MOptima
Manual

MOptima Manual

Source: docs/manual/index.md

This manual is written for the package website. It is organized by user workflow rather than by source code, so future features can be added as new chapters without rewriting the whole document.

What MOptima does

MOptima is a desktop molecular workflow application built around four connected parts:

  • A 3D molecule viewer
  • A visual molecule editor
  • Setup panels for optimization, conformer generation, and other classical structure workflows
  • Result tabs with vistualization for these workflows

The application starts a local service in the background and keeps the full workflow inside one desktop interface. In practice, a typical session is:

  1. Create or open a project.
  2. Import or build a molecule.
  3. Edit atoms, bonds, angles, or torsions.
  4. Run a single task or a process task.
  5. Review the generated result tabs.
  6. Save the project or export figures and reports.

How to use this manual

  • Start with the interface chapter if you are new to the program.
  • Read the mouse chapter before using the 3D editor.
  • Follow the workflow chapters in order for a first project.
  • Read the Batch Mode chapter before working with multiple molecules in one session.

Table of contents

  1. Overview
  2. Interface and Navigation
  3. Mouse and View Controls
  4. Projects and File Organization
  5. Importing and Building Molecules
  6. Editing and Selection
  7. Single Tasks
  8. Process Tasks
  9. QM Workflow
  10. Results, Export, and Reports
  11. Batch Mode
  12. Installation and Platform Notes
  13. Licensing

Screenshot convention

Use the same three-part placeholder format throughout the manual:

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  • Suggested filename: a stable asset name for the screenshot file
  • Caption: the sentence that should appear below the image

Store the actual screenshot files in docs/manual/figure/ and use the Suggested filename value as the real file name there.

The PDF builder and the website renderer both look up that file automatically. In the rendered output, screenshot blocks display only the image and its caption.