molgif 0.2.1

creates smooth gifs of rotating molecules

molgif

create smooth gifs of rotating molecules

Installation

pip install molgif

Examples

Easily create gif with rot_gif function

import molgif
import ase.build

# load in molecule (ase.Atoms object)
c4h4o = ase.build.molecule('c4h4o')
c4h4o.rotate(60, 'z')

# create rotating gif
molgif.rot_gif(atoms)

Use smart_rotate to find best viewing angle and add a legend

molgif.rot_gif(c4h4o, smart_rotate=True, add_legend=True)

# can also smart_rotate atoms object using pca in utils
c4h4o = molgif.utils.smart_rotate_atoms(c4h4o)

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'] * 2

# list length much match number of atoms
rainbow = rainbow[:len(c4h4o)]

molgif.rot_gif(c4h4o, colors=rainbow)

Use a dictionary to quickly color by atom type and add a legend that's ordered by size

# default colors will be used for types not specified
# can also order legend by size
molgif.rot_gif(c4h4o, colors=dict(C='hotpink'),
               add_legend=True, leg_order='size')

Anchor an atom to be at the center of rotation

# define index of atom to anchor
anchor = 3

colors = ['white'] * len(c4h4o)
colors[anchor] = '#0892d0'

molgif.rot_gif(c4h4o, colors=colors,
               anchor=anchor)

Adjust loop time and FPS

# loop_time = time to complete one rotation (seconds)
molgif.rot_gif(c4h4o, loop_time=2, fps=60)

Turn off bonds and scale atomic sizes

molgif.rot_gif(c4h4o, add_bonds=False,
               scale=0.9)

Change rotation axis

# switch between x, y (Default), or z
molgif.rot_gif(c4h4o, rot_axis='x')

Switch rotation direction

# "negative" rot_axis = opposite direction
molgif.rot_gif(c4h4o, rot_axis='-x')

Visualize charges

# random charges [-1, 1]
chgs = np.linspace(-1, 1, len(atoms))
np.random.shuffle(chgs)

# add the charges to atoms object
atoms.set_initial_charges(chgs)

molgif.rot_gif(atoms, max_px=max_px, use_charges=True)

Requirements

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