Molecular Blender

An import plugin specialized for .xyz files of molecules used in, for example, quantum chemistry

Capabilities

• imports using linked objects making rapid changes to the aesthetics feasible
• basic styling (stick model, VDW, ball and stick, wireframe) and sensible defaults
• support for animations (input as multiframe .xyz files) including dynamically drawing bonds
• find and fill in aromatic rings
• draw spheres sitting on atoms to represent atomic charges and dynamically scale them during an animation
• draw molecular orbital isosurfaces with .cube files or .molden files

Installation

There are two basic ways to install Molecular Blender, depending on whether you want to use the optional cython enhanced isosurface routines (highly recommended, if you're drawing isosurfaces at all).

Using setup.py (cython compatible)

The most robust way to install is to use the included setup.py.

cd /path/to/molecular/blender/repo
python3 setup.py build
python3 setup.py link

This will build the cython extensions to the code and then create symlinks to all of the versions of blender found in the normal blender install directories (only tested on macOS). For this to work, you'll need to use python 3.7 (the same version used in Blender 2.80), and have cython installed for it. The same setup can be used to export a build:

python3 setup.py build
python3 setup.py export

This will create a zip file that should be compatible with the add-on installation machinery of blender itself.

Direct symlink (no cython)

If you are okay with skipping sython, you can directly symlink from the python package to the blender scripts directory. The non-cython version has all the same functionality as the cython version, but may be significantly slower for certain tasks (cython version is roughly 100 times faster at drawing orbitals from molden files).

ln -s /path/to/molecular/blender/repo/molecular_blender /path/to/blender/scripts/addons/

and then it should appear in the list of Import-Export addons that can be activated like any other addon.

On Mac OS X, the path for a user supplied addon is

/Users/<username>/Library/Application\ Support/Blender/<version>/scripts/addons

where <username> and <version> should be replaced with your username and the Blender version you are using.

Design

The only guiding design principle so far has been to try and separate the molecular data structures (Molecule, Bond, Atom) from the Blender manipulations. This is subject to change.