MOptima
Chapter 11

Batch Mode

Batch Mode is the multi-structure workflow in MOptima. Use it when one import action produces more than one molecule that you want to review without leaving the main editor.

When Batch Mode appears

Batch Mode can be offered in three common cases:

  1. You open a file that contains multiple molecules.
  2. You paste or enter multiple SMILES lines.
  3. You import one structure that contains multiple disconnected fragments.

When MOptima detects more than one structure, it asks whether you want to separate them and open Batch Mode.

Selecting No (Keep as one) does not discard the additional structures. It keeps all detected molecules together in the ordinary non-batch Editor, where they can be translated, rotated, or connected by new bonds. Initially overlapping fragments are rigidly separated by at least 3 Å.

When MOptima detects multiple molecules or fragments, it offers to separate them and open Batch Mode.

What changes in the interface

When Batch Mode is active, the editor shows a side panel with one card per structure. Use those cards to switch the active molecule before you edit or run a task.

In Batch Mode, the editor keeps a separate card for each imported molecule so you can switch the active structure explicitly.

Supported and restricted actions

Batch Mode is designed for structure-by-structure review. During that mode:

  • Edit workflows remain available.
  • Energy evaluation remains available.
  • Geometry optimization remains available.
  • Generation is disabled.
  • Low-energy conformer search is disabled.
  • PES scan is disabled.
  • Constrained optimization is disabled; Batch Optimization always uses the ordinary run.

For MMFF94 Batch Optimization, each molecule is still optimized in one continuous minimization. Its result records the initial structure, every 10th BFGS iteration, and the exact final structure. Batch result cards report both the final optimizer iteration and the number of stored frames.

If you enter Batch Mode while an unsupported panel is active, MOptima returns you to a supported panel.

Typical Batch Mode workflow

  1. Import the multi-molecule source.
  2. Confirm that you want to open Batch Mode.
  3. Click a structure card to make one molecule active.
  4. Inspect or edit that molecule in the viewer.
  5. Run a supported task if needed.
  6. Switch to the next card and repeat.

Removing structures from the batch

You can remove an unwanted structure from the batch card list, but MOptima does not let you delete the final remaining molecule. If only one structure is left, continue in single-molecule mode instead of trying to trim the batch further.

Saving and reloading

Batch state belongs to the project. If you save the project while Batch Mode is active, the grouped structures and the current selection state can be restored when you load the project again.

Only one Batch Energy or Batch Optimization queue can run in a MOptima window at a time. If a second Batch or an Interrupted-Batch Retry is started before the first queue finishes, MOptima rejects it with a warning. Independently launched MOptima windows have separate queues; avoid saving both windows to the same project path simultaneously.