traincraft/examples/08_smiles_molecule.toml at main · basillicus/traincraft · GitHub

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# Example 08 — Build a molecule from SMILES and run MD
#
# What it shows:
#   1. smiles source: ethanol (CCO) built with RDKit ETKDG and MMFF94 optimization.
#      Fragment 0 = entire molecule (set automatically by the source).
#      Canonical SMILES stored in provenance.extra for conformer moves.
#   2. EMT MD — a cheap sanity check; replace with tblite or mace for real sampling.
#
# Requires the science environment (rdkit):
#   pixi install -e science
#   pixi run -e science example-08

[run]
name   = "08_smiles_ethanol"
outdir = "runs"
seed   = 7

[geometry.source]
type         = "smiles"
smiles       = "CCO"       # ethanol
n_conformers = 1
optimize     = true
vacuum       = 8.0

[calculator]
type = "emt"

[sampling]
type        = "md"
temperature = 300.0
steps       = 50
interval    = 10

[selection]
steps  = ["physicality", "dedup"]
budget = 3

[dataset]
path = "dataset"