Aqua-Duct installation was tested on macOS Sierra and is quite straightforward. It can be installed either with existing system Python or with custom Python installation. In both cases one have to install Xcode for the App Store.
System native Python
sudo easy_install pip sudo pip install aquaduct
The drawback of using system Python installation is a lack of PyMOL. It should be, however, relatively easy to compile PyMOL on your own. Try to follow compilation instruction under BSD systems.
This is recommended way of Aqua-Duct installation. If you do not have custom Python installation you can get it by using one of package managers available for macOS, for example homebrew. With this package manager you can do following:
brew install python sudo easy_install pip sudo pip install aquaduct
Next, you can install PyMOL:
brew install pymol brew cask install xquartz
Once XQuartz is installed you should reboot. The above procedure installs PyMOL, however, PyMOL Python modules are not visible. To fix it you can issue following commands:
cd /usr/local/lib/python2.7/site-packages sudo ln -s /usr/local/Cellar/pymol/*/libexec/lib/python2.7/site-packages/* ./
The above instruction assumes that you are using brew and you have only one PyMOL installation.