Repository for refactoring the "MAWS 2023" repository by dtu-denmark for integration in the pyaptamer package

Refactoring aims

• remove or replace binary dependencies
• remove or replace subprocess calls
• full python bindings

Sampling region

MAWS samples the initial nucleotide pose around the ligand surface using SAS-style rejection: candidate poses inside the protein bulk (within vdW + probe, default 1.4 Å water-equivalent) are skipped before the energy evaluator sees them. The envelope is a single sphere auto-sized from the ligand geometry (radius = R_max + reach) around its mass-weighted centre of mass. Two CLI flags control behavior:

• --reach FLOAT — how far the envelope extends past the ligand's bounding radius, in Å (default 10.0).
• --probe FLOAT — vdW probe radius for the SAS rejection, in Å (default 1.4, water-equivalent).

The same options are available as keyword arguments on maws.run.MawsRunner for programmatic use. An opt-in surface-following sampling mode (maws.space.make_sampler(..., mode="surface-following", d_max=...)) is also implemented for users who want accepted poses concentrated near the molecular surface; see docs/space.md for the full API.

Implicit-solvent salt screening

Energies are evaluated with the GB-OBC1 implicit solvent. The monovalent salt concentration used for Debye–Hückel screening is configurable:

• --salt-conc FLOAT — monovalent salt concentration in mol/L (default 0.15, ~physiological). Also available as the salt_conc keyword on maws.run.MawsRunner and maws.complex.Complex.

Behavior change: earlier releases ran unscreened (effectively 0.0 mol/L). Because screening changes the GB energies that drive sequence selection, results will differ from prior versions unless you pass --salt-conc 0. The screening is monovalent only and does not model divalent ions such as Mg²⁺.

original readme

https://github.com/gc-os-ai/MAWS_2025/blob/main/README_orig.md