Re: [Ambit-users] Problems when applying transformations using stereochemistry

By the way,

 In addition to the information I just sent, I am using ambit 3.0.3.

Best,
Yannick

On Thu, Jun 8, 2017 at 1:38 PM, Yannick .Djoumbou <y.d...@gm...>
wrote:

> Hi all,
>
> I have an issue with the transformation of compounds while handling
> stereochemistry.
>
> I have the following compound CID54424913 (PubChem) with SMILES "C[C@H
> ]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]2[C@@H]([C@H]([C@@H](O[C@H
> ]2OC3=CC=C(C=C3)C4CC(=O)C5=C(C=C(C=C5O4)O)O)C)O)O)O)O)O". I would like to
> transform it, and obtain the product that also has the correct isomeric
> information.
>
> 1) These are the settings for my SMIRKSManager:
>
> this.smrkMan.setFlagApplyStereoTransformation(true); this.smrkMan.
> setFlagCheckResultStereo(true); this.smrkMan.
> setFlagFilterEquivalentMappings(true); this.smrkMan.
> setFlagProcessResultStructures(true);
>
> 2) This is my SMIRKSReaction
>
> "[H:20][#8:9][C@@:5]1([H:18])[C@:6]([H:19])([#8:8]-[#6:23])[#8:7][C@
> @:2]([H:15])([C:1]([H:12])([H:13])[H:14])[C@:3]([H:16])([#8:11][H:22])[C@
> @:4]1([H:17])[#8:10][H:21]>>[H][#8]-[#6:23].[H][#8:8][C@@:6]1([H:
> 19])[#8:7][C@@:2]([H:15])([C:1]([H:12])([H:13])[H:14])[C@:
> 3]([H:16])([#8:11][H:22])[C@@:4]([H:17])([#8:10][H:21])[C@@:
> 5]1([H:18])[#8:9][H:20]".
>
> It implements the removal of the rhamnose moiety from a
> alpha-L-rhamnoside. The compound is a valid substrate, as it matches the
> SMARTS string from the reactant/substrate. When I apply the following
> reaction to the compound, I do not get any result. However, I do get
> results when I set the FlagApplyStereoTransformation to false ( as in
> this.smrkMan.setFlagApplyStereoTransformation(false) ), I get the
> following results:
>
> (a) InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3
> (b) InChI=1S/C21H22O9/c1-9-18(25)19(26)20(27)21(28-9)29-12-
> 4-2-10(3-5-12)15-8-14(24)17-13(23)6-11(22)7-16(17)30-15/
> h2-7,9,15,18-23,25-27H,8H2,1H3
>
> As you can see, the resulting structures do no include any stereochemical
> information at all. In an earlier e-mail exchange a long time ago, I got
> the confirmation that AMBIT now supports stereochemistry in the
> transformations.
>
> Is there anything that I am missing in my settings? If yes, what?
> How can I get the resulting products with stereochemical information?
>
> Thank you for your help.
>
> Best,
> Yannick
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