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Funct read_xyz_file expanded #29

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Funct read_xyz_file expanded #29

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29 changes: 25 additions & 4 deletions xyz2mol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -529,8 +529,16 @@ def get_proto_mol(atoms):
return mol


def read_xyz_file(filename, look_for_charge=True):
def read_xyz_file(filename):
"""
Takes xyz file. Also accept xyz files without title lines and
xyz files containing connectivity info (Tinker format) as well
as ones which have leading atomic numbers before the atomic symbols.

args:
filename for xyz file
returns:
RDKit mol object
"""

atomic_symbols = []
Expand All @@ -542,20 +550,33 @@ def read_xyz_file(filename, look_for_charge=True):
for line_number, line in enumerate(file):
if line_number == 0:
num_atoms = int(line)
elif line_number == 1:
elif line_number == 1 and len(line.split()) < 4:
title = line
if "charge=" in line:
charge = int(line.split("=")[1])
elif line_number == 1 and len(line.split()) >= 4 and not \
((line.split()[0].strip('-')[0].isdigit() and \
line.split()[2].strip('-')[0].isdigit() and \
line.split()[3].strip('-')[0].isdigit()) or \
(line.split()[1].strip('-')[0].isdigit() and \
line.split()[2].strip('-')[0].isdigit() and \
line.split()[3].strip('-')[0].isdigit())):
title = line
if "charge=" in line:
charge = int(line.split("=")[1])
elif line.split()[0].isnumeric():
atomic_symbol, x, y, z = line.split()[1:5]
atomic_symbols.append(atomic_symbol)
xyz_coordinates.append([float(x), float(y), float(z)])
else:
atomic_symbol, x, y, z = line.split()
atomic_symbol, x, y, z = line.split()[0:4]
atomic_symbols.append(atomic_symbol)
xyz_coordinates.append([float(x), float(y), float(z)])

atoms = [int_atom(atom) for atom in atomic_symbols]

return atoms, charge, xyz_coordinates


def xyz2AC(atoms, xyz, charge, use_huckel=False):
"""

Expand Down