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Converting group to pseudo atom in the standardization
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cd2002

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Link to postPosted: Thu Sep 23, 2010 11:37 amPost subject: Converting group to pseudo atom in the standardization Reply with quote

We are facing a new problem about standardization. we set two transform(convert nitro to NO2 pseudo atom and convert azide to N3 pseudo atom) as the method you taught us.  But we found the pseudo atom had an effect to the chiral structure when we made a standardization using jchem for linux(5.3.7). The chiral information was removed. Could you help us to find out which setting  need to be modified.

Thank you very much

The attahced file(contract-1-standardized.sdf was standardized from contract-1.sdf)




 Filename: config.xml    Filesize: 6.48 KB    Downloaded: 90 Time(s)
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 Filename: contract-1-standardized.sdf    Filesize: 8.13 KB    Downloaded: 107 Time(s)
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 Filename: contract-1.sdf    Filesize: 8.04 KB    Downloaded: 103 Time(s)
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Zsolt
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Link to postPosted: Fri Sep 24, 2010 6:22 pmPost subject: Reply with quote

We cannot reproduce the error. I attached  the generated output (out.sdf), it seems fine.

Please let us know which Java version are you using on your system. Use the "java -version" command to identify the Java version.

$ java -version
java version "1.6.0_21"
Java(TM) SE Runtime Environment (build 1.6.0_21-b07)
Java HotSpot(TM) 64-Bit Server VM (build 17.0-b17, mixed mode)

ChemAxon products support only Sun distributed Java versions (see more details in System requirements). If your have a non-Sun distributed Java version, then you have the following options:

A.) Use the JChem installer with bundled Java (jchem-VERSION-linux_with_jre.sh). In this case, installer and installed components will use the bundled Sun Java.

B.) Install a Sun distributed Java to your machine and prefer this Java version in your PATH.

Let us know if this solves the problem.

Regards,
Zsolt




 Filename: out.sdf    Filesize: 8.13 KB    Downloaded: 87 Time(s)
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cd2002

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Link to postPosted: Mon Sep 27, 2010 11:28 amPost subject: Reply with quote

 

Zsolt wrote:

We cannot reproduce the error. I attached  the generated output (out.sdf), it seems fine.

Please let us know which Java version are you using on your system. Use the "java -version" command to identify the Java version.

$ java -version
java version "1.6.0_21"
Java(TM) SE Runtime Environment (build 1.6.0_21-b07)
Java HotSpot(TM) 64-Bit Server VM (build 17.0-b17, mixed mode)

ChemAxon products support only Sun distributed Java versions (see more details in System requirements). If your have a non-Sun distributed Java version, then you have the following options:

A.) Use the JChem installer with bundled Java (jchem-VERSION-linux_with_jre.sh). In this case, installer and installed components will use the bundled Sun Java.

B.) Install a Sun distributed Java to your machine and prefer this Java version in your PATH.

Let us know if this solves the problem.

Regards,
Zsolt

Hi, I  Use the JChem installer with bundled Java (jchem-5.3.7-linux_with_jre.sh),

linux-wim4:~ # java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01, mixed mode)

java code:

String molfiles = request.getParameter("molfile");
Standardizer sta = new Standardizer(new File("config.xml"));
Molecule mols=MolImporter.importMol(molfiles);
Molecule molfilea=sta.standardize(mols);

String molfile=molfilea.toFormat("MRV");

When  put the molfile into database, it has such problems。

Thanks!

Zsolt
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Link to postPosted: Mon Sep 27, 2010 1:33 pmPost subject: Reply with quote

cd2002 wrote:

When  put the molfile into database, it has such problems。

So the error occurs only if  molecules are read from database?

Could you run the Standardizer command line application on your system, and post here the output (out.sdf)?

standardize -c config.xml contract-1.sdf -f sdf -o out.sdf

 Zsolt

cd2002

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Link to postPosted: Tue Sep 28, 2010 9:12 amPost subject: Reply with quote

Zsolt wrote:
cd2002 wrote:

When  put the molfile into database, it has such problems。

So the error occurs only if  molecules are read from database?

Could you run the Standardizer command line application on your system, and post here the output (out.sdf)?

standardize -c config.xml contract-1.sdf -f sdf -o out.sdf

 Zsolt

Hi, Zsolt

Thanks for your suggest.

Our purpose was that the structure can be input into the structure database one by one after it was standardized using the above java code, rather than all the standardized structures were output as SDF.  I forget to say that the structure was saved in the database in mrv format.

Could you test if the error can be reproduced by standardizing the structure in mrv format? Is there  some bug with "Pseudo Transform"?

 




 Filename: contract-1.mrv    Filesize: 15.08 KB    Downloaded: 91 Time(s)
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Zsolt
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Link to postPosted: Wed Sep 29, 2010 12:36 pmPost subject: Reply with quote

Hi,

We can reproduce the bug now. The error occurs if the input structures are in mrv format (see outFromMrv.mrv). If the input comes from sdf file, then the result is correct (see outFromSdf.mrv). The output format does not matter.

$ standardize -c config.xml contract-1.mrv -f mrv -o outFromMrv.mrv

$ standardize -c config.xml contract-1.sdf -f mrv -o outFromSdf.mrv

We will fix the error, the fix can be expected in JChem 5.4.1 (maybe earlier).

Workaround: convert the structures to sdf before standardization.

Note: the error occurs only if there are pseudo atom transforms in the Standardzier config

Zsolt




 Filename: outFromSdf.mrv    Filesize: 15.21 KB    Downloaded: 81 Time(s)
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 Filename: outFromMrv.mrv    Filesize: 13.45 KB    Downloaded: 112 Time(s)
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cd2002

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Link to postPosted: Mon Mar 14, 2011 7:45 amPost subject: Reply with quote

Zsolt wrote:

Hi,

We can reproduce the bug now. The error occurs if the input structures are in mrv format (see outFromMrv.mrv). If the input comes from sdf file, then the result is correct (see outFromSdf.mrv). The output format does not matter.

$ standardize -c config.xml contract-1.mrv -f mrv -o outFromMrv.mrv

$ standardize -c config.xml contract-1.sdf -f mrv -o outFromSdf.mrv

We will fix the error, the fix can be expected in JChem 5.4.1 (maybe earlier).

Workaround: convert the structures to sdf before standardization.

Note: the error occurs only if there are pseudo atom transforms in the Standardzier config

Zsolt

Hi,

We are glad to find Jchem 5.4.1 had been released, but this error is still exist. If the MRV file was input for standardized, the chiral information was removed with N3 or NO2 pseudo atom.  Could you fix this error? we are planning to upgrade the version of Jchem when we got a satisfying version. Thank you very much

Zsolt
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Link to postPosted: Wed Mar 16, 2011 11:19 amPost subject: Reply with quote

This bug will be fixed in JChem 5.5, it will be released in April 2011. Sorry for the inconvenience, it took more time to fix the issue than we expected.

Zsolt

cd2002

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Link to postPosted: Tue May 31, 2011 10:51 amPost subject: Reply with quote

Zsolt wrote:

This bug will be fixed in JChem 5.5, it will be released in April 2011. Sorry for the inconvenience, it took more time to fix the issue than we expected.

Zsolt


Hi, We downloaded the JChem 5.5 and was disappointed to find we can not standardize the structure with N3 and NO2 and other special structure.  Those structures can be stanardized in old version. The chiral problem is still existed. Could you help us to deal with them?




 Filename: error.txt    Filesize: 915 Bytes    Downloaded: 83 Time(s)
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 Filename: 20110314.xml    Filesize: 6.79 KB    Downloaded: 50 Time(s)
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 Filename: Structures.mrv    Filesize: 30.08 KB    Downloaded: 51 Time(s)
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Zsolt
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Link to postPosted: Fri Jun 10, 2011 5:42 pmPost subject: Reply with quote

Hi,

The original bug was fixed. JChem 5.5 generates the same output for MRV and SDF inputs:

$ standardize -c config.xml contract-1.mrv -f mrv -o outFromMrv.mrv

$ standardize -c config.xml contract-1.sdf -f mrv -o outFromSdf.mrv

cd2002 wrote:


Hi, We downloaded the JChem 5.5 and was disappointed to find we can not standardize the structure with N3 and NO2 and other special structure.  Those structures can be stanardized in old version. The chiral problem is still existed. Could you help us to deal with them?
 

Unfortunately it's a different bug: the created structures cannot be exported to MRV format. If the output format is SDF, then  the output is created.

$ standardize -c 20110314.xml Structures.mrv -f sdf -o out.sdf

I attached the output (out.sdf). It's still not correct, so we do not recommend converting groups to pseudo atoms, and then converting them back to groups using the "Alias To  Group" action (this was a workaround we suggested earlier). We will implement a Standardizen action that can convert the selected parts of the molecule (given as a substructure query) into groups in one step.

Sorry for the late answer.

Zsolt




 Filename: out.sdf    Filesize: 19.44 KB    Downloaded: 47 Time(s)
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cd2002

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Link to postPosted: Tue Jun 14, 2011 9:44 amPost subject: Reply with quote

Thank a lot

Our purpose is to standardize various type of N3, NO2 to a same type in MRV file. In order to display more beautifully, the N3, NO2 will be displayed as contract group. Certainly, the property of structure must be kept  no changed. Could you help us to recommend the suitable method? will we need to wait for the next version?

Thank very much for help

Zsolt
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Link to postPosted: Thu Jun 30, 2011 9:52 amPost subject: Reply with quote

cd2002 wrote:

Our purpose is to standardize various type of N3, NO2 to a same type in MRV file. In order to display more beautifully, the N3, NO2 will be displayed as contract group. Certainly, the property of structure must be kept  no changed. Could you help us to recommend the suitable method? will we need to wait for the next version?

Yes, you will have to wait for JChem 5.7 version.

Zsolt

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