What is Molecular Constructor?

Molecular Constructor (MC) is a free 3D molecular builder and editor. Using this application, the user can design a molecule and optimize its geometry at the same time.

Is MC free?


What platforms are supported?

  • MC Desktop is available on Windows.
  • MC Mobile is available on Android and iOS.

Are desktop and mobile versions compatible?

No, but will be one day.

Can I contribute?

Currently, we have no plans on extending our team.

What are we working on right now?

Switching to Vulkan API to make MC Desktop cross-platform (Windows, MacOS, and Linux).


What is the energy? What are the units?

The energy is calculated using a force field method, which includes contributions from bond lengths, angles, torsion angles and out-of-plane distortions. All components are described using a harmonic model. Force field constants were manually adjusted to improve geometry convergence and should not be treated as the potential energy of a molecule. This is why the energy is printed without any units.

Also, MC Desktop includes van-der-Waals and Coulomb terms, whereas MC Mobile does not. The lack of the intermolecular interaction in MC Mobile causes two molecules to overlap if they are placed very close to each other.

How does geometry optimization work?

The optimization algorithm is energy-driven and is greedy. On each iteration a slightly distorted configuration is generated and the algorithm accepts it only of the energy is smaller than the energy of the current configuration. This way, the search always ends up at a local minimum. The user is encouraged to use their fingers (MC Mobile) or mouse (MC Desktop) to manually guide convergence wherever they want. This is where your chemical intuition shines.

How can I add more atoms or change the physical model?

  • MC Desktop: please read help and edit config.ini appropriately.
  • MC Mobile: no editing available.

Can I build and optimize simultaneously?

Absolutely yes. You may want to have the shaping feature always on.

Does MC calculate atomic charges?

  • MC Desktop: yes.
  • MC Mobile: not yet.

How atomic charges are calculated?

Sigma and pi electrons are treated separately (sigma-pi separability). The Del Re method of calculating charge distribution is used for sigma (localized) electrons and the Hückel method is used for pi (delocalized) electrons.


What molecular file formats are supported?

MC uses its own file formats.

  • MC Mobile stores molecular data in a file with extension "*.mc".
  • MC Desktop stores molecular geometry in a standard ".pdb" file, molecular connectivity in "*.mctopology" and atomic charges in "*.mcatoms". We are planning to replace MC Desktop file formats with MC Mobile one.

All files are simple text files. Please feel free to parse them or convert to your favorite molecular data format.

How to transfer MC molecular files between mobile phone and PC?

  • Android
    1. Connect the phone to your computer in copy / file-transfer mode.
    2. The files can be found in Android -> data -> com.alextepl.molconstr -> files.
  • iOS
    1. Open iTunes app on your computer.
    2. Click device button near the top left -> File Sharing -> Molecular Constructor.
    3. The files will appear on the right.