JChem does not recognize the following smiles

Marvin has difficulty interpreting the following smiles. For example, the first smiles plotted fine with ChemDraw (See attached picture), also fine with Daylight. Marvin complains: Ring (2) formed from two neighboring atoms ... The smiles looks fine when I hand trace it.





I check all smiles with Daylight, they all can be depicted.





C(C1(C=C(C2=CC=1)OC)C(C(C3=CNC4=C3C=C(C=C4)CC(CC5)C(N5CCC)=O)2C)CC)(=O)OC


C([C@@]1(N(C([C@@]2([H])N3OC4CCCCC4)=O)[C@@]2(SC1(C)(C)3C5N=C(SC=5)N)[H])NC(CCCCCCCCCCCCCCC)=O)(=O)OC(OC(C6C=CC=CC=6)=O)NC(CN)=O.[H]Cl


N1(C(=C2N=CC1)C3C(=CC(=CC=3Cl)Cl)Cl)(C(C4C(=CC=CN=4)OC(N(C)C)=O)2C)I


N1(C(C2C13C(CCCC3)=O)=O)[Si](O[Si](C(C)C)2C(C)C)(C(C)C)C(C)C


N1(C(C2C13CCCCC3)=O)[Si](O[Si](C(C)C)2C(C)C)(C(C)C)C(C)C


N1([C@@H](CCC1)C(=O)NCC2(CC(N3CC2)C(CCC)=O)N(N(C)3NC(=O)OC(C)(C)C)C(=O)OC(C)(C)C)S(=O)(=O)C4C(=C(C(=CC=4)Cl)COC5C=CC=C6C=5N=C(C=C6)C)Cl


[Bi+]1([Si](C(=O)N1NC2=O)(C34NC([Si](C[Si](C(=O)N5)(C)C)4C)=O)C56NC([Si](C[Si]2(C)C)6C)=O)NC([Si](C)3C)=O


[Bi]1([Si](C(=O)N1NC2=O)(C34NC([Si](C[Si](C(=O)N5)(C)C)4C)=O)C56NC([Si](C[Si]2(C)C)6C)=O)NC([Si](C)3C)=O


[Na+].C(N(C(=S)N12C3C=CC=CC=3)CC)(C(C=N(C4)OC5C4=CC=CC=5)2CCCS(=O)(=O)[O-])C1=O


[Na+].[Na+].C(N(C(=S)N12C3C=CC=CC=3)CC(=O)[O-])(C(C=N(C4)OC5C4=CC=CC=5)2CCCS(=O)(=O)[O-])C1=O


[Sn]1([Si](C(=O)N1)(C23NC4=O)C)([Si](C(=O)N3)(C[Si]4(C)C)C)NC([Si](C)2C)=O

I too noticed that sometimes I can't paste SMILES into Marvin. Yet, the web application generates an image from this SMILES. Is this problem limited to pasting operation or there are there SMILES that are problematic in general?

Thank you for the report, we will investigate these errors ASAP.

Thank you for the report.


The bug is fixed. The next release will contain the fix.

Could you send the SMILES which cannot be pasted?

At the moment I can't give you any additional SMILES. But none from the in the original post can be pasted. When I will encounter any new strings that don't work I will post here.

Yes sure.


It was a bug. We have fixed it.


If smiles import is not successful then the paste doesn't work also.


You can test your smiles easily with the molconvert application.


molconvert smiles something.smi


(see http://www.chemaxon.com/product/molcon.html )

I am also having problems pasting SMILES into the web-based Marvin application, even something as simple as "C".  The stand-alone version works (5.1.2).  Can anyone help?

Hi Erin,

I can paste SMILES in Marvin applets without any problem. Would you please try this functionality on the following page as well?

http://www.chemaxon.com/marvin/sketch/index.jsp

Please inform me whether it works or not.

Thank you and best regards,

Akos

 

Hi, Akos.

That was what I had referred to in my original post.  I can also paste SMILES in Marvin applets (stand-alone, on local computer), but it does not work (and has not worked) on the link you provided.

 

akospapp wrote:

Hi Erin, I can paste SMILES in Marvin applets without any problem. Would you please try this functionality on the following page as well? http://www.chemaxon.com/marvin/sketch/index.jsp Please inform me whether it works or not. Thank you and best regards, Akos

 

Being curious, I tried it. The paste really does not work there. BTW, the applet is quite slow.

Even if I draw a structure, select, Ctrl+C to copy, then Ctrl+V does not do anything.

After doing a little searching, it appears that a Java error may be causing the problem:

Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
 at chemaxon.marvin.util.ClipboardHandler.getDataFromClipboardOLE(Unknown Source)
 at chemaxon.marvin.util.ClipboardHandler.getObjectFromClipboard(Unknown Source)
 at chemaxon.marvin.common.swing.MolPanel.getMClipboardMol(Unknown Source)
 at chemaxon.marvin.sketch.swing.SketchPanel.d(Unknown Source)
 at chemaxon.marvin.sketch.swing.SketchPanel.doPaste(Unknown Source)
 at chemaxon.marvin.sketch.swing.actions.PasteAction.actionPerformed(Unknown Source)
 at chemaxon.marvin.uif.module.support.ShortcutBinding$DelegatingAction.actionPerformed(Unknown Source)
 at javax.swing.SwingUtilities.notifyAction(Unknown Source)
 at javax.swing.JComponent.processKeyBinding(Unknown Source)
 at javax.swing.JComponent.processKeyBindings(Unknown Source)
 at javax.swing.JComponent.processKeyEvent(Unknown Source)
 at java.awt.Component.processEvent(Unknown Source)
 at java.awt.Container.processEvent(Unknown Source)
 at java.awt.Component.dispatchEventImpl(Unknown Source)
 at java.awt.Container.dispatchEventImpl(Unknown Source)
 at java.awt.Component.dispatchEvent(Unknown Source)
 at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
 at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)
 at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Source)
 at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)
 at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
 at java.awt.Component.dispatchEventImpl(Unknown Source)
 at java.awt.Container.dispatchEventImpl(Unknown Source)
 at java.awt.Component.dispatchEvent(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)

I just upgraded Java 6 SE this morning to version 6, update 13.  However, I experienced the same inability to copy/paste with version 6, update 10.  My co-workers and I did not discover this problem until a few days ago.  Up until that point, we had no problems at all.

Hi Erin,

What kind of browser do you use? IE6?

Best regards,

Akos

Hi, Akos.

I am currently using Internet Explorer 7.0.5730.11.  I have not tried accessing Marvin in any other browser, but a co-worker informs me that he experienced the same error in Google Chrome.

 

akospapp wrote:

Hi Erin, What kind of browser do you use? IE6? Best regards, Akos

 

Hi Yingyao,

Do you also use java 1.6.0_13?

I try to identify the source of the problem (whether it is connected to java or the browser or their combination), because I do not have any problem with the copy/paste on that page.

Best regards,

Akos

 

Hi Erin,

I've just tried with exactly the same version of IE you use, and copy/paste worked perfectly. The only difference now is that I use java 1.6.0_11, so we will investigate the issue with java 1.6.0_13 as well.

Best regards,

Akos

 

Probably, there is a compatibility issue between the new Marvin code (5.2.x) and the previously installed (earlier Marvin OLE server). We are debugging the issue and fix it asap.