mooonpy.template.ntafile module

NTA-file writer for atom_typing/all2lmp consumption.

Format:

mooonpy NTA file for <basename> at <date>
style id

<atom_id> <nta_string>
<atom_id> <nta_string>
...

The file uses style id (per-atom-id NTA assignments). Atom NTA strings come from atom.comment after canonicalization (only the NTA token is kept, any verbose atom_typing-style preamble is stripped).

mooonpy.template.ntafile.canonicalize_ntas(mol)[source]

Reduce every atom.comment in mol to just its NTA token, in place.

Idempotent: running it on a Molspace whose comments are already plain NTAs is a no-op.

mooonpy.template.ntafile.extract_nta(comment)[source]

Pull the NTA token out of an atom_typing comment string.

atom_typing writes verbose comments like "C        Sp2     avg-angle: 120.000000      type: cp". After a ReactionTemplate.changed_typ rewrite the field may already be just "cp". This handles both: returns "cp" either way, or "" for an empty comment.

mooonpy.template.ntafile.write_ntafile(filename, mol, edge_external_ntas=None)[source]

Write a per-atom NTA assignment file for mol.

Parameters:

  • filename (str or Path) – Output path.

  • mol – Molspace whose atom.comment carries the NTA tokens. The comment is canonicalized (verbose atom_typing preambles stripped) before writing.

  • edge_external_ntas (dict[int, list[str]] or None) – Optional {edge_atom_id: [nta, ...]} mapping each template edge atom to the NTA strings of its bonded neighbors outside the template. When given (and non-empty), an edge id section is appended so downstream charge-equilibration can account for the severed bonds. Empty lists are skipped.