a .pdb file, a .txt/.fa file containing a sequence, or directly from a provided sequence string.

For example, we can create a Pose object for Histatin5 (Hst5), an intrinsically disordered peptide with 24 aminoacid residues.

Assuming the path to your .pdb file is assigned to a variable named HST5_PDB, you should run:

>>> import ensemblify.modelling as em
>>> em.setup_pose(HST5_PDB)

Create a full-length PDB structure from ordered and disordered fragments

The ensemblify.modelling.fuse_structures function can be used to fuse PDB structures of folded protein domains with the sequences of connecting disordered regions. For this you need: a list of FASTA files, containing the sequences of all protein domains (folded + disordered) to be included in the final fused structure; a list of PDB or PDBx/mmCIF files, containing the structure of folded domains to be fused.

Assuming the paths to your (Multi-)FASTA and (Multi-Model)PDB files are assigned to variables named FASTAS and PDBS, respectively, you should run:

>>> import ensemblify.modelling as em
>>> em.fuse_structures(FASTAS, PDBS, 'myprotein')

Available Functions

apply_basic_idealize

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

apply_constraints

Apply energy constraints to desired regions of a Pose object.

apply_pae_constraints

Apply energy constraints to a Pose created from an AlphaFold structure based on its Predicted Aligned Error (PAE) matrix.

create_fusion_pose

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

fuse_structures

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

pack_sidechains

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

process_pdb_structure

Apply FASPR and PULCHRA to PDB structure.

setup_minmover

Setup a PyRosetta MinMover object given the necessary parameters.

setup_pose

Initialize a Pose object from a sequence, a .txt file containing the sequence or a PDB file.

Submodules