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Reading a Gromacs topology fails with insertion code or negative number #1222

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merged 5 commits into from
Feb 15, 2022
Merged

Reading a Gromacs topology fails with insertion code or negative number #1222

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d4755e4
reading gromacs topologies with insertion codes fixed
Valdes-Tresanco-MS Feb 7, 2022
d0d6050
reading gromacs topologies with insertion codes and negative number f…
Valdes-Tresanco-MS Feb 15, 2022
73ae4f7
Merge branch 'v3.4' into fix_icode_resn
Valdes-Tresanco-MS Feb 15, 2022
a8d0e3f
using conditional instead of try-except clause
Valdes-Tresanco-MS Feb 15, 2022
bea9d1b
Merge branch 'v3.4' into fix_icode_resn
swails Feb 15, 2022
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4 changes: 2 additions & 2 deletions parmed/gromacs/gromacstop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -491,10 +491,10 @@ def _parse_atoms(self, line, params):
atom = Atom(atomic_number=atomic_number, name=words[4],
type=words[1], charge=charge, mass=mass)
# check for insertion code
if words[2].isnumeric():
try:
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It looks like the problem is that a leading - leads to isnumeric() returning False. What about we change line 494 to this instead:

if words[2].isnumeric() or (words[2].startswith('-') and words[2][1:].isnumeric()):

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Done via a8d0e3f

icode = ''
resnum = int(words[2])
else:
except:
icode = words[2][-1]
resnum = int(words[2][:-1])
return atom, words[3], resnum, icode
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