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Installation for Windows

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Hiromichi Yokoyama edited this page Aug 5, 2026 · 6 revisions

Installation for Windows

MoleditPy supports Python 3.9 through 3.14 (requires-python = ">=3.9, <3.15"). On Python 3.9 specifically, PyQt6 is pinned to <6.10 (all other supported versions use <6.12); pip resolves this automatically, you don't need to pin it yourself.

There are two supported ways to install MoleditPy on Windows:

  • Recommended: moleditpy-installer — installs the moleditpy package for you and can create a Start Menu/Desktop shortcut and register the .pmeprj file association. See Method A below.
  • Conda-based install — a manually managed environment, useful if you want to pin exact dependency versions or already use Conda. See Method B.

Method A: moleditpy-installer (recommended)

  1. Install the Python package

    Open a terminal (PowerShell, Command Prompt, or a Conda Prompt) and run:

    pip install moleditpy-installer

    This automatically installs the moleditpy package (the Windows/macOS build) as a dependency.

  2. Run the installer

    moleditpy-installer

    In an interactive terminal this opens a TUI where you pick the components (Desktop shortcut, application-menu entry, .pmeprj file association) and the scope (per-user or system-wide), then press Install. Defaults: Desktop shortcut off, Start Menu entry on, file association on, per-user scope.

    For scripted/non-interactive installs, skip the TUI with explicit flags, e.g.:

    moleditpy-installer --no-tui        # install with the defaults
moleditpy-installer --desktop       # also create a Desktop shortcut
# From an elevated (Run as Administrator) prompt, for a system-wide install:
moleditpy-installer --system

  3. Launch

    moleditpy

  4. Upgrade

    pip install --upgrade moleditpy moleditpy-installer

  5. Uninstall

    moleditpy-installer --uninstall
pip uninstall moleditpy

    moleditpy-installer --uninstall removes the shortcuts and file association only; pip uninstall moleditpy removes the application itself.

See the moleditpy-installer README for the full option list (--check, --version, --help), or the Shortcut (Windows) page if you'd rather set up the shortcut and file association manually.

Method B: Conda environment

This procedure is designed to ensure library compatibility, which can often be an issue with GUI applications, by replicating the development environment and required library versions as closely as possible.

Prerequisites

  • Anaconda or Miniconda must be installed on your PC.

Step 1: create and activate a new Conda environment

First, create a clean virtual environment dedicated to moleditpy.

  1. Open the Conda Prompt
    Find and launch "Anaconda Prompt" or "Miniconda Prompt" from the Windows Start Menu.

  2. Create a New Environment
    Create an environment named moleditpy-env specifying a compatible Python version (e.g., 3.12).

    conda create -n moleditpy-env python=3.12
    • If prompted with Proceed ([y]/n)?, type y and press Enter.

  3. Activate the Created Environment
    All subsequent operations will be performed within this new environment.

    conda activate moleditpy-env

    Confirm that the command prompt line now starts with (moleditpy-env).

Step 2: install moleditpy

With all the necessary dependencies in place, install moleditpy itself using pip.

  1. Install moleditpy with pip
    Run the following command in the activated conda environment. 
    pip install moleditpy
    If you want to install specific versions that are confirmed to be compatible, run this command: 
    pip install numpy==2.3.3 openbabel-wheel==3.1.1.22 PyQt6==6.9.1 QtPy==2.4.3 rdkit==2025.3.6 vtk==9.5.2 pyvista==0.46.3 pyvistaqt==0.11.3 moleditpy

Step 3: launch moleditpy

Once the installation is complete, launch moleditpy as a GUI application. The initial launch may take some time.

  1. Run the Launch Command
    In the command prompt (with moleditpy-env activated), execute the following: 
    moleditpy
    If the moleditpy GUI window appears, the environment setup is successful. You can confirm the installed version with moleditpy --version.

Upgrading and uninstalling (Conda method)

conda activate moleditpy-env
pip install --upgrade moleditpy

To remove the environment entirely (this also removes moleditpy and every pinned dependency):

conda deactivate
conda env remove -n moleditpy-env

If you also ran moleditpy-installer inside this environment to create a shortcut/file association, run moleditpy-installer --uninstall first, since its own uninstall command needs moleditpy-installer to still be resolvable on the path.

See also

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