Problem with positive Charged Smiles

Hello,

when we open a SMILEs of a positive charged molecule we got the following exeption:

Molfile cannot be loaded because an error occured:
chemaxon.formats.MolFormatException: Cannot read molecule file.

#ffffffffffffffff

STACK TRACE:
chemaxon.formats.MolFormatException: Cannot read molecule file.
    at chemaxon.formats.MolInputStream.a(Unknown Source)
    at chemaxon.formats.MolInputStream.<init>(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.JMView.createGUI(Unknown Source)
    at chemaxon.marvin.applet.AbstractMarvinApplet.init(Unknown Source)
    at chemaxon.marvin.applet.JMViewLaunch.showApplet(Unknown Source)
    at chemaxon.marvin.applet.AppletLaunch$3.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:241)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: chemaxon.formats.MolFormatException: Cannot recognize format (?)
Unrecognized file contents:
Cc1ccc(OCCN2C(=O)c3cccc(c3C2=O)[N ]([O-])=O)cc1
    at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(Unknown Source)
    at chemaxon.formats.MolInputStream.c(Unknown Source)
    at chemaxon.formats.MolInputStream.a(Unknown Source)
    ... 23 more

 

The original SMILES is:

C(c1cc2ccccc2c2ccccc12)[P+](c1ccccc1)(c1ccccc1)c1ccccc1

and the code is:

<!-- et CODEBASE="js/marvin" ARCHIVE="appletlaunch.jar" CODE="chemaxon/marvin/applet/JMViewLaunch" WIDTH=300 HEIGHT=300>

        <PARAM NAME="mol" VALUE=<%=smiles%> >

        <strong>Your browser does not support the applet tag.</strong>

</app -->

 

How can we fix that Problem?

Thanks for help.

 

Bernd

Hello,

From the stack trace, it seems that it is not the same molecule, its not 

C(c1cc2ccccc2c2ccccc12)[P+](c1ccccc1)(c1ccccc1)c1ccccc1

but instead 

Cc1ccc(OCCN2C(=O)c3cccc(c3C2=O)[N ]([O-])=O)cc1

and the problem is that there is one space after the second nitrogen between the brackets.

Best regards,

Tamas Fazekas-Vigh

Hello tfazekas,

 

i get this Problem too always when the Structure has positive charge ??

like

[O-][N+](=O)c1cc(ccc1Cl)S(=O)(=O)C(F)F

[O-][N+](=O)c1ccc(OCCCl)c(OCCCl)c1 

CC(C1CC1)N(C(=O)c1ccccc1[N+]([O-])=O)c1ccccc1


and the same will happen if we have P+ 


i tried with MolHandler to get a MoleculeObject from Smiles but 
i get the same Result -->  Exception 


ERROR: 
Molfile cannot be loaded because an error occured:
chemaxon.formats.MolFormatException: Cannot read molecule file.

#ffffffffffffffff

STACK TRACE:
chemaxon.formats.MolFormatException: Cannot read molecule file.
    at chemaxon.formats.MolInputStream.a(Unknown Source)
    at chemaxon.formats.MolInputStream.<init>(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.JMView.createGUI(Unknown Source)
    at chemaxon.marvin.applet.AbstractMarvinApplet.init(Unknown Source)
    at chemaxon.marvin.applet.JMViewLaunch.showApplet(Unknown Source)
    at chemaxon.marvin.applet.AppletLaunch$3.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:241)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: chemaxon.formats.MolFormatException: Cannot recognize format (?)
Unrecognized file contents:
Molecule@22df4e2c[16a,16b]
    at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(Unknown Source)
    at chemaxon.formats.MolInputStream.c(Unknown Source)
    at chemaxon.formats.MolInputStream.a(Unknown Source)
    ... 23 more


with best Regards,

Raed 

Ups, this was my fault:

the original smiles was:

Cc1ccc(OCCN2C(=O)c3cccc(c3C2=O)[N+]([O-])=O)cc1

 

but the stack trace show that the plus is replaced by a space with the shown code.

Thanks

 

Bernd

Which Marvin version did you use ? I tried to reproduce your case with 6.1 and 6.0 but it did not threw any exception.

 

 

 

Tamás Fazekas-Vígh 

Hello,

we use 6.1, 6.0 and 5.12..

How did you transfer the SMILES string into the applet?

We saw that we have the correct string in the Page source but during the interpretation of the source in the browser we lost the plus!?

We found some copy and paste problems in the first code example on the threat.

Here the Corrected code:

<applet CODEBASE="js/marvin" ARCHIVE="appletlaunch.jar" CODE="chemaxon/marvin/applet/JMViewLaunch" WIDTH=300 HEIGHT=300>

        <PARAM NAME="mol" VALUE=<%=smiles%> >

        <strong>Your browser does not support the applet tag.</strong>

</applet>

 

 

Thanks for help,

 

Bernd

Hi ,

you can start JavaScript to show the Structure (Molecule) as smiles in MarvinView if it has a positive Charge

without Exception but if you want to show the Structure with Applet and the Structure has a positive Cahrge

you can't do that because you will get an Exception  ?

i tried with it and always i get the same result as i mention Exception, i prefer to use Applet

because if you get Java-update in your Browser JS doesn't work well sometimes.

i speak only about WebApplication e.g JSP (No Swing & AWT or Desktop/-Application).

 

thanks,

Raed

The problem is described here : http://stackoverflow.com/questions/7842547/request-parameter-losing-plus-sign

When we deploy the applet using marvin.js we encode the string what you give to the applet by a param, so the plus sign is not lost, however if you deploy manually within an applet tag this conversion doesn't happen.

I recommend to use marvin.js to deploy the applet, or try to apply the solution mentioned in the stackoverflow link.

Hope this helps,

Tamas Fazekas-Vigh

Hello Tamas Fazekas-Vigh

thanks alot for your Answer, i tried it and it goes well as i read here

http://stackoverflow.com/questions/7842547/request-parameter-losing-plus-sign

 

 

thank you.

Raed