ambit-users — Ambit users

[Ambit-users] Ambit-Tautomer

[Gerrit M. <ger...@tu...>]

Hi,

 

I am working with the commando line tool of the Tautomer application to generate all possible tautomers (1-3 Proton Shifts) and get the ranking. I’ve used a SDF file as Input and Output. The input file contained 1680 molecules and it led to a new file, that contains now 3360 entries. The first 1680 entries contain an entry for the rank and in all all cases the entry is “Original structure”. 

Does it mean that the input structure is the most stable one? It seems kind of suspicious, that all input strcutures are the most stable one.

 

Is there a way to get the specific energy values, which the algorithm uses?

 

Thanks in advance and best regards,

Gerrit

 

 

[Ambit-users] how to encode in RDF that a compound or substance is mentioned in some article?

[Egon W. <ego...@gm...>]

Hi all,

I'm doing text mining for JRC representative nanomaterials, and need a
way to encode that a compound/substance is discussed in some
(research) article... I know how AMBIT (for eNanoMapper, at least) can
link assay data to a publication, but not sure how to do this for a
compound/substance itself... I now have:

    ex:M17 cito:isDiscussedBy pmc:PMC5450058 .

Basically, I have two questions:

1. does AMBIT already support something like this?
2. if not, how would AMBIT store this information in its data model?

The latter is relevant as it would allow me to hack up a patch...

Egon

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

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

[Nikolay K. <ni...@un...>]

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

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

[Nina J. <jel...@gm...>]

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

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

[Yannick .D. <y.d...@gm...>]

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
>
>
>
>
>
>
>
>
>
>

[Ambit-users] Problems when applying transformations using stereochemistry

[Yannick .D. <y.d...@gm...>]

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

Re: [Ambit-users] Comparing wo reactions

[Nina J. <jel...@gm...>]

Hi Yannick,



On 15 February 2017 at 23:29, Yannick .Djoumbou <y.d...@gm...>
wrote:

> Hi all,
>
> I have a question in regard to SMIRKS. Using AMBIT, is it possible to
>
> 1) take a generic SMIRKS, and a substrate/Product pair and determine is
> the product can be generated from the substrate using the SMIRKS
>

You could just apply the reaction to the substrate, and check if the
products match (by InChI, SMILES, etc)

>
> 2) take 2 SMIRKS for generic reactions and see if they have a parent child
> relation. For instance "aliphatic hydroxylation" would be an instance of
> "hydroxylation". This would be the equivalent of a substructure search for
> chemical reactions.
>

I'm not aware of a generic way to do this. Eventually  Nick may have
 suggestions.

Regards,
Nina

>
> If any of these tasks is possible with AMBIT, what tools can help perform
> those? If not, may be I would have to compare the reactants of one reaction
> to that of the other, as well as their products, etc... Is there another
> tool you are aware of that could help in this regard?
>
> Thank you for your help.
>
>
> Regards,
>
> Yannick
>

Re: [Ambit-users] Comparing wo reactions

[Yannick .D. <y.d...@gm...>]

On Wed, Feb 15, 2017 at 2:29 PM, Yannick .Djoumbou <y.d...@gm...>
wrote:

> Hi all,
>
> I have a question in regard to SMIRKS. Using AMBIT, is it possible to
>
> 1) take a generic SMIRKS, and a substrate/Product pair and determine is
> the product can be generated from the substrate using the SMIRKS
>
> 2) take 2 SMIRKS for generic reactions and see if they have a parent child
> relation. For instance "aliphatic hydroxylation" would be an instance of
> "hydroxylation". This would be the equivalent of a substructure search for
> chemical reactions.
>
> If any of these tasks is possible with AMBIT, what tools can help perform
> those? If not, may be I would have to compare the reactants of one reaction
> to that of the other, as well as their products, etc... Is there another
> tool you are aware of that could help in this regard?
>
> Thank you for your help.
>
>
> Regards,
>
> Yannick
>

[Ambit-users] Comparing wo reactions

[Yannick .D. <y.d...@gm...>]

Hi all,

I have a question in regard to SMIRKS. Using AMBIT, is it possible to

1) take a generic SMIRKS, and a substrate/Product pair and determine is the
product can be generated from the substrate using the SMIRKS

2) take 2 SMIRKS for generic reactions and see if they have a parent child
relation. For instance "aliphatic hydroxylation" would be an instance of
"hydroxylation". This would be the equivalent of a substructure search for
chemical reactions.

If any of these tasks is possible with AMBIT, what tools can help perform
those? If not, may be I would have to compare the reactants of one reaction
to that of the other, as well as their products, etc... Is there another
tool you are aware of that could help in this regard?

Thank you for your help.


Regards,

Yannick

[Ambit-users] [URGENT] Problem connecting to the ambit repository via Maven

[Yannick .D. <y.d...@gm...>]

[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ProjectX
[INFO] ------------------------------------------------------------------------
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/nz/ac/waikato/cms/weka/weka-dev/maven-metadata.xml
[WARNING] Could not transfer metadata nz.ac.waikato.cms.weka:weka-dev/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/tw/edu/ntu/csie/libsvm/maven-metadata.xml
[WARNING] Could not transfer metadata tw.edu.ntu.csie:libsvm/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/net/idea/modbcum/1.0.5-SNAPSHOT/maven-metadata.xml
[WARNING] Could not transfer metadata net.idea:modbcum:1.0.5-SNAPSHOT/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[WARNING] Failure to transfer net.idea:modbcum:1.0.5-SNAPSHOT/maven-metadata.xml from http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots was cached in the local repository, resolution will not be reattempted until the update interval of ambit-plovdiv-snapshots has elapsed or updates are forced. Original error: Could not transfer metadata net.idea:modbcum:1.0.5-SNAPSHOT/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/net/idea/modbcum/1.0.5-SNAPSHOT/modbcum-1.0.5-SNAPSHOT.pom
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/ambit/ambit2-smarts/3.0.0-SNAPSHOT/maven-metadata.xml
[WARNING] Could not transfer metadata ambit:ambit2-smarts:3.0.0-SNAPSHOT/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[WARNING] Failure to transfer ambit:ambit2-smarts:3.0.0-SNAPSHOT/maven-metadata.xml from http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots was cached in the local repository, resolution will not be reattempted until the update interval of ambit-plovdiv-snapshots has elapsed or updates are forced. Original error: Could not transfer metadata ambit:ambit2-smarts:3.0.0-SNAPSHOT/maven-metadata.xml from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed)
[INFO] Downloading: http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots/ambit/ambit2-smarts/3.0.0-SNAPSHOT/ambit2-smarts-3.0.0-SNAPSHOT.pom
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 26.699 s
[INFO] Finished at: 2016-11-22T14:12:13-07:00
[INFO] Final Memory: 9M/245M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project biotransformer: Could not resolve dependencies for project wishartlab:biotransformer:jar:1.0.0-SNAPSHOT: Failed to collect dependencies at net.idea:modbcum:jar:1.0.5-SNAPSHOT: Failed to read artifact descriptor for net.idea:modbcum:jar:1.0.5-SNAPSHOT: Could not transfer artifact net.idea:modbcum:pom:1.0.5-SNAPSHOT from/to ambit-plovdiv-snapshots (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots): Network is unreachable (connect failed) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

Re: [Ambit-users] [URGENT] Issues with my SMIRKS reaction. Need help

[Yannick .D. <y.d...@gm...>]

Hello Nina,
Hello Nick,

I will do so. I was afraid I would have to write two different SMIRKS as a
solution, as this might significantly increase the total number of SMIRKS
in my system.
Again, thanks a lot.

Best regards,

Yannick

On Tue, Sep 13, 2016 at 2:09 AM, Nikolay Kochev <ni...@un...>
wrote:

> Dear Yannick
> If you need to transform/remove/add H atoms in Ambit-SMART it can be done
> only treating them as explicit H atoms. The SMIRKS must define explicitly
> what happens with each H atom.
>
> The indicated implicit H atoms are used only for defining logical
> expression in order to match the substructure (target fragment) that is to
> be transformed according to the SMIRKS.
>
> Here I suggest to you a working solution based on explicit H atoms:
>
> (1) First you need two different SMIRKS for both cases since the H atom
> configuration is different (It is impossible with explicit H managing to
> handle both cases with a single SMIRKS):
>
> (2) Secondly your target molecule must be set with explicit H atoms
>
> (3) here are the SMIRKS for both cases:
>
> [#6;A;H2X4:7]([H:99])([H])!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:
> 4]([#8;X2:2])([#8;A;X2:3][H])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=
> [O;X1:1])[#8;A;X:3][#6;A;H1X4:7]([H:99])!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>
> [#6;A;H2X4:7]([H:99])([H])!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:
> 4]([#8;X2:2])([#8;A;X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[
> O;X1:1])[#8;A;X:3][#6;A;H1X4:7]([H:99])!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>
> Notice that also the explicit H atoms are treated on atom 7
> [#6;A;H2X4:7]([H:99])([H])  because when you close the ring one of the H
> atoms must be removed (i.e. this is the unmapped H atom) the other H atom
> stays (i.e. this is the mapped H atom: [H:99])
>
>
> With best regards
> Nick
>
>
>
>
>
> On 9/12/16 22:29, Yannick .Djoumbou wrote:
>
>
>
> On Sun, Jul 10, 2016 at 7:57 PM, Yannick .Djoumbou <y.d...@gm...>
> wrote:
>
>> Hi all,
>>
>> I have some issues with my SMIRKS manager.
>> have written the SMIKRS below that I am applying on one compounds:
>>
>> [#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])
>> ([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[
>> #8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>>
>>
>> I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
>>  the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
>> negatively charged (case 2). The problem is that in the product, the O3 has
>> a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).
>>
>> The examples are illustrated in the attached file.
>>
>>
>> Could anyone help?
>>
>>
>> Thanks.
>>
>>
>> Regards,
>>
>
>
>

Re: [Ambit-users] [URGENT] Issues with my SMIRKS reaction. Need help

[Nikolay K. <ni...@un...>]

Dear Yannick

If you need to transform/remove/add H atoms in Ambit-SMART it can be 
done only treating them as explicit H atoms. The SMIRKS must define 
explicitly what happens with each H atom.

The indicated implicit H atoms are used only for defining logical 
expression in order to match the substructure (target fragment) that is 
to be transformed according to the SMIRKS.

Here I suggest to you a working solution based on explicit H atoms:

(1) First you need two different SMIRKS for both cases since the H atom 
configuration is different (It is impossible with explicit H managing to 
handle both cases with a single SMIRKS):

(2) Secondly your target molecule must be set with explicit H atoms

(3) here are the SMIRKS for both cases:

[#6;A;H2X4:7]([H:99])([H])!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X2:3][H])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]([H:99])!@-[#6;A;H2X4:6]!@-[#8;X2:5]1

[#6;A;H2X4:7]([H:99])([H])!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]([H:99])!@-[#6;A;H2X4:6]!@-[#8;X2:5]1

Notice that also the explicit H atoms are treated on atom 7 
[#6;A;H2X4:7]([H:99])([H])  because when you close the ring one of the H 
atoms must be removed (i.e. this is the unmapped H atom) the other H 
atom stays (i.e. this is the mapped H atom: [H:99])


With best regards
Nick




On 9/12/16 22:29, Yannick .Djoumbou wrote:
>
>
> On Sun, Jul 10, 2016 at 7:57 PM, Yannick .Djoumbou 
> <y.d...@gm... <mailto:y.d...@gm...>> wrote:
>
>     Hi all,
>
>     I have some issues with my SMIRKS manager.
>     have written the SMIKRS below that I am applying on one compounds:
>
>     [#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>
>
>     I am trying to join two atoms here to form a cycle, The C7 and the
>     O3. In  the reactant,O3 can be linked to a Hydrogen atom (case 1)
>      or can be negatively charged (case 2). The problem is that in the
>     product, the O3 has a valence of 3 (with an implicit H) (case 1),
>     or a valence of 2 (case 2).
>
>     The examples are illustrated in the attached file.
>
>
>     Could anyone help?
>
>
>     Thanks.
>
>
>     Regards,
>
>

Re: [Ambit-users] [URGENT] Issues with my SMIRKS reaction. Need help

[Nina J. <jel...@gm...>]

Yannick,

Could you please file an issue https://sourceforge.net/p/ambit/bugs/ if not
already.

SMIRKS processing has number of updates and cleanups since this spring, do
try to use the version in trunk 3.0.3-SNAPSHOT.

Best regards,
Nina

On 12 September 2016 at 22:29, Yannick .Djoumbou <y.d...@gm...>
wrote:

>
>
> On Sun, Jul 10, 2016 at 7:57 PM, Yannick .Djoumbou <y.d...@gm...>
> wrote:
>
>> Hi all,
>>
>> I have some issues with my SMIRKS manager.
>> have written the SMIKRS below that I am applying on one compounds:
>>
>> [#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])
>> ([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[
>> #8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>>
>>
>> I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
>>  the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
>> negatively charged (case 2). The problem is that in the product, the O3 has
>> a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).
>>
>> The examples are illustrated in the attached file.
>>
>>
>> Could anyone help?
>>
>>
>> Thanks.
>>
>>
>> Regards,
>>
>
>

[Ambit-users] [URGENT] Issues with my SMIRKS reaction. Need help

[Yannick .D. <y.d...@gm...>]

On Sun, Jul 10, 2016 at 7:57 PM, Yannick .Djoumbou <y.d...@gm...>
wrote:

> Hi all,
>
> I have some issues with my SMIRKS manager.
> have written the SMIKRS below that I am applying on one compounds:
>
> [#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])
> ([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[
> #8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>
>
> I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
>  the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
> negatively charged (case 2). The problem is that in the product, the O3 has
> a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).
>
> The examples are illustrated in the attached file.
>
>
> Could anyone help?
>
>
> Thanks.
>
>
> Regards,
>

[Ambit-users] Calculating multiple descriptors

[Patrick O'C. <pat...@ho...>]

Hi


I've got a local machine install up an working and I'm trying to add multiple chemoinformatic descriptors to my imported sdf set.  Unfortunately I'm only able to load one descriptor at a time.  Say I load XlogP, and then when I go to Enhanced functions -> algorithms -> Descriptor calculation -> TPSA,  then when that loads up the XlogP is gone.  I want to calculate a bunch of stuff and then export  the results.  Is there something simple I'm doing wrong?


This is a fantastic program by the way, congrats to the developers [😊]


Regards

Patrick O'Connor

[Ambit-users] Fwd: Issues with my SMIRKS reaction

[Yannick .D. <y.d...@gm...>]

---------- Forwarded message ----------
From: Yannick .Djoumbou <y.d...@gm...>
Date: Sun, Jul 10, 2016 at 7:57 PM
Subject: Issues with my SMIRKS reaction
To: amb...@li..., Nikolay Kochev <ni...@un...>,
Nina Jeliazkova <jel...@gm...>


Hi all,

I have some issues with my SMIRKS manager.
have written the SMIKRS below that I am applying on one compounds:

[#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1


I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
 the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
negatively charged (case 2). The problem is that in the product, the O3 has
a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).

The examples are illustrated in the attached file.


Could anyone help?


Thanks.


Regards,

[Ambit-users] Issues with my SMIRKS reaction

[Yannick .D. <y.d...@gm...>]

Hi all,

I have some issues with my SMIRKS manager.
have written the SMIKRS below that I am applying on one compounds:

[#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1


I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
 the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
negatively charged (case 2). The problem is that in the product, the O3 has
a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).

The examples are illustrated in the attached file.


Could anyone help?


Thanks.


Regards,

[Ambit-users] May you please give me some help on AMBIT?

[TungTX <tun...@gm...>]

Dear colleges,


I am studying nanotoxicity prediction and I just have found that AMBIT is a
good model to start.

I have a connection to the database of AMBIT which is this link:
http://www.oscube.co.kr/ambit2/

I am trying to test an algorithm (Bayes Network learning) on a data-set (
http://www.oscube.co.kr/ambit2/dataset/15). However, I always get the
result "Bad request".

May you please give me some help? Is it possible for me to access some
"Starting Guides" for  modelings and algorithms of AMBIT.

I am really appreciate if I could use your help.

Best wishes,

XuanTung Trinh

[Ambit-users] May you please give me some help on AMBIT?

[TungTX <tun...@gm...>]

Dear colleges,


I am studying nanotoxicity prediction and I just have found that AMBIT is a
good model to start.

I have a connection to the database of AMBIT which is this link:
http://www.oscube.co.kr/ambit2/

I am trying to test an algorithm (Bayes Network learning) on a data-set (
http://www.oscube.co.kr/ambit2/dataset/15). However, I always get the
result "Bad request".

May you please give me some help

[Ambit-users] ERROR 1293 (HY000)

[Sorin S. <Sor...@or...>]

Hi all,

I inherited an ancient Ambit2-appliance running off of a virtualised instance 
of Linux Mint 13, aka Maya.

A few hours ago I set out to update Ambit to run off of our standard 
virtualised Linux environment by using CentOS 6.7 x64.

I found and used the guide available on 
http://ambit.sourceforge.net/install_ambitrest.html.

Managed to install Java, Tomcat and MySQL, and all three work properly.

Next step was to use the script on the above link, and I immediately ran into 
some problems.

Please note that my sql-proficency is pretty basic at best, I can list 
databases, drop them etc., therefore the below error put me pretty much out of 
my league.
Some google searches later I learned that I can't use the same time stamps or 
something to that effect.

root@ambit ~/ [0]# mysql ambit2 -u root -p < ~/Downloads/create_tables.sql
Enter password:
ERROR 1293 (HY000) at line 240: Incorrect table definition; there can be only 
one TIMESTAMP column with CURRENT_TIMESTAMP in DEFAULT or ON UPDATE clause
root@ambit ~/ [0]#

Seems it's the two lines in the "bundle"-table that are the culprits.

`created` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE 
CURRENT_TIMESTAMP,
...
`updated` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,


However, I've no idea how to go about this.

Could somebody with more knowledge please give me a hint to a fix, or maybe 
suggest some further reading in order to fix this?

Thanks.

-- 
BW,
	Sorin
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Re: [Ambit-users] Transforming compounds using SMIRKS and while respecting stereochemistry.

[Nikolay K. <ni...@un...>]

Dear Yannick,

Concerning the stereo-chemistry:

Currently the code does not support the stereo-chemistry transformation 
(e.g. cis/trans double bonds, chirals atoms) due to the poor support of 
the stereo-chemistry in previous CDK versions (1.4.x) since we have just 
recently migrated to cdk 1.5.x. (this is ambit3)
So now the stereo-chemistry can be implemented fully on the base of new 
CDK 1.5.x.
It will take time to do it however. I expect in the following months to 
finish the stereo support.

With best regards
Nick




On 8/5/15 11:59 PM, Yannick .Djoumbou wrote:
> Hi all,
>
> I have an issue with the use of SMIRKS to transform molecules while 
> taking into account the stereochemistry. I have a smarts that depicts 
> a steroid analog carrying a 3-alpha hydroxyl group. I would like to 
> transform molecules matching this constraint, but I realized that 
> AMBIT is transforming any molecule that has the same skeleton depicted 
> in the reactant smarts independent of the stereochemistry (i.e. 
> 3-hydroxy, 3-alpha hydroxy, 3-beta hydroxy). Moreover, the 3D 
> arrangement of other chemical bonds is not conserved in the product.
>
> I use the SMIRKS:
> [#8;H1X2:1]-[#6;H1X4;@@:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1>>[O;X1:1]=[#6;X3;@@:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1
>
> And the function: applyTransformationWithSingleCopyForEachPos
>
> This is the smiles with the 3-alpha-hydroxyl group, the 3-beta-hydroxy 
> group, and a generic 3-hydroxyl group, respectively:
>
> A: CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
>
> B: CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
>
> C: CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4CC(O)CC[C@]4(C)[C@H]3CC[C@]12C
>
> 1) Is it possible get AMBIT to transform only the 3-alpha-hydroxyl 
> bearing compounds based solely on the SMIRKS?  If yes, how?
>
> 2) I used a two step process where I first used CDK's SMARTSQueryTool 
> to do substructure matching and then transformed the molecules that 
> had a match.
>
> 3) One issue I had when using SMIRKS with or without prefiltering was 
> that the resulting structure did not contain any stereochemistry 
> information. The information stored in the input was lost throughout 
> the process.  How do I avoid this?
>
>
> Looking forward to hearing from you.
>
> Thank you for your consideration.
>
>
> Regards,
>
> Yannick

Re: [Ambit-users] Transforming compounds using SMIRKS and while respecting stereochemistry.

[Yannick .D. <y.d...@gm...>]

Hi Nina,

I have updated to the latest snapshot. I still have the same issue.
Hopefully, I will get some help soon.

Thank you.

Best,

Yannick.

On Wed, Aug 5, 2015 at 11:11 PM, Nina Jeliazkova <jel...@gm...>
wrote:

> Yannick,
>
> While waiting for Nick's answer (who's on vacation), please make sure you
> are using the latest 3.0.0-SNAPSHOT
>
>
> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~ambit2-smarts~3.0.0-SNAPSHOT~~
>
> There were a number of SMIRKS-related updates during the last month, and
> judging from your other email you are using an older snapshot.
>
> Best regards,
> Nina
>
> On 5 August 2015 at 23:59, Yannick .Djoumbou <y.d...@gm...> wrote:
>
>> Hi all,
>>
>> I have an issue with the use of SMIRKS to transform molecules while
>> taking into account the stereochemistry. I have a smarts that depicts a
>> steroid analog carrying a 3-alpha hydroxyl group. I would like to transform
>> molecules matching this constraint, but I realized that AMBIT is
>> transforming any molecule that has the same skeleton depicted in the
>> reactant smarts independent of the stereochemistry (i.e. 3-hydroxy, 3-alpha
>> hydroxy, 3-beta hydroxy). Moreover, the 3D arrangement of other chemical
>> bonds is not conserved in the product.
>>
>> I use the SMIRKS:
>> [#8;H1X2:1]-[#6;H1X4;@
>> @:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1>>[O;X1:1]=[#6;X3;@
>> @:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1
>>
>> And the function: applyTransformationWithSingleCopyForEachPos
>>
>> This is the smiles with the 3-alpha-hydroxyl group, the 3-beta-hydroxy
>> group, and a generic 3-hydroxyl group, respectively:
>>
>> A:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@
>> ]12C
>>
>> B:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@
>> ]12C
>>
>> C:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4CC(O)CC[C@]4(C)[C@H]3CC[C@]12C
>>
>> 1) Is it possible get AMBIT to transform only the 3-alpha-hydroxyl
>> bearing compounds based solely on the SMIRKS?  If yes, how?
>>
>> 2) I used a two step process where I first used CDK's SMARTSQueryTool to
>> do substructure matching and then transformed the molecules that had a
>> match.
>>
>> 3) One issue I had when using SMIRKS with or without prefiltering was
>> that the resulting structure did not contain any stereochemistry
>> information. The information stored in the input was lost throughout the
>> process.  How do I avoid this?
>>
>>
>> Looking forward to hearing from you.
>>
>> Thank you for your consideration.
>>
>>
>> Regards,
>>
>> Yannick
>>
>
>

Re: [Ambit-users] SMIRKS MANAGER's Flags have to be set using different calls when on Mac compared to Windows.

[Yannick .D. <y.d...@gm...>]

Hi Nina,

Thanks for the reply. We were using the same version already. Well, I have
updated the snapshot version and had to change the code and use setter
functions instead. So, regarding this issue, it's all OK now.

Thank you.

Yannick

On Wed, Aug 5, 2015 at 10:26 PM, Nina Jeliazkova <jel...@gm...>
wrote:

> Yannick,
>
> Could you please ensure you are using the very same AMBIT snapshot .  My
> guess is the ones in MAC are using slightly outdated snapshot. Please note
> ambit.3.0.0-SNAPSHOT is a snapshot, not release, hence you should take care
> of working with the most recent one.
>
> I don't think this is OS issue (We are also using both MacOs and Windows).
>
> Regards,
> Nina
>
>
> On 6 August 2015 at 00:01, Yannick .Djoumbou <y.d...@gm...> wrote:
>
>>
>> ---------- Forwarded message ----------
>> From: Yannick .Djoumbou <y.d...@gm...>
>> Date: Fri, Jun 12, 2015 at 11:28 AM
>> Subject: SMIRKS MANAGER's Flags have to be set using different calls when
>> on Mac compared to Windows.
>> To: amb...@li...
>>
>>
>> Hi guys,
>>
>> I have been using the AMBIT library for a project. My colleague and I and
>> are developing a JAVA-based  application and are peer-programming on
>> Windows and MacOS X, respectively. We have not had any issue so far.
>> However, we realized that when trying to set the flags for the SMIRKS
>> Manager, we have to use a different from one platform to another.
>>
>> After creating a new SMIRKS manager:
>>    new SMIRKSManager(SilentChemObjectBuilder.getInstance());
>>
>> On MacOSX, we have to use:
>>      smrkMan.FlagFilterEquivalentMappings = true;
>>
>> On Windows, we have to use:
>>      smrkMan.setFlagProcessResultStructures(true);
>>
>> This is kind of troublesome since we are peer programming and have to
>> commit/push/pull the code that lies on the same repository.
>>
>> We are using the version 3.0.0 of AMBIT. How can we go around this?
>>
>> Thank you for your consideration.
>>
>> Regards,
>>
>> Yannick
>>
>>
>

Re: [Ambit-users] Transforming compounds using SMIRKS and while respecting stereochemistry.

[Nina J. <jel...@gm...>]

Yannick,

While waiting for Nick's answer (who's on vacation), please make sure you
are using the latest 3.0.0-SNAPSHOT

http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~ambit2-smarts~3.0.0-SNAPSHOT~~

There were a number of SMIRKS-related updates during the last month, and
judging from your other email you are using an older snapshot.

Best regards,
Nina

On 5 August 2015 at 23:59, Yannick .Djoumbou <y.d...@gm...> wrote:

> Hi all,
>
> I have an issue with the use of SMIRKS to transform molecules while taking
> into account the stereochemistry. I have a smarts that depicts a steroid
> analog carrying a 3-alpha hydroxyl group. I would like to transform
> molecules matching this constraint, but I realized that AMBIT is
> transforming any molecule that has the same skeleton depicted in the
> reactant smarts independent of the stereochemistry (i.e. 3-hydroxy, 3-alpha
> hydroxy, 3-beta hydroxy). Moreover, the 3D arrangement of other chemical
> bonds is not conserved in the product.
>
> I use the SMIRKS:
> [#8;H1X2:1]-[#6;H1X4;@
> @:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1>>[O;X1:1]=[#6;X3;@
> @:2]-1-[#6,#8,#7,#16:3]-,=[#6,#8,#7,#16:4]-,=[#6,#8,#7,#16:5]-,=2-,=[#6,#8,#7,#16;A;R2:6](-,=[#6,#8,#7,#16:7]-,=[#6,#8,#7,#16;A;R1:8]-,=[#6,#8,#7,#16;A;R2:9]-,=3-,=[#6,#8,#7,#16;A;R2:10]-,=4-,=[#6,#8,#7,#16;A;R1:11]-,=[#6,#8,#7,#16:12]-,=[#6,#8,#7,#16:13]-,=[#6,#8,#7,#16:14]-,=4-,=[#6,#8,#7,#16:15]-,=[#6,#8,#7,#16;A;R1:16]-,=[#6,#8,#7,#16:17]-,=2-,=3)-,=[#6,#8,#7,#16:18]-1
>
> And the function: applyTransformationWithSingleCopyForEachPos
>
> This is the smiles with the 3-alpha-hydroxyl group, the 3-beta-hydroxy
> group, and a generic 3-hydroxyl group, respectively:
>
> A:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@
> ]12C
>
> B:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@
> ]12C
>
> C:    CO[C@H]1[C@@H](O)C[C@H]2[C@@H]3CC=C4CC(O)CC[C@]4(C)[C@H]3CC[C@]12C
>
> 1) Is it possible get AMBIT to transform only the 3-alpha-hydroxyl bearing
> compounds based solely on the SMIRKS?  If yes, how?
>
> 2) I used a two step process where I first used CDK's SMARTSQueryTool to
> do substructure matching and then transformed the molecules that had a
> match.
>
> 3) One issue I had when using SMIRKS with or without prefiltering was that
> the resulting structure did not contain any stereochemistry information.
> The information stored in the input was lost throughout the process.  How
> do I avoid this?
>
>
> Looking forward to hearing from you.
>
> Thank you for your consideration.
>
>
> Regards,
>
> Yannick
>

Re: [Ambit-users] SMIRKS MANAGER's Flags have to be set using different calls when on Mac compared to Windows.

[Nina J. <jel...@gm...>]

Yannick,

Could you please ensure you are using the very same AMBIT snapshot .  My
guess is the ones in MAC are using slightly outdated snapshot. Please note
ambit.3.0.0-SNAPSHOT is a snapshot, not release, hence you should take care
of working with the most recent one.

I don't think this is OS issue (We are also using both MacOs and Windows).

Regards,
Nina

On 6 August 2015 at 00:01, Yannick .Djoumbou <y.d...@gm...> wrote:

>
> ---------- Forwarded message ----------
> From: Yannick .Djoumbou <y.d...@gm...>
> Date: Fri, Jun 12, 2015 at 11:28 AM
> Subject: SMIRKS MANAGER's Flags have to be set using different calls when
> on Mac compared to Windows.
> To: amb...@li...
>
>
> Hi guys,
>
> I have been using the AMBIT library for a project. My colleague and I and
> are developing a JAVA-based  application and are peer-programming on
> Windows and MacOS X, respectively. We have not had any issue so far.
> However, we realized that when trying to set the flags for the SMIRKS
> Manager, we have to use a different from one platform to another.
>
> After creating a new SMIRKS manager:
>    new SMIRKSManager(SilentChemObjectBuilder.getInstance());
>
> On MacOSX, we have to use:
>      smrkMan.FlagFilterEquivalentMappings = true;
>
> On Windows, we have to use:
>      smrkMan.setFlagProcessResultStructures(true);
>
> This is kind of troublesome since we are peer programming and have to
> commit/push/pull the code that lies on the same repository.
>
> We are using the version 3.0.0 of AMBIT. How can we go around this?
>
> Thank you for your consideration.
>
> Regards,
>
> Yannick
>
>