Molecular utilities

mlcg.mol_utils contains useful tools for creating systems via ASE

mlcg.mol_utils._ASE_prior_model(mol='CH3CH2NH2', sum_out=True, device='cpu')

Wrapper that returns a simple prior-only model of an ASE molecule with HarmonicBonds and HarmonicAngles priors whose parameters are estimated from coordinates artifically perturbed by some small Gaussian noise.

Parameters:

• mol (str) – Molecule specifying string found in ase.build.molecule

• sum_out (bool) – If True, the model constituents are wrapped within a SumOut instance

• device – Device on which to place the model

Returns:

Dictionary that contains the fitted prior-only model under the key “model” and the noisey data, as a collated AtomicData instance, used for fitting under the key “collated_prior_data”

Return type:

model_with_data

mlcg.mol_utils._get_initial_data()