def save_pictures(git_path="", species_path="", overwrite=False):
"""
Save a folder full of molecule pictures, needed for the pretty dot files.
Saves them in the results directory, in a subfolder "species_pictures".
Unless you set overwrite=True, it'll leave alone files that are
already there.
"""
dictionary_filename = git_path + "/base/chemkin/species_dictionary.txt"
specs = Database().get_species(dictionary_filename, resonance=False)
images_dir = os.path.join(species_path)
os.makedirs(images_dir, exist_ok=True)
for name, species in specs.items():
filepath = os.path.join(images_dir, name + ".png")
if not overwrite and os.path.exists(filepath):
continue
species.molecule[0].draw(filepath)
