Mview error: Molfile cannot be loaded ...

Hi, 

I have many errors for the visualization of big structures with Marvin view 5 and 6 used in a script :

mview_begin("marvin/", 250, 120); //arguments: codebase, width, height

<?php if ($tabstru[$ligdata[$i]["STRU_ID"]]!='') { ?>

mview_param("mol", "<?php echo $tabstru[$ligdata[$i]["STRU_ID"]];?>");

<?php } ?>

mview_param("molbg", "#ffffff");

mview_param("rendering", "wireframe");

mview_end();

ERROR: 

Molfile cannot be loaded because an error occured:

chemaxon.formats.MolFormatException: Error parsing SMILES string 'CC(=O)OC[C@H]1O[C@@H](Oc2ccc(cc2)C2=C3C=CC(=N3)C(c3ccc(O[C@@H]4O[C@H](COC(C)=O)[C@@H](O[C@H]5O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]5OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)cc3)=c3ccc4=C(C5=NC(C=C5)=C(/c5cccn5[Mn](Cl)n34)c2ccc(O[C@@H]3O[C@H](COC(C)=O)[C@@H](O[C@H]4O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)[C@H](OC(C)=O)[C@H]3OC(C)=O)cc2)c2ccc(O[C@@H]3O[C@H](COC(C)=O)[C@@H](O[C@H]4O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)[C@H](OC(C)=O)[C@H]3OC(C)=O)cc2)[C@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H]1O[C@H]1O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]1OC(C)=O |r,c:16,18,20,85,87,t:76,80,82|' at character 215 ('')

#ffffffffffffffff

STACK TRACE:

chemaxon.formats.MolFormatException: Error parsing SMILES string 'CC(=O)OC[C@H]1O[C@@H](Oc2ccc(cc2)C2=C3C=CC(=N3)C(c3ccc(O[C@@H]4O[C@H](COC(C)=O)[C@@H](O[C@H]5O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]5OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)cc3)=c3ccc4=C(C5=NC(C=C5)=C(/c5cccn5[Mn](Cl)n34)c2ccc(O[C@@H]3O[C@H](COC(C)=O)[C@@H](O[C@H]4O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)[C@H](OC(C)=O)[C@H]3OC(C)=O)cc2)c2ccc(O[C@@H]3O[C@H](COC(C)=O)[C@@H](O[C@H]4O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]4OC(C)=O)[C@H](OC(C)=O)[C@H]3OC(C)=O)cc2)[C@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H]1O[C@H]1O[C@H](COC(C)=O)[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]1OC(C)=O |r,c:16,18,20,85,87,t:76,80,82|' at character 215 ('')

at chemaxon.marvin.io.formats.smiles.SmilesImport.a(Unknown Source)

at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(Unknown Source)

at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(Unknown Source)

at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readStructure(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.a(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.b(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)

at chemaxon.marvin.util.MolLoader.a(Unknown Source)

at chemaxon.marvin.util.MolLoader.run(Unknown Source)

at chemaxon.marvin.common.swing.MolPanel.startLoader(Unknown Source)

at chemaxon.marvin.view.swing.ViewPanel.startstop(Unknown Source)

at chemaxon.marvin.applet.AbstractMarvinApplet$3.run(Unknown Source)

at java.awt.event.InvocationEvent.dispatch(Unknown Source)

at java.awt.EventQueue.dispatchEventImpl(Unknown Source)

at java.awt.EventQueue.access$200(Unknown Source)

at java.awt.EventQueue$3.run(Unknown Source)

at java.awt.EventQueue$3.run(Unknown Source)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)

at java.awt.EventQueue.dispatchEvent(Unknown Source)

at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.awt.EventDispatchThread.run(Unknown Source)

Hi,

The smiles in the error message is not the same as in the end of the document.

Could you double check it and send the one which you would like to import, please?

If it is confidential, please send it to my email address directly.

Thank you,

Efi

Hi, 

the smiles in the error message is coming from the cd_smiles column

The original smiles from the structure is  well :

Cl[Mn]1N2C3=CC=C2\C(=C2\C=CC(=N2)\C(\C2=CC=C(C=C2)O[C@@H]2O[C@H](COC(=O)C)[C@@H](O[C@H]4O[C@H](COC(=O)C)[C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]4OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)=C2\C=C/C(/N12)=C(/C1=N/C(/C=C1)=C3/C1=CC=C(C=C1)O[C@@H]1O[C@H](COC(=O)C)[C@@H](O[C@H]2O[C@H](COC(=O)C)[C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)C1=CC=C(C=C1)O[C@@H]1O[C@H](COC(=O)C)[C@@H](O[C@H]2O[C@H](COC(=O)C)[C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)C1=CC=C(C=C1)O[C@@H]1O[C@H](COC(=O)C)[C@@H](O[C@H]2O[C@H](COC(=O)C)[C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C

Hi!

   After I have discussed it with JChem Team I was informed that cd_smiles is an internal use only column, that should not be used this way. If you want to use the source you have added to the table you should use cd_structure column.

   It would be much better if you have chosen to use any export options of JChem. These tables are only for representation of our inner structures, and various things can happen with the seem-to-be plain text data according to the current Java version and the type of the database table. 

   In the error message it complains about the 215th character which is an invisible control character that might be visible for PHP or the Database but would be removed with the built-in Java connector.

   Inserting the source of the smiles string to "mol" param, or linking this source through a file both has been acceptable for Marvin View without any problem. It is also possible that somehow the PHP script or the database connector left this unwanted control character inside the stream.

   I hope I could help.

Regards:
Balázs 

I used cd_smiles field because I need the standardized representation of the structure.

The cd_structure field doesn't contain the standardized structure.

cd_smiles does not always contain anything, it depends on various settings. cd_structure holds the structure in the form what you have used to import. However it would be better to use one of the export functions. I forward your request to a JChem expert, who can tell you more about this topic.

Hi,

I close this topic because we discuss the standardization questions in the other topic.

Krisztina