creates smooth gifs of rotating molecules
Project description
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)
Project details
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molgif-0.1.5.tar.gz
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