def read_energy_from_mae(filename):
"""
Reads energies from *.mae files.
Energies are read and saved as kJ/mol.
"""
path_of_this_file = os.path.dirname(os.path.realpath(__file__))
path_of_q2mm = os.path.join(path_of_this_file, '../q2mm')
sys.path.append(path_of_q2mm)
import filetypes
mae = filetypes.Mae(filename)
energies = [float(x.props[ENERGY_LABEL]) for x in mae.structures]
return energies
def main(args):
parser = return_parser()
opts = parser.parse_args(args)
# ~~~ STRUCTURE AND CHARGE READING ~~~
mae = ft.Mae(opts.mae)
mmo = ft.MacroModel(opts.mmo)
# Select 1st structure of .mae. Sure hope your MM charges are there.
str_mae = mae.structures[0]
# Select 1st structure of .mmo.
# This structure should only contain bonds that are particular to our
# substructure.
str_mmo = mmo.structures[0]
substr_bonds = str_mmo.select_stuff('bonds', com_match=opts.subnames)
substr_atoms = atom_nums_from_bonds(substr_bonds)
# Now that we have the atoms in the substructure, we need to select
# every other atom and get those MM charges.
non_substr_atoms = []
for atom in str_mae.atoms:
if atom.index not in substr_atoms:
non_substr_atoms.append(atom)
# ~~~ WORKING ON GENERATING THE OUTPUT ~~~
if opts.format == 'jaguar':
atomic_lines = gen_atomic_section(non_substr_atoms)
# Now we just need to add these to the atomic section.
# Read or generate the .in file.
if opts.jin:
jin = ft.JaguarIn(opts.jin)
else:
jin = None
new_lines = gen_jaguar_output(mae, jin, opts.charge)
# Add the charge section.
new_lines[0:0] = atomic_lines
elif opts.format == 'gaussian':
non_substr_atom_indices = [x.index for x in non_substr_atoms]
new_lines = gen_gaussian_output(
mae,
indices_use_charge=non_substr_atom_indices,
title=mae.filename.split('.')[0],
charge=opts.charge,
multiplicity=opts.multiplicity)
# ~~~ WRITE OUTPUT ~~~
if opts.output:
with open(opts.output, 'w') as f:
for line in new_lines:
f.write(line + '\n')
else:
for line in new_lines:
print(line)
parser = argparse.ArgumentParser()
parser.add_argument('--display', '-d', type=str, default='3d')
parser.add_argument('--filename', '-f', type=str)
parser.add_argument('--extension',
'-e',
type=str,
nargs='+',
default=['jpg'])
parser.add_argument('--key', '-k', type=str, nargs='+', default=[])
parser.add_argument('--output', '-o', type=str)
opts = parser.parse_args(sys.argv[1:])
path, ext = os.path.splitext(opts.filename)
if ext == '.mae':
mae = filetypes.Mae(opts.filename)
x_data = []
y_data = []
z_data = []
for structure in mae.structures:
x_data.append(float(structure.props[X_LABEL]))
y_data.append(float(structure.props[Y_LABEL]))
z_data.append(float(structure.props[Z_LABEL]))
logger.info('x: {} y: {} z: {}'.format(len(x_data), len(y_data),
len(z_data)))
minimum = min(z_data)
z_data = [x - minimum for x in z_data]
x_set = np.array(sorted(set(x_data)))