2 problems upgrading my web page from Marvin 3.3.2 to 3.5.1

Hi


On our Intranet site, we are using MarvinSketch.





As recommended by you in another post in this forum, I am trying to upgrade the version of Marvin in use from 3.3.2 to 3.5.1





However, there are two problems I have seen so far, which are making this not possible. Both of problems issues were not a problem using version 3.3.2





PROBLEM ONE


The first problem is that if the user specifies the SMARTS property Hydgrogen Count on an atom, this is not preserved in the Applet when the user returns to the Search page. All of the other SMARTS properties (Ring count, Ring Size, Connections and Valency) seem to be preserved OK. I have included the HTML which the client receives at the end of this message, and this shows that the SMARTS are still set in the applet parameter.





The way the application works is that client script runs on the search page when the user presses the search button. This client vbscript extracts the drawn molecule using this code





form1.hiddenSMILES.value = document.applets(0).getMol("SMARTS:a")'aromaticise


form1.hiddenMolFile.value = document.applets(0).getMol("mol")





and stores it in two formats - SMILES/SMARTS and the molfile. These are stored in hidden fields on the form.





When the user returns to the search page, the structure they had drawn is set by one of the applet parameters using server side code. I had to do this, rather than using client script to set the applet molecule, because there is no way for client script to detect when the applet has finished its initialisation.





I think problem one is something to do with the following - using version 3.3.2, I used the client script getMol("SMILES:a"), and this produced for example [C;H0] which was OK. If you used getMol("SMARTS:a"), this produced [CH0]. This only happened with Hydrogen count - all the other SMARTS produced for example [CR0] regardless of which parameter you passed to the getMol method.





However, using getMol("SMILES:a") in 3.5.1 does not work if the molecule contains SMARTS (it returns an empty string), so you have to use "SMARTS:a" all the time.





PROBLEM TWO


The second problem is that specifying the applet parameter CleanOpts, which using version 3.3.2 I had set to "e", now causes an error. If you take out the


parameter altogether, the error goes away, but I need to set this parameter. If I do not, then, as you have documented on your webstite, the applet does not behave


correctly where the E/Z stereochemistry around a double bond is unknown. Instead of marking it as unknown, it marks it either as E or Z. I have included the error stack trace at the end of this message.





Thanks


Mark





Applet HTML follows (showing that mol parameter still shows the hydrogen count, but the Marvin applet does not display it)





<APPLET id=Sketcher codeBase=../marvin_3.5.1/ height=350 archive=jmarvin.jar width=550 code=JMSketch name=MarvinSketch VIEWASTEXT>


<PARAM NAME="preload" VALUE="SmilesExport">


<PARAM NAME="molbg" VALUE="#ffffff">


<PARAM NAME="mol" VALUE="\ Marvin 12090417552D\\ 1 0 0 0 0 0 999 V2000\ -0.2187 0.8750 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0\M MRV SMA 1 [CH0]\M END\">


<PARAM NAME="background" VALUE="#ffffff">


<PARAM NAME="implicitH" VALUE="heteroterm">


<PARAM NAME="explicitH" VALUE="true">


<PARAM NAME="chiralitySupport" VALUE="all">


<PARAM NAME="ezVisible" VALUE="true">


<PARAM NAME="atomStrings" VALUE="smarts">


<PARAM NAME="reactionSupport" VALUE="false">


<PARAM NAME="molFormat" VALUE="mol">


<PARAM NAME="importConv" VALUE="">


<PARAM NAME="queryAtoms" VALUE="any,arom,conn,H,hetero,list,notlist,rings,srs,val">


<PARAM NAME="tmpls0" VALUE=":Generic:chemaxon/marvin/templates/generic.t">


<PARAM NAME="tmpls1" VALUE=":Rings:chemaxon/marvin/templates/rings.t">


<PARAM NAME="tmpls2" VALUE=":Amino acids:chemaxon/marvin/templates/aminoacids.t">


<PARAM NAME="tmpls3" VALUE=":Polycyclics:chemaxon/marvin/templates/polycyclics.t">


<PARAM NAME="tmpls4" VALUE=":Custom:chemaxon/marvin/templates/custom.t">


<PARAM NAME="tmpls5" VALUE=":Alpha-D-Sugars:chemaxon/marvin/templates/ADSUGAR.t">


<PARAM NAME="tmpls6" VALUE=":Aromatics:chemaxon/marvin/templates/aromatics.t">


<PARAM NAME="tmpls7" VALUE=":Bases:chemaxon/marvin/templates/bases.t">


<PARAM NAME="tmpls8" VALUE=":Beta-D-Sugars:chemaxon/marvin/templates/bdsugar.t">


<PARAM NAME="tmpls9" VALUE=":Bicyclics:chemaxon/marvin/templates/bicyclics.t">


<PARAM NAME="tmpls10" VALUE=":Carbonyls:chemaxon/marvin/templates/carbonyls.t">


<PARAM NAME="tmpls11" VALUE=":Chains:chemaxon/marvin/templates/chains.t">


<PARAM NAME="tmpls12" VALUE=":Crown Ethers:chemaxon/marvin/templates/crown.t">


<PARAM NAME="tmpls13" VALUE=":D-Sugars:chemaxon/marvin/templates/dsugars.t">


<PARAM NAME="tmpls14" VALUE=":Functional Groups:chemaxon/marvin/templates/functional_groups.t">


<PARAM NAME="tmpls15" VALUE=":Fused Rings:chemaxon/marvin/templates/fused_rings.t">


<PARAM NAME="tmpls16" VALUE=":Heterocyclic Rings:chemaxon/marvin/templates/heterocyclic_rings.t">


<PARAM NAME="tmpls17" VALUE=":More Rings:chemaxon/marvin/templates/more_rings.t">


<PARAM NAME="tmpls18" VALUE=":Nitrogen:chemaxon/marvin/templates/Nitrogen.t">


<PARAM NAME="tmpls19" VALUE=":Phosphorous:chemaxon/marvin/templates/Phosphorous.t">


<PARAM NAME="tmpls20" VALUE=":Polycyclics_ISIS:chemaxon/marvin/templates/Polycyclics_isis.t">


<PARAM NAME="tmpls21" VALUE=":Rings_ISIS:chemaxon/marvin/templates/rings_isis.t">


<PARAM NAME="abbrevgroups" VALUE="chemaxon/marvin/templates/mcr.abbrevgroup">


<PARAM NAME="xtmpls" VALUE="chemaxon/marvin/templates/custom.t">


<PARAM NAME="extraBonds" VALUE="arom,any,wedge,either">


(YOU CANNOT SEE A JAVA APPLET HERE)</strong></APPLET>





Error message stack trace follows (showing the result of setting the cleanOpts parameter to "e" in the applet HTML)





java.lang.NullPointerException at chemaxon.marvin.common.UserSettings.d(Unknown Source) at





chemaxon.marvin.common.swing.MolPanel.setClean2dOpts(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.propertyChange(Unknown





Source) at chemaxon.marvin.sketch.swing.SketchPanel.propertyChange(Unknown Source) at





java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source) at chemaxon.marvin.common.swing.m.a(Unknown Source) at





chemaxon.marvin.common.swing.MolPanel.setClean2dOpts(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.propertyChange(Unknown





Source) at chemaxon.marvin.sketch.swing.SketchPanel.propertyChange(Unknown Source) at





java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source) at chemaxon.marvin.common.UserSettings.d(Unknown Source) at





chemaxon.marvin.common.swing.MolPanel.setClean2dOpts(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.z(Unknown Source) at





chemaxon.marvin.sketch.swing.SketchPanel.z(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source) at





chemaxon.marvin.common.swing.MolPanel.init(Unknown Source) at JMSketch.init(Unknown Source) at sun.applet.AppletPanel.run(Unknown Source) at





java.lang.Thread.run(Unknown Source)

Problem 1:


If I understand well you have both SMARTS and Molfile version of the query molecule.


In the earlier version you could export your molecule to SMARTS even if you have specified SMILES export. In the new version you cannot export a molecule to SMILES if it has SMARTS features, that is why you get empty string.


But I found that the problem is in the Molfile Import.


This bug is already fixed. The fix will be included in the next Marvin release.








The PROBLEM 2 must be a bug also, but it is not fixed yet.


I'll send a post here if it is fixed.

Yes I think you understand perflectly.





Just to clarify with Problem 1 - I don't care whether I have to use getMol("SMILES:a") or getMol("SMARTS:a") - I will try SMILES and if this returns empty, try SMARTS if it turns out to be necessary. You have correctly identified that the problem is in the MolFile import from the applet initialisation parameters.





Thanks for your reply.





Mark

About the PROBLEM 2


In the current release, MarvinSketch and MarvinView do not accept "O2e" clean 2D option.


MarvinSketch and MarvinView support only those options which are enumerated as base options in the documentation ( http//www.chemaxon.com/marvin/doc/user/cleanoptions.html ).


Since, "O2e" is not a base option, MarvinSketch drops an exception.





Now, I have modified the code. MarvinSketch/MarvinView accepts also extra cleaning options.


This feature will be available in the next release.