Clean the drawing and prepare 3D geometry

Open lactic-acid.vsk. This exercise keeps a specified stereocentre while separating 2D layout from 3D geometry. Use lactic-acid-3d.vsk to inspect the prepared result directly.

  1. Move an atom with the selection tool so the drawing has an uneven bond. Click Clean up or press Ctrl/Cmd+Shift+L. Standard bond lengths and angles return while the molecule keeps its position and orientation.

  2. Use Undo and Redo to compare. A molecule that cannot be cleaned without changing stereo is left as drawn with a warning; do not assume every molecule was changed just because the command completed.

  3. Click Generate 3D in the Species heading for all missing geometries. Use Generate on an individual card for just that species. The lactic acid card should show a 12-atom structure, including hydrogens.

  4. Redo replaces that species’ cached structure. Ordinary Generate keeps existing conformers. Editing the chemical identity, charge or multiplicity invalidates a geometry that no longer matches.

Lactic acid in the browser with a species-card entry reporting twelve atoms and the ETKDG plus MMFF94 geometry method.

The geometry is an RDKit starting structure, not a completed vibe-qc optimisation.

The preparation uses ETKDG, followed by MMFF94 or UFF where available. Geometries without force-field coverage carry a warning. Specified R/S and E/Z must survive in 3D; unspecified centres are reported because embedding must choose coordinates. These checks do not establish conformational convergence or quantum-chemical accuracy.

Request several conformers through the CLI or API

vibe-sketch clean lactic-acid.vsk -o lactic-clean.vsk
vibe-sketch embed lactic-clean.vsk --count 3 -o lactic-acid-3d.vsk
vibe-sketch embed lactic-acid-3d.vsk --species m1 --count 3 --replace -o redone.vsk
vibe-sketch input redone.vsk --species m1 --program xyz --output-dir geometry

Use the real species ids from info. The count is between 1 and 20; pruning can leave fewer distinct conformers than requested. Writers use the first conformer, rather than generating a calculation for every conformer. The example generator checks stereo identity, cached geometry and explicit replacement and also writes XYZ and QCSchema molecule files.

POST /api/chem/embed3d embeds an isolated SMILES and reports conformers, force-field energies, open stereo and warnings without storing a document. POST /api/documents/{id}/embed updates the shared document at its current revision. The REST example exercises both.

Reference-database geometry, FIRE cleanup and constrained 3D relaxation are planned. Clean up does not invoke those methods. Use vibe-view for detailed 3D structure editing, and vibe-qc inputs for an optimisation.