openmolecules.org Forum: Cheminformatics » Visualising SMILES string

Home » DataWarrior » Cheminformatics » Visualising SMILES string

Show: Today's Messages :: Polls :: Message Navigator

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

Sat, 20 March 2021 15:07

thomas
Messages: 747
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

Report message to a moderator

[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

Previous Topic:	Drug Likeness vs Drug Score
Next Topic:	Count # scaffolds by plate ID

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Tue Jun 30 04:16:33 CEST 2026

Total time taken to generate the page: 0.00655 seconds