molgif 0.1.5

creates smooth gifs of rotating molecules

molgif

create smooth gifs of rotating molecules

Examples

Use auto_rotate to find the best viewing angle

import molgif
import ase.build

# load in molecule (ase.Atoms object)
molecule = ase.build.molecule('biphenyl')

# specify save path
save_path = 'biphenyl.gif'

# create rotating gif with rot_gif function
molgif.rot_gif(molecule, save_path, auto_rotate=True)

Add a legend

molgif.rot_gif(molecule, save_path, add_legend=True)

Specify the color of each atom

# can be a string for one color or a list of custom colors
rainbow = ['red', 'orange', 'yellow',
           'green', 'blue', 'violet'] * 4

# list much match number of atoms
rainbow = rainbow[:len(molecule)]

molgif.rot_gif(molecule, save_path, colors=rainbow)

Use a dictionary to quickly color by atom type

# default colors will be used for types not specified
molgif.rot_gif(molecule, save_path, colors=dict(C='hotpink'),
               add_legend=True)

Anchor an atom to be at the center of rotation

# define index of atom to anchor
anchor = 3

colors = ['white'] * len(molecule)
colors[anchor] = '#0892d0'

molgif.rot_gif(molecule, save_path, colors=colors,
               anchor=anchor)

Adjust loop time and FPS

# loop_time = time to complete one rotation (seconds)
molgif.rot_gif(molecule, save_path, loop_time=2, fps=60)

Turn off bonds and scale atomic sizes

molgif.rot_gif(molecule, save_path, add_bonds=False,
               scale=0.9)

Change rotation axis

# switch between x, y (Default), or z
molgif.rot_gif(molecule, save_path, rot_axis='z')

Switch rotation direction

# counterclockwise (ccw)[Default] or clockwise (cw)
# based on rot_axis
# 'x': view from left
# 'y': view from top
# 'z': view into screen
molgif.rot_gif(molecule, save_path, direction='cw')

Visualize charges

import random

# random charges [-1, 1]
chgs = [-1 + 2 * random.random() for i in molecule]

# manually set the colorbar range (optional)
cb_range = (-1, 1)

molecule.set_initial_charges(chgs)

molgif.rot_gif(molecule, save_path, use_charges=True,
               cb_range=cb_range)

Requirements

• ase
• matplotlib
• ImageMagick (command line tools must be installed)