moleculekit.tools.mutate module#

Side-chain reconstruction for residue mutation.

Rotamer library data from:: Shapovalov & Dunbrack (2011) “A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions.” Structure 19(6):844-858. Licensed under Creative Commons CC BY 4.0.

moleculekit.tools.mutate.mutate_residue(mol, sel, newres, rotamer_mode='best', minimize=False)#

Mutate a residue, fully reconstructing the side-chain.

The mutation proceeds in up to three phases:

Kabsch superposition – the ideal template for newres is aligned onto the existing backbone (N, CA, C) atoms.
Rotamer selection – the Dunbrack backbone-dependent rotamer library is queried using the residue’s phi/psi angles, and the best rotamer (lowest VdW clash energy with surroundings) is selected.
Optional OpenMM minimization – if minimize is True and OpenMM is installed, a soft-potential energy minimization gently resolves remaining clashes.

Parameters:

mol (Molecule) – The molecule to mutate (modified in place).
sel (str) – Atom selection string identifying a single residue.
newres (str) – 3-letter code of the target residue (e.g. "ARG"). Protonation variants such as "HID", "HIE", "HIP", "CYX", "ASH", "GLH", "LYN" etc. are also accepted – the heavy-atom geometry is taken from the parent residue and the requested name is preserved. The non-standard natural amino acids "SEC" (selenocysteine) and "PYL" (pyrrolysine) and the modified amino acids "MSE", "MLZ", "MLY", "M3L", "SEP", "TPO" and "PTR" are also supported – they use their own CIF templates but reuse their parent residue’s rotamer library entries.
rotamer_mode (str, optional) – "best" (lowest clash energy, default), "first" (highest probability), or "random" (sampled by probability).
minimize (bool, optional) – If True, run soft-potential OpenMM minimization after rotamer placement. Requires OpenMM. Default False.