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Installing Python and pip
MoleditPy is installed with pip, so you need a working Python first. This page covers getting Python and pip onto Windows, macOS and Linux, and the problems people most often hit along the way. If you already have Python, check the version below and go straight to your platform's installation page.
MoleditPy supports Python 3.9 through 3.14. Any of them works; a recent version such as 3.12 or 3.13 is a good choice.
Prefer conda? If you use Anaconda or Miniconda, you already have Python and pip. Follow the Conda method on the Windows or macOS page instead.
Open a terminal (Windows: PowerShell or Command Prompt; macOS: Terminal) and run:
python --version
python -m pip --versionOn macOS and Linux the command is usually python3:
python3 --version
python3 -m pip --versionIf both print a version and the Python version is 3.9–3.14, you are ready — skip to Next steps.
Use
python -m pip, not barepip. If more than one Python is installed,pipmay belong to a different one thanpython, and MoleditPy ends up installed somewhere you are not running.python -m pipalways uses the Python you named. The commands on this page follow that rule.
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Download the installer from python.org/downloads.
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Run it and, on the first screen, tick "Add python.exe to PATH" before clicking Install Now. pip is included.
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Open a new PowerShell window and check:
python --version python -m pip --version
If python is still not found, the Python Launcher always works: use py in place of python (for example py -m pip install moleditpy-installer).
Windows ships a placeholder python command that opens the Store. Either install Python from python.org as above, or turn the placeholder off: Settings › Apps › Advanced app settings › App execution aliases, and switch off python.exe and python3.exe.
macOS may already have a python3 command, but it belongs to Apple's developer tools and can be older than you want. Install your own Python with one of these:
Option 1: python.org installer (recommended)
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Download the macOS installer from python.org/downloads and run it.
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When it finishes, a Finder window opens on /Applications/Python 3.x. Double-click Install Certificates.command in it. Do not skip this step — see SSL certificate errors on macOS for why.
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Open a new Terminal window and check:
python3 --version python3 -m pip --version
Option 2: Homebrew
If you use Homebrew:
brew install pythonHomebrew's Python uses Homebrew's own certificates, so the certificate step above is not needed. Homebrew's Python refuses pip install into itself (externally-managed-environment), so install MoleditPy into a virtual environment.
Most distributions include Python 3. Install pip and the venv module from the package manager:
# Debian / Ubuntu
sudo apt update
sudo apt install python3 python3-pip python3-venv
# Fedora
sudo dnf install python3 python3-pipRecent distributions block pip install into the system Python (externally-managed-environment), so install MoleditPy into a virtual environment — see Method B on Installation for Linux.
Install MoleditPy with:
python -m pip install moleditpy-installer
python -m moleditpy_installer(python3 on macOS and Linux.) The platform pages explain the options and how to upgrade and uninstall:
Symptom: MoleditPy itself installs and works normally, but plugins that connect to the internet do not — for example the Plugin Installer cannot load the plugin list, PubChem name lookups fail, and AI chat plugins cannot reach their service. The plugin's error message, the log, or the terminal contains:
[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed
often followed by unable to get local issuer certificate.
Cause: the python.org installer for macOS does not set up the root certificates that Python uses to check HTTPS connections. pip is not affected, because it carries its own certificate bundle — which is why installing MoleditPy succeeds and only the plugins' own connections fail.
Fix: run the certificate installer that came with Python. Double-click Install Certificates.command in /Applications/Python 3.x (use the folder for the version you installed), or run it from Terminal, adjusting the version number:
open "/Applications/Python 3.13/Install Certificates.command"Then restart MoleditPy. If you install another Python version later, run that version's Install Certificates.command too.
Pythons from Homebrew or conda do not have this problem.
On a university or company network, downloads can fail with timeouts or ProxyError. If your network uses an HTTP proxy, give it to pip:
python -m pip install --proxy http://proxy.example.com:8080 moleditpy-installerTo let MoleditPy and its plugins use the proxy too, set it in the environment before starting the app:
# macOS / Linux
export HTTPS_PROXY=http://proxy.example.com:8080
export HTTP_PROXY=http://proxy.example.com:8080# Windows (PowerShell)
$env:HTTPS_PROXY = "http://proxy.example.com:8080"
$env:HTTP_PROXY = "http://proxy.example.com:8080"Ask your IT department for the proxy address. If the network inspects HTTPS traffic with its own certificate, you will also see CERTIFICATE_VERIFY_FAILED; IT can give you that certificate to install.
Use python -m pip (or python3 -m pip, or py -m pip on Windows). If that also fails, pip is missing: reinstall Python from python.org, or on Linux install the python3-pip package.
Your system or Homebrew Python is protected from pip install. Create a virtual environment and install MoleditPy into it:
python3 -m venv ~/moleditpy-env
source ~/moleditpy-env/bin/activate
python -m pip install moleditpy-installerActivate the environment (source ~/moleditpy-env/bin/activate) each time before running moleditpy from a terminal; the shortcut created by moleditpy-installer remembers the environment for you.
moleditpy needs Python 3.9–3.14. If pip says it cannot find a matching version, check python --version. On Windows, py -0 lists every installed Python and py -3.13 -m pip ... picks one; on macOS and Linux, call a specific version such as python3.13.