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Render multi-bond first partner as flat !N!N, not !N![N] #80

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Merged
jrfaeder merged 1 commit into from
May 11, 2026
+5 −1
Merged

Render multi-bond first partner as flat !N!N, not !N![N] #80

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6 changes: 5 additions & 1 deletion bionetgen/modelapi/xmlparsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,11 @@ def resolve_xml(self, bonds_xml):
if bond_partner_1 not in self.bonds_dict:
self.bonds_dict[bond_partner_1] = [ibond + 1]
else:
self.bonds_dict[bond_partner_1].append([ibond + 1])
# B13: must append the int, not a [int] list — the
# rendered Component.__str__ emits ``f"!{bond}"`` per
# entry, so a list ``[2]`` would render as ``![2]``,
# which BNG2.pl reads as a compartment specifier.
self.bonds_dict[bond_partner_1].append(ibond + 1)
if bond_partner_2 not in self.bonds_dict:
self.bonds_dict[bond_partner_2] = [ibond + 1]
else:
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