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Unable to get the structure of pentaspiro[2.0.24.0.27.0.210.0.213.03]pentadecane #254

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vthimmakondu opened this issue Apr 26, 2024 · 2 comments

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@vthimmakondu
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Hi,

I am unable to get the structure of this molecule, pentaspiro[2.0.24.0.27.0.210.0.213.03]pentadecane, in OPSIN. The error message that I got is as follows: "Disagreement between number of atoms in spiro descriptor: 484 and number of atoms in chain: 15". If I try without superscripts then I get the usual error message like "Bonds must be made between different atoms". But, if I try with superscripts then it says there is a disagreement between number of atoms in spiro descriptor and the total length of the chain.

To me it looks like, if the spiro molecule is highly symmetric then OPSIN is unable to generate the structure. The reason I say so is because, I have also tried to get the structure of tetraspiro[2.0.24.0.27.0.210.03]dodecane. In that case too, I got an error message - "Disagreement between number of atoms in spiro descriptor: 270 and number of atoms in chain: 12".

Any help is appreciated.

Thank you.

@dan2097
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dan2097 commented Apr 27, 2024

Presumably pentaspiro[2.0.2^4.0.2^7.0.2^10.0.2^13.0^3]pentadecane gives the expected structure?

I'll have a look into whether OPSIN can be adjusted to autodetect which numbers were intended to superscripted. If I recall this is implemented for Von Baeyer nomenclature but not spiro nomenclature.

OPSIN supports the following ways of specifying superscripts:

A carat with bracketing e.g. N^(2)
A carat e.g. N^2
Bracketing e.g. N(2)
Using tildes e.g. N~2~
Using stars e.g. N*2*
Using angle brackets e.g. N<2>

@vthimmakondu
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Thank you. But, what I have observed in the past is that OPSIN works without carat with bracketing, carat, tildes, etc.,
image

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