tetramol

Idealized molecular structures for illustrations, rendered as SVGs with xyzrender.

Atoms are placed on a tetrahedral "diamond" grid, with ideal bond lengths (1.1 Å to hydrogen, 1.5 Å otherwise) and angles (arccos(-1/3) ≈ 109.47°), so neighboring centers are always staggered. This is meant for clean, schematic pictures, not for real geometries.

Installation

pixi run init      # first time only
pixi run local start   # use the local ../automol checkout (see below)

tetramol depends on automol (from the avcopan conda channel) for geometry handling, and on xyzrender (from PyPI) for rendering. To develop against a local automol checkout next to this repository, toggle it with pixi run local start and pixi run local stop.

Usage

from automol import geom
from tetramol import Builder, orient, render

b = Builder(up=(0, 1, 0), left=(-1, 0, 0))  # y is up the page, z toward you
c = b.add("C")  # the first atom goes at the origin
n = b.add("N", c, toward=(0, 1, 0))  # bond through the slot closest to a direction
b.add("C", c, toward=(-1, 0, 0))  # ... or through a slot by index: b.add("C", c, 2)
b.add_hydrogens(avoid=(0, 0, -1))  # fill valences; N's lone pair points back
geo = b.geometry()  # an automol Geometry

rot = orient(geo)  # optional: rotate by hand in the browser,
geo = geom.rotate(geo, rot)  # ... and apply the rotation
render(geo, "drawing.svg")

Each atom has four slots, one per tetrahedral direction, and bonded atoms bond back through the same slot, which fills in the diamond lattice. Use automol.geom for anything off the grid (e.g. geom.rotate(geo, rot, origin=..., keys=[...])).

To draw an umbrella inversion, b.umbrella_image(n) adds the mirror image of the branch on atom n (through the plane of its parent bond, perpendicular to its lone pair), keeping both, so that one side can be faded afterwards.

Drawings live in drawings/, one folder per molecule.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Credits

This package was created with copier and the avcopan/copier-pixi-python project template.