molgif 0.0.5

creates smooth gifs of rotating molecules

molgif

create smooth gifs of rotating molecules

Examples

Automatically rotate molecule for better view

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)

Adjust loop time and FPS

# time to complete one rotation (seconds)
loop_time = 2

# frames per second
fps = 60

molgif.rot_gif(molecule, save_path, auto_rotate=True,
               loop_time=loop_time, fps=fps)

Turn off bonds and scale atomic sizes

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

Visualize charges and include a colorbar

import random

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

molecule.set_initial_charges(chgs)

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

Specify 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, auto_rotate=True,
               colors=rainbow)

Switch rotation direction and adjust bond widths

# counterclockwise (ccw) or clockwise
# based on top-down perspective
direction = 'cw'

# specify bond width in Angstrom
bond_width = 0.4

molgif.rot_gif(molecule, save_path, auto_rotate=True,
               direction=direction, bond_width=bond_width)

Requirements

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