def read_propka(input_file, parameters, molecule):
"""Read PROPKA input file for molecular container.
Args:
input_file: input file
parameters: parameters for parsing/setup
molecule: molecular container
Returns:
list with [conformations, names of conformations]
"""
conformations = {}
# read in all atoms in the input file
lines = get_atom_lines_from_input(input_file)
for (name, atom) in lines:
if not name in conformations.keys():
conformations[name] = ConformationContainer(
name=name, parameters=parameters, molecular_container=molecule)
conformations[name].add_atom(atom)
# make a sorted list of conformation names
names = sorted(conformations.keys(), key=conformation_sorter)
return [conformations, names]