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Fix bug in GRO reader #775

Merged
merged 10 commits into from
Jan 15, 2024
22 changes: 11 additions & 11 deletions gmso/formats/gro.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,12 @@
coords = u.nm * np.zeros(shape=(n_atoms, 3))
for row, _ in enumerate(coords):
line = gro_file.readline()
content = line.split()
res_id = int(line[:5])
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res_name = line[5:10].strip()
atom_name = line[10:15].strip()
atom_id = line[15:20].strip()
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positions = line[20:].split()
if not line:
msg = (
"Incorrect number of lines in .gro file. Based on the "
Expand All @@ -66,22 +71,17 @@
)
raise ValueError(msg.format(n_atoms))

res = content[0]
atom_name = content[1]
atom_id = content[2]
coords[row] = u.nm * np.array(
[
float(content[3]),
float(content[4]),
float(content[5]),
float(positions[0]),
float(positions[1]),
float(positions[2]),
]
)
site = Atom(name=atom_name, position=coords[row])

r = re.compile("([0-9]+)([a-zA-Z]+)")
m = r.match(res)
site.molecule = (m.group(2), int(m.group(1)))
site.residue = (m.group(2), int(m.group(1)))
site.molecule = (res_name, res_id)
site.residue = (res_name, res_id)
top.add_site(site, update_types=False)
top.update_topology()

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