Source code for vibesketch.inputs.xyz

"""The XYZ writer: the geometry of one species, nothing else.

XYZ carries element symbols and Cartesian coordinates in angstrom. Charge and
multiplicity go into the comment line as ``key=value`` pairs, the extended
XYZ convention that ASE and vibe-view read; a plain XYZ reader ignores them.
Anything that describes a calculation is refused: an XYZ file cannot say
which method or basis to use.
"""

from __future__ import annotations

from collections.abc import Sequence
from typing import ClassVar

from vibesketch.document.model import JobSpec, Species, Task
from vibesketch.inputs.base import InputFile, InputWriter, first_conformer, needs_conformer




class XyzWriter(InputWriter):
    name: ClassVar[str] = "xyz"
    description: ClassVar[str] = "Cartesian geometry in angstrom, charge and spin in the comment"
    tasks: ClassVar[frozenset[Task]] = frozenset({"geometry"})

    def _refusals(self, species: Species, spec: JobSpec) -> list[str]:
        return needs_conformer(self.name, species)

    def _render(self, species: Species, spec: JobSpec) -> Sequence[InputFile]:
        from vibesketch import __version__

        conformer = first_conformer(species)
        comment = (
            f"charge={species.charge} multiplicity={species.multiplicity} "
            f"species={species.id} generator=vibe-sketch-{__version__}"
        )
        lines = [str(len(conformer.symbols)), comment]
        for symbol, (x, y, z) in zip(conformer.symbols, conformer.xyz_angstrom, strict=True):
            lines.append(f"{symbol:<2} {x:16.10f} {y:16.10f} {z:16.10f}")
        return [InputFile(f"{species.id}.xyz", "\n".join(lines) + "\n", "chemical/x-xyz")]