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ghutchis / avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
http://avogadro.cc/
GNU General Public License v2.0
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SMILES import makes cis amide and carbamate bonds #701

Closed ghutchis closed 8 years ago

ghutchis commented 10 years ago

trying to create structures of amides and carbamates via a SMILES import gives back after the create 3D step, compounds which have the amide bonds cis, not trans. The SMILES strings are created in ChemDraw. Pasting back into Chemdraw yields the correct structure. If I instead export out of Chemdraw as a .mol file, then the import and conversion to 3D produced the correct trans isomer.

an example structure I am having issues with is: O=C(O)C@@HCC(NC(C)(C)C)=O

Reported by: *anonymous

ghutchis commented 10 years ago

This was my ticket, Martin Stoermer, seem not to have been logged in when I posted it

Original comment by: vcpmartin

ghutchis commented 10 years ago

This is an ill-formed SMILES. Even if I clean it up a bit:

O=C(O)[C@@H]CC(NC(C)(C)C)=O

There still isn't any stereochemistry on that carbon. It has one bond to the hydrogen, two bonds to the carbons, and then the other bond (for a tetrahedral carbon) is left undefined.

Now, you may have indicated wedges and hashes with ChemDraw, but it'd really help if you had more SMILES that you think cause problems.

And yes, there is specific code to create trans amide bonds. There may be bugs, but I'm not even sure what the code is supposed to do with that string.

Original comment by: @ghutchis