x, y, z = map(float, (x, y, z))
res.append([path,
Atom(sym,
coords=(x, y, z))]) # new key for each coord
found = False
counter = 0
for line in read_file(logfile):
if 'NET CHARGES:' in line:
found = True
if 'RMS DEVIATION' in line:
break
if found:
if re.search(charge_regex, line):
res[counter].append(float(line.split()[1]))
counter += 1
coords = [atom[1] for atom in res]
mol = Molecule(atoms=coords)
mol.separate()
# bad practice, should use for i, j in zip(mol.coords, res):
for atom, r in zip(mol.coords, res):
path, _, geodesic_charge = r
results.append([
path, atom.index, atom.symbol, geodesic_charge, atom.x, atom.y,
atom.z, f"{mol.fragments[atom.mol]['name']}_{atom.mol}"
])
write_csv_from_nested(results,
col_names=('Path', 'Index', 'Element', 'Geodesic', 'Rx',
'Ry', 'Rz', 'Fragment'),
filename='charges.csv')
#!/usr/bin/env python3
from autochem import Molecule, write_xyz
from glob import glob
import os
import sys
from tqdm import tqdm
base = os.path.basename(__file__)
if len(sys.argv) != 2 or sys.argv[1] == '-h':
print(
'Extract all ions of a particular name from all xyz files in the current directory.'
)
print(
f'i.e. `{base} dhp` pulls out all dhp anions from all xyz files and place them in a subdirectory'
)
print(f'Syntax: {base} molecule')
sys.exit(1)
if not os.path.isdir('extracted'):
os.mkdir('extracted')
for f in tqdm(glob('*xyz')):
mol = Molecule(f)
newname = os.path.join(os.getcwd(), 'extracted', f)
extracted = [atom for atom in mol.coords if sys.argv[1] in atom.fragment]
write_xyz(extracted, newname)
#!/usr/bin/env python3
from autochem import Molecule
import sys
if len(sys.argv) not in [2, 3] or '-h' in sys.argv:
print(f'Syntax: {sys.argv[0]} xyzfile')
sys.exit(1)
try:
output = sys.argv[2]
except IndexError:
output = 'connected.in'
mol = Molecule(sys.argv[1])
bonds = []
for atom in mol.coords:
for a in atom.connected_atoms:
if f'{a.symbol}{a.index} - {atom.symbol}{atom.index}' not in bonds:
bonds.append(f'{atom.symbol}{atom.index} - {a.symbol}{a.index}')
for b in bonds:
print(b)
from collections import namedtuple
info = namedtuple("info", "xyz atom1 mol1 atom2 mol2 dist")
def distances(namedtup, molecule):
return [
namedtup(
molecule.xyz,
f"{atom1.symbol}_{atom1.index}",
atom1.fragment,
f"{atom2.symbol}_{atom2.index}",
atom2.fragment,
atom1.distance_to(atom2),
) for frag1, frag2 in itertools.combinations(
molecule.fragments.values(), 2) for atom1 in frag1["atoms"]
for atom2 in frag2["atoms"]
]
dists = []
for xyz in glob('*xyz'):
mol = Molecule(xyz)
dists += distances(info, mol)
df = df_from_namedtuples(info, dists)
mindists = df.groupby(["xyz", "mol1",
"mol2"])["dist"].min().reset_index().sort_values(
["xyz", "mol1", "mol2"])
mindists.to_csv('min_dists_between_frags.csv', index=False)