vibesketch.document.relax

Relaxed 3D structures for a document’s species, kept in the document.

Each named species’ first conformer goes through vibesketch.chem.relax.relax_3d() and is replaced by the result; its other conformers stay. Constraints name atoms of one species, so a call with constraints names exactly one species.

Functions

relax(document[, species, constraints, ...])

document with the 3D structures of species (default: all) relaxed.

Classes

RelaxReport([relaxed, results, failed, warnings])

What relaxing did, per species id.

class vibesketch.document.relax.RelaxReport(relaxed=<factory>, results=<factory>, failed=<factory>, warnings=<factory>)

Bases: object

What relaxing did, per species id.

Parameters:

• relaxed (list[str])

• results (dict[str, Relaxed])

• failed (dict[str, str])

• warnings (list[str])

relaxed: list[str]

results: dict[str, Relaxed]

energies, steps, constraint checks.

Type:

The relaxation of each relaxed species

failed: dict[str, str]

Species that could not be relaxed, with the reason.

warnings: list[str]

vibesketch.document.relax.relax(document, species=None, *, constraints=None, force_field='mmff94', fmax=None, max_steps=None)

document with the 3D structures of species (default: all) relaxed.

fmax and max_steps default to the relaxation’s own. Raises UnknownSpecies for an id the document does not have and ValueError when constraints come with more than one species.

Parameters:

• document (Document)

• species (Sequence[str] | None)

• constraints (Sequence[Constraint] | None)

• force_field (Literal['mmff94', 'uff'])

• fmax (float | None)

• max_steps (int | None)

Return type:

tuple[Document, RelaxReport]