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How to identify chiral compounds in exact structure search
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Rui

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Link to postPosted: Wed Jun 09, 2010 8:28 amPost subject: How to identify chiral compounds in exact structure search Reply with quote

Hi, Chemaxon

I have a urgent question to identify chiral compounds, my customer draw a compound with up chiral as picture one and use exact search, but the result contains compound with down chiral as picture two, now customer expect the result only contains the picture one.

Who can give me some suggestions about it?

thanks in advance!




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 Description:  picture two
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 Filename: one.jpg    Filesize: 2.52 KB    Viewed: 12269 Time(s)
 Description:  picture one
one.jpg
Szabolcs
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Link to postPosted: Wed Jun 09, 2010 8:39 amPost subject: Reply with quote

Hi Zhou,

Your structure has an invalid stereochemistry. Stereochemistry can only be specified on an atom with four different ligands, and in your case the carbon atom has two (implicit) Hydrogens.

Structure Checker in the latest Marvin Sketch already notifies users about this error. See picture attached.

 

This is why searching behaves as there was no stereo specified.

 

Best regards,

Szabolcs




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stereo_error_checker.png
Rui

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Link to postPosted: Wed Jun 09, 2010 8:58 amPost subject: Reply with quote

Hi, Szabolcs

Sorry, the two pictures i just want to describe what I need, now I just want to identify chiral compounds in jchem base api. in other case, if customer want to create a new compound in database, how to know whether this compound already exists in the database?

thanks

Szabolcs
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Link to postPosted: Wed Jun 09, 2010 9:05 amPost subject: Reply with quote

By default, stereochemistry is considered by all search types. However, you can switch it off by the stereoSearchType search option. Please check that this search option is left on default.

See more details here:

https://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html

 

Best regards,

Szabolcs

yao

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Link to postPosted: Wed Jun 09, 2010 9:56 amPost subject: Reply with quote

Szabolcs wrote:

By default, stereochemistry is considered by all search types. However, you can switch it off by the stereoSearchType search option. Please check that this search option is left on default.

See more details here:

https://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html

 

Best regards,

Szabolcs


Hi Szabolcs:

    I  used jchemSearch api to search chiral structure,  but  the result was not i want. 
................................
    ch.setConnection(conn);
   options.setAbsoluteStereo(JChemSearch.ABS_STEREO_ALWAYS_ON);
    options.setStereoModel(JChemSearch.ABS_STEREO_CHIRAL_FLAG);
     jChemSearch.setInfoToStdError(true);
      jChemSearch.setStructureTable(structureTableName);
      jChemSearch.setQueryStructure(mol);
      jChemSearch.setSearchOptions(options);
      jChemSearch.setConnectionHandler(ch);
..................................
    Please give us some code example for search chiral structure.  
    Thank you very much in advance.
 Andy
Szabolcs
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Link to postPosted: Wed Jun 09, 2010 12:12 pmPost subject: Reply with quote

Hi Andy,

This part of the code looks OK, except the constant given for setStereoModel().

See possible values here: http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/SearchOptions.html#setStereoModel%28int%29

 

But I don't think it would cause any problem. Do you have any non-default setting or standardization on your JChem table?

Furthermore, it would also be helpful if you could give an example that does not work.

 

Best regards,

Szabolcs

yao

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Link to postPosted: Thu Jun 10, 2010 7:05 amPost subject: Reply with quote

Hi, Szabolcs,

      Thanks for your answer! 

        Sorry, I still failed.  My Jchem table is created by jchem management, and we already used defalut setting.  Please see pictures as below.

    code:

   ch.setConnection(conn);
   options.setAbsoluteStereo(JChemSearch.ABS_STEREO_ALWAYS_ON);
   options.setStereoModel(JChemSearch.STEREO_MODEL_GLOBAL);
   jChemSearch.setInfoToStdError(true);
   jChemSearch.setStructureTable(structureTableName);
   jChemSearch.setQueryStructure(mol);
   jChemSearch.setSearchOptions(options);
   jChemSearch.setConnectionHandler(ch); ...

    Thanks!

Andy




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 Description:  table[ JChemProperties ]
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 Description:  default setting on jchem management.
one.jpg
Szabolcs
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Link to postPosted: Thu Jun 10, 2010 8:52 amPost subject: Reply with quote

Hi,

Can you confirm that the following two molecules are recognized different:

CC[C@@H](C)O

CC[C@H](C)O

 

Could you attach two example chiral structures that you think are not working correctly?

Thanks,

Szabolcs

Rui

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Link to postPosted: Fri Jun 11, 2010 6:05 amPost subject: Reply with quote

Hi, Szabolcs

there are three compounds in acd database, i use marvinsketch to check these compounds, the last two compounds are error(wedge error). i have no idea about it. This is the ACD data problems, or Marvinsketch check problems? and when i use the first compound for the exact search condition, it returns these three compounds.




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 Description:  acd data
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Volfi
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Link to postPosted: Fri Jun 11, 2010 6:45 pmPost subject: Reply with quote

Hi,

Actually we treat phosphanes and amines in the same category in question of chirality:

These atoms are under normal circumstances not stereocenters since they are flexible enough to invert but if the N or P atom itself is in ring and all its' ligands are also in ring (smaller than size 12) this flexibility vanish.

So the wedge information in the given compounds are neglected.

Andras

Rui

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Link to postPosted: Sat Jun 12, 2010 3:38 amPost subject: Reply with quote

Hi, Andras

thanks for your reply, and then how to identify these three compounds by exact search?

 

Eric

Szabolcs
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Link to postPosted: Mon Jun 14, 2010 7:53 amPost subject: Reply with quote

Hi Eric,

András's post means that JChem identifies all above three phosphane molecules as equivalent. Currently there is no way to distinguish them by searching.

 

Best regards,

Szabolcs

Volfi
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Link to postPosted: Mon Jun 14, 2010 9:31 amPost subject: Reply with quote

Hi Eric,

Do you have some information about the thermal stability of these compounds?

As we found that IUPAC also assigns chirality for such compounds we consider to support chirality for Phosphanes in the next major release.

All the best

Andras

Rui

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Link to postPosted: Thu Jun 17, 2010 2:27 amPost subject: Reply with quote

Hi, Andras

I am sorry, i have no information about it. thanks for your reply.

I very much hope that early to see the next major version :)

Eric

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