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Re: Visualising SMILES string [message #1257 is a reply to message #1256]

Sat, 20 March 2021 15:07

thomas
Messages: 742
Registered: June 2014

Senior Member

Hi Angus,

if you replace [*:1] by *, then the atom is interpreted as wildcard query feature, which is drawn as a '?'.
In this case the new molecule is considered as sub-structure rather than as normal structure. The difference is
that a sub-structure may have query features and all unspecified atom valences are not implicitly considered
to be blocked by hydrogen atoms. Therefore, a single bonded oxygen is shown as -O in contrast to -OH in a normal molecule.

DataWarrior makes this distinction, which is not made by most other software, possibly, because the SMILES definition itself does not distinguish between these two structure flavors.

Thomas

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[Message index]

		Visualising SMILES string By: amorrison on Thu, 18 March 2021 10:55
		Re: Visualising SMILES string By: thomas on Sat, 20 March 2021 15:07
		Re: Visualising SMILES string By: amorrison on Sun, 21 March 2021 05:00
		Re: Visualising SMILES string By: thomas on Tue, 23 March 2021 16:38
		Re: Visualising SMILES string By: amorrison on Fri, 26 March 2021 09:31

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