Render multi-bond first partner as flat !N!N, not !N![N]#80
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jrfaeder merged 1 commit intoMay 11, 2026
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`BondsXML.resolve_xml` had an off-by-one-character bug: when the SAME
site is the first partner of two or more bonds (the `hub(x!1!2)` shape),
the second-and-later bond IDs were appended to `self.bonds_dict` as a
one-element LIST `[ibond + 1]` instead of as the int `ibond + 1`. The
second partner's branch already appended the int correctly, so the bug
only surfaced for sites that appeared as `bond_partner_1` in multiple
bonds.
`Component.__str__` then ran `f"!{bond}"` over the flat bonds list,
which turned `[2]` into `![2]`. BNG2.pl reads `![N]` as a compartment
specifier in pattern syntax and aborts with `Invalid syntax at ![2]`
when it re-loads the regenerated BNGL.
Fix: append the int (parity with the second-partner branch).
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Summary
`BondsXML.resolve_xml` has an off-by-one-character bug: when the SAME site is the first partner of two or more bonds (the `hub(x!1!2)` shape), the second-and-later bond IDs are appended to `self.bonds_dict` as a one-element LIST `[ibond + 1]` instead of as the int `ibond + 1`. The second partner's branch already appends the int correctly, so the bug only surfaces for sites that appear as `bond_partner_1` in multiple bonds.
`Component.str` then runs `f"!{bond}"` over the flat bonds list, which turns `[2]` into `![2]`. BNG2.pl reads `![N]` as a compartment specifier in pattern syntax and aborts with `Invalid syntax at ![2]` when it re-loads the regenerated BNGL.
Fix
Append the int (parity with the second-partner branch).
Test plan