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Polymers extension unclear #8

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merkys opened this issue Feb 2, 2021 · 2 comments
Open

Polymers extension unclear #8

merkys opened this issue Feb 2, 2021 · 2 comments

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@merkys
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merkys commented Feb 2, 2021

This issue has been discussed before, however somewhat inconclusively.

I would intuitively expect C&1&1 meaning a self-bond, i.e., a bond with another repeating unit. Thus, C atom constitutes a monomer with one outgoing and one incoming bond, hence the valence of 2. So I understand C&1&1 as depicting an endless saturated alkane chain. So the polystyrene example is clear to me.

However, I cannot understand the diamond and graphite depictions. Based on the previous example, in c&1&1&1 there are two outgoing and two incoming bonds at each c atom, resulting in valence of 4. Or am I missing something?

Moreover, I cannot locate Daylight (Weininger) proposal for this extension, which is referenced in the OpenSMILES specification. It would be interesting to understand this notation, as it seems quite an elegant way to denote polymeric structures.

@johnmay
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johnmay commented Mar 20, 2022

Looks like a mistake Polystyrene should be

c1ccccc1C&1C&1
c1ccccc1C(*)C* |$;;;;;;;_AP1;;_AP1$,Sg:n:0,1,2,3,4,5,6,8::ht|

but

c1ccccc1C&1&1

is not wrong per-say

c1ccccc1C(*)* |$;;;;;;;_AP1;_AP1$,Sg:n:0,1,2,3,4,5,6::ht|

Which would be polymer like this:

*C(c1ccccc1)C(c1ccccc1)C(c1ccccc1)C(c1ccccc1)*

@johnmay
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johnmay commented Mar 20, 2022

Those are CXSMILES BTW

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