MOptima
Chapter 05

Importing and Building Molecules

Source: docs/manual/05-import-and-build.md

Main entry points

MOptima supports three practical starting routes:

  1. Draw a molecule.
  2. Input a SMILES string.
  3. Open an existing structure file.
You can begin from a drawn structure, a SMILES string, or an imported file, depending on what information you already have.

Draw a molecule

Use the drawing workflow when you want to sketch a new structure manually. This route is useful for quick ideation, small organic systems, and structures that are easier to define graphically than by file import.

Input SMILES

Use the SMILES dialog when you already know the connectivity in text form. This is often the fastest route from a literature structure or notebook idea into a 3D-editable model.

Open a file

Use file import when the geometry already exists and you want to continue editing or calculation from that structure.

After import

After any import route, do the same short validation pass:

  1. Inspect the 3D structure.
  2. Use the Edit panel if the geometry needs correction.
  3. Confirm atom picking works as expected.
  4. Save the project before large calculations.
After import, inspect the loaded geometry in the viewer before moving to editing or calculations.