Attachment point handling is not supported for S-groups with

HI there,

We have recently updated our standardisation rules and the chemaxon version to 5.10.0. And we have also updated the associated relational database using the JCHemManager. But there seems to be some issues with the data which was already loaded with the previous versions. One of the issues I see is as below. Can there be an alterntive to fix this type of an issue, without reloading the content?

 

2012-09-04 11:09:31,999 ERROR [http-192.168.55.157-9091-12] chemaxon.jchem.db.JChemSearch.handleQTCError : 6403 : chemaxon.formats.MolFormatException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds

2012-09-04 11:09:32,001 ERROR [http-192.168.55.157-9091-12] chemaxon.jchem.db.JChemSearch.report : 123 : QT search error Query=<?xml version="1.0"?><cml version="ChemAxon file format v5.10.0, generated by v5.10.1">\n<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="" elementType="" x2="" y2=""></atomArray><bondArray></bondArray></molecule></MChemicalStruct></ ... (19 more characters) CD_ID=19840 index=273

chemaxon.formats.MolFormatException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds

at chemaxon.marvin.io.MRecordImporter.readStructure(MRecordImporter.java:775) ~[MarvinBeans-formats-2.0.jar:5.10.1 2012-07-12]

.....

at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2017) [jchem-db-2.0.jar:5.10.1 2012-07-12]

.....

Caused by: java.lang.UnsupportedOperationException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds

at chemaxon.struc.sgroup.SuperatomSgroup.calculateAttachmentPoints(SuperatomSgroup.java:1367) ~[MarvinBeans-2.0.jar:5.10.1 2012-07-12]

at chemaxon.marvin.io.formats.mdl.MolImport.readPropertiesBlockV2(MolImport.java:1621) ~[MarvinBeans-formats.mdl-2.0.jar:5.10.1 2012-07-12]

.....

at chemaxon.marvin.io.MRecordImporter.readStructure(MRecordImporter.java:764) ~[MarvinBeans-formats-2.0.jar:5.10.1 2012-07-12]

... 60 common frames omitted

 

java.lang.RuntimeException: chemaxon.jchem.db.DatabaseSearchException: An error occured for structure with cd_id: 19840

Caused by:

Attachment point handling is not supported for S-groups with more than 2 crossing bonds

at chemaxon.jchem.db.JChemSearch.retrieveBatchAndSearch(JChemSearch.java:5166)

......

at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2017)

. ... 44 more

Caused by: chemaxon.formats.MolFormatException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds

at chemaxon.marvin.io.MRecordImporter.readStructure(MRecordImporter.java:775)

.....

at chemaxon.formats.MolImporter.readMol(MolImporter.java:860)

.....

at chemaxon.jchem.db.JChemSearch.retrieveBatchAndSearch(JChemSearch.java:5151)

... 51 more

Caused by: java.lang.UnsupportedOperationException: Attachment point handling is not supported for S-groups with more than 2 crossing bonds

at chemaxon.struc.sgroup.SuperatomSgroup.calculateAttachmentPoints(SuperatomSgroup.java:1367)

at chemaxon.marvin.io.formats.mdl.MolImport.readPropertiesBlockV2(MolImport.java:1621)

....

at chemaxon.marvin.io.MRecordImporter.readStructure(MRecordImporter.java:764)

... 60 more

 

Thanks,

Isha

Hi Isha, 

Unfortunately we can't represent abbreviations with 3 attachment points at the moment. Before 5.10.0 we imported these structures, but the result was incorrect. We decided not to import these structures until we can handle 3 or more attachment points. 

You have to expand abbreviations with 3 attachment point in an other program.

We are working on the support of such structures, in 5.11.1 (coming in October) we will provide a workaround that will ungroup Sgroups in these structures so we can work with them.  We have planned to support multiple attachment points in 5.12, scheduled to the end of this year.

 

Regards,

Peter

Hi Peter,

 

Can you please elaborate on followin? 

You have to expand abbreviations with 3 attachment point in an other program.

 

How can this be done? 

 

Thanks,

Isha

Hi,

We will create an sdf/molfile import option which will ungroup these (and only
these) sgroups with more than two attachment points and import them.

I hope this workarund is acceptable.

The import option will be included in Marvin 5.10.4.

Hopefully in 5.12 the ungroup option will not be necessary any more
as we will handle these structures properly.

Sorry for the inconvenience.

We have fixed this issue in V2000 sdf and molfiles. Do you use V3000 molfiles as well?

 

 

Thanks for the fix.

We use mostly v2000, but some issues have v3000 files as well.

Can you please let us know when the new version would be available? 

Marvin 5.10.4 release date: 2012.09.12.

Many thanks,

Isha

Hi there,

Has this been released? Can you kindly confirm when it would be available? 

Thanks,

Isha

Hi Isha,

No, not yet. I will inform you.

Janos

JChem 5.10.4 has been released. 

For the list of changes please see:  
http://www.chemaxon.com/jchem/changes.html style="text-align: -webkit-auto; font-size: 14px; line-height: 20px;">   

JChem home:  
http://www.chemaxon.com/jchem/ style="text-align: -webkit-auto; font-size: 14px; line-height: 20px;">   

Download: 
http://www.chemaxon.com/download/jchem/  

volfi wrote:

JChem 5.10.4 has been released.  For the list of changes please see:   http://www.chemaxon.com/jchem/changes.html style="text-align: -webkit-auto; font-size: 14px; line-height: 20px;">    JChem home:   http://www.chemaxon.com/jchem/ style="text-align: -webkit-auto; font-size: 14px; line-height: 20px;">    Download:  http://www.chemaxon.com/download/jchem/

Hello everyone,

I'm using  the lateest released version of marvin beans (5.11.4), But i'm still having problems to export some structures. The message that is returned to me is something like that: (Attachment point handling is not supported for S-groups with more than 2 crossing bonds). 

Attached is the structure that i'm trying to export 

Does Someone have any tip?

Hi,

The problem probably comes from the import of the file. Use the import option "mol:Fsg".

For example:

 

MolImporter mi = new MolImporter(new FileInputStream(fileName), "mol:Fsg");

Molecule mol = mi.read();

mi.close();

 

After import those s-groups will be ungroupped that have more than 2 attachment points.

Best regards,

Domi