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Fragment cannot be converted to 2D structural [message #1365] Tue, 03 August 2021 05:28 Go to next message
dreamfly is currently offline  dreamfly
Messages: 1
Registered: August 2021
Junior Member
Hi,
When I converted fragment to 2D structural,the cell was blank. But the fragment can be converted to 2D structural rightly in the MarvinSketch19.21.The fragment smiles is "[*:1]Nc1cnc(OC)cc1C(=O)NC" and I've attached images of the error.

Thanks in advance!

Dreamfly

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Re: Fragment cannot be converted to 2D structural [message #1377 is a reply to message #1365] Thu, 19 August 2021 20:27 Go to previous message
thomas is currently offline  thomas
Messages: 722
Registered: June 2014
Senior Member
till recently DataWarrior didn't support SMARTS features and it will never fully implements SMARTS, because some of DataWarrior's query features cannot be expressed in SMARTS and some SMARTS query features are not compatible with DataWarrior. However, very recently DataWarrior's SMILES support was extended to some SMARTS features. Soon exclude groups will be translated into negated recursive SMARTS. This will also work backwards.

When pasting your example "[*:1]Nc1cnc(OC)cc1C(=O)NC" into the DataWarrior 5.5.0, then I get one row with structure. If I paste it into the editor, then it is also correctly translated into a substructure with the exception that the ':'-bond converted into a single bond. With the SMARTS support ':'-bonds will be translated into an 'aromatic' bond query feature.

Expect this to happen very soon...

Thomas

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