Molecular Constructor

FAQ

General

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?

Yes.

What platforms are supported?

  • MC Desktop is available on Windows, MacOS and Ubuntu (X11, no Wayland).
  • MC Mobile is available on Android and iOS.
  • MC Legacy is available on Windows.

Which graphics API is used?

  • MC Desktop: Vulkan 1.0
  • MC Mobile: OpenGL ES 2.0
  • MC Legacy: DirectX 9.x

Are desktop and mobile versions compatible?

Yes. Molecules created in the mobile app can be loaded in the desktop version and vice versa.

Are desktop and mobile versions different?

Yes. The desktop version has more features:

  • physical model customization by editing config file (for example, adding more elements)
  • custom fluctuation for shaping
  • multiple ways to select atoms: rectangular, free-form, double-click to select, (de)select all
  • copy and paste
  • molecule centering and view reset

Can I contribute?

Currently, we have no plans on extending our team.

Can I use MC for XYZ?

You can use MC in any environment, including personal, educational, academic, commercial, government etc. Do not sell.

Can I customize?

Yes, please feel free to edit config in the app directory to add more atoms and bonds or to adjust any other parameters.

What are we working on right now?

Nothing major, just keeping everything up to date.

Science

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 Legacy includes van-der-Waals and Coulomb terms. The lack of the intermolecular interaction in MC Desktop and 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.

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: no
  • MC Mobile: no
  • MC Legacy: yes

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.

Technical

How can I add more elements?

  • MC Desktop: edit config in the app directory and restart the app.
  • MC Mobile: no editing available.
  • MC Legacy: please read help and edit config.ini accordingly.

What molecular file formats are supported?

MC uses its own text-based file format with extension *.mc.

Please feel free to parse files or convert them to your favorite molecular data format.

Line-endings when saving a molecule (loading supports both):

  • Windows: CR/LF
  • Non-Windows: LF

MC Legacy files:

  • molecular geometry in a standard *.pdb file
  • molecular connectivity in *.mctopology
  • atomic charges in *.mcatoms.

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.

Alternatively, you can use cloud storage apps to access your molecules across all devices.