ambit-users Mailing List for AMBIT:Chemical Structure DB&Web Service

Hi Yannick,

I did some tests at my site and the SMIRKS transformation looks to be 
working.
Stereo is preserved in both cases
        smrkMan.setFlagApplyStereoTransformation(true)
and
        smrkMan.setFlagApplyStereoTransformation(false)

Here are the results:
(1) case: smrkMan.setFlagApplyStereoTransformation(true)

  
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 
  -->
C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc2ccc(cc2)C3CC(=O)c4c(cc(cc4O3)O)O)O)O)O.C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O)O1)O)O)O

Here is a web link that depicts the reactant
https://apps.ideaconsult.net/ambit2/depict?search=C%5BC%40H%5D1%5BC%40%40H%5D%28%5BC%40H%5D%28%5BC%40H%5D%28%5BC%40%40H%5D%28O1%29O%5BC%40%40H%5D2%5BC%40%40H%5D%28%5BC%40H%5D%28%5BC%40%40H%5D%28O%5BC%40H%5D2OC3%3DCC%3DC%28C%3DC3%29C4CC%28%3DO%29C5%3DC%28C%3DC%28C%3DC5O4%29O%29O%29C%29O%29O%29O%29O%29O&smarts=#

Here is a web link that depicts the obtained product
https://apps.ideaconsult.net/ambit2/depict?search=C%5BC%40H%5D1%5BC%40%40H%5D%28%5BC%40H%5D%28%5BC%40H%5D%28%5BC%40%40H%5D%28O1%29Oc2ccc%28cc2%29C3CC%28%3DO%29c4c%28cc%28cc4O3%29O%29O%29O%29O%29O.C%5BC%40H%5D1%5BC%40%40H%5D%28%5BC%40H%5D%28%5BC%40H%5D%28%5BC%40%40H%5D%28O%29O1%29O%29O%29O&smarts=#


(2)It also works good enough for this case 
smrkMan.setFlagApplyStereoTransformation(false)
Only one stereo center is lost (9 chiral atom remain out of 10)

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 
  -->  
C[C@H]1[C@@H]([C@H](C([C@@H](O1)Oc2ccc(cc2)C3CC(=O)c4c(cc(cc4O3)O)O)O)O)O.C[C@H]1[C@@H]([C@H]([C@H]([C@H](O)O1)O)O)O

In order to be more helpful to you,
please, can you sent us the java code that performs the reaction 
including the molecule pre-processing and post-processing?

With best regards
Nick



On 2017-06-08 22:38, Yannick .Djoumbou 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

Dear Yannick,

Could you please submit a ticket ?

Yes, AMBIT supports stereochemistry in SMIRKS, including in version 3.0.3.
The current version is 3.1.0-SNAPSHOT in trunk.

Best regards,
Nina

On 9 June 2017 at 00:48, Yannick .Djoumbou <y.d...@gm...> wrote:

> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

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
>
>
>
>
>
>
>
>
>
>

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