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flag to use spaces instead of tabs in molSimplify construction #275

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merged 2 commits into from
Oct 24, 2024
Merged

flag to use spaces instead of tabs in molSimplify construction #275

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7c1cf6a
flag to use spaces instead of tabs in molSimplify construction
gianmarco-terrones Oct 24, 2024
f56041b
adjusting test case
gianmarco-terrones Oct 24, 2024
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4 changes: 4 additions & 0 deletions molSimplify/Scripts/inparse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -582,6 +582,8 @@
args.jobdir = l[1]
else:
args.jobdirblank = True
if (l[0] == '-no_tabs'):
args.no_tabs = True

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molSimplify/Scripts/inparse.py#L586 

Added line #L586 was not covered by tests
### parse structure generation arguments ###
if (l[0] == '-bind' and len(l[1:]) > 0):
l = [_f for _f in re.split(' |,|\t', line) if _f] # noqa: E741
Expand Down Expand Up @@ -1194,6 +1196,8 @@
"-reportonly", help='add this flag if you just want the report, without actual structure generation. Currently does not support pentadentates.')
parser.add_argument(
"-jobmanager", help='use jobmanager naming convention.', default=False)
parser.add_argument(
"-no_tabs", help="add this flag to use spaces instead of tabs in written xyz files", default=False)
if len(p) == 1: # only one input, printing help only
args = parser.parse_args()
return args
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2 changes: 1 addition & 1 deletion molSimplify/Scripts/structgen.py
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Expand Up @@ -3015,7 +3015,7 @@ def structgen(args: Namespace, rootdir: str, ligands: List[str], ligoc: List[int

# write xyz file
if (not args.reportonly) and (write_files):
core3D.writexyz(fname)
core3D.writexyz(fname, no_tabs=args.no_tabs)
strfiles.append(fname)
if write_files:
# write report file
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2 changes: 1 addition & 1 deletion tests/test_inparse.py
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Expand Up @@ -40,7 +40,7 @@ def test_parseinputs_advanced(monkeypatch):
defaults = dict(MLbonds=False, antigeoisomer=None, calccharge=True,
charge=None, decoration=False, decoration_index=False,
distort='0', genall=False, isomers=None, langles=False,
ligalign=False, nconfs='1', oldANN=None, pangles=False,
ligalign=False, nconfs='1', no_tabs=False, oldANN=None, pangles=False,
reportonly=None, scoreconfs=False, stereos=None,
jobmanager=False)
assert args.__dict__ == defaults
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