using marvin applet : returns mol file of created molecule

Dear support,

 

I try to replace JME applet by marvin applet :

Fisrt I have 2 problems :

- the elements table are not represented because of my htaccess rules :

RewriteRule ^.*\.zip sdfile.php [QSA,L]

 

=> all zip files of marvin packages are not read because of the rule (elements.zip)

 

How to do?

 

- second problem that I don't see in your help :

which function to use to return MDL mol file of created (drawn) molecule like with JME (http://www.molinspiration.com/jme/doc/jme_functions.html) : public void JME.molFile(void)

 

Thanks for your help!

 

Kiet TRAN

Dear Kiet TRAN,

we need some time to investigate the first question. It is possible that we have to wait for a colleague who is out of office this week.

For the second question:
we have an API to retrieve the molecule in MOL file format, though it is returned as a String that you can write to a file.

http://www.chemaxon.com/marvin/help/developer/applets/api/JMSketch.html#getMol(java.lang.String)

This is an example of usage, though covers more than you need: http://www.chemaxon.com/marvin/examples/applets/sketch/js_io.html

Kind regards,
Judit

Dear Kiet TRAN,

For the first question i can suggest you to extend your rewriting rules to not match any file in marvin applet package.

If i think well you are using Apache webserver, so you could use a RewriteCond before the rule in your configuration for example like this:

RewriteCond {%REQUEST_URI} !^marvin_applet_package_uriwhere the marvin_applet_package_uri is the relative path from your site's document root to the directory of your Marvin Applet package.

Bets regards,
Istvan

Thank you for your help

The real rule is :

 

RewriteCond %{REQUEST_URI} !marvin

 

and not  : RewriteCond {%REQUEST_URI} !^marvin

 

 

Kiet

In apache log, I have these warning :

 

 File does not exist: /data-dev/abonne/marvin/META-INF
[Wed Jul 22 15:34:51 2009] [error] [client 192.XX] File does not exist: /data-dev/abonne/marvin/META-INF
[Wed Jul 22 15:35:20 2009] [error] [client 192.XX] File does not exist: /data-dev/abonne/marvin/chemaxon/marvin/dict.class
[Wed Jul 22 15:35:20 2009] [error] [client 192.XX] File does not exist: /data-dev/abonne/marvin/plugins/plugins.properties

 (70014)End of file found: mod_mime_magic: read failed /www-data-dev/abonne/marvin/chemaxon/isotopes.data

Have you seen already this log?

Good to hear, thanks for the refinement.

Just a question: if i remember well, the ^ character in regexp matches at the begining of the expression, is it possible that the relative path of your applet package contains special chars, and therfore not matched? If i am right, your RewriteCond will match for any REQUEST_URI contains the string marvin, for example the file example.org/datadir/marvinmolfiles.zip too.

Best regards,
Istvan

About the warning:

The META-INF searching could be a missconfiguration of the codebase for the applet. It should search the META-INF directory in appletlaunch.jar, or in jmarvin.jar depending on the codebase.

The dict.class searched by the classloader, while loading a property file for Marvin.

The plugins.properties file is searched because it is possible to add third party calculator plugins for Marvin, and that file is responsible to contain the third party plugins' properties. More information on this topic can be found at http://www.chemaxon.com/marvin/examples/plugin-integration/index.html

The last error message seems to be an Apache configuration problem, Apache use mime magic to determine mime-types for files, and maybe treats the file somthing else than it is and run into an internal error. Due the mod_mime_magic cause the lack of performace of the webserver, i suggest you to turn mod_mime_magic off unless you do not need it for special ocassions.

Regards,
Istvan

<For the second question:
<we have an API to retrieve the molecule in MOL file format, though it is returned as a String that <you can write to a file.

http://www.chemaxon.com/marvin/help/developer/applets/api/JMSketch.html#getMol(java.lang.String)

<This is an example of usage, though covers more than you need: http://www.chemaxon.com/marvin/examples/applets/sketch/js_io.html

<Kind regards,
<Judit

 

OK it's works :

 

//var smile = document.JME.molFile();
var molfile = document.MSketch.getMol("mol");
document.formulaire.requ_smile.value = molfile;

 

i'm looking for the same function that jmeFile() : (http://www.molinspiration.com/jme/doc/jme_functions.html)

 

    //var jmef = document.JME.jmeFile();
    var jmef = document.MSketch.setMol();
    document.formulaire.requ_structure.value = jmef;

 

I try with setMol() but it doesn't work.

have you the solution?

No, unfortunately we do not have JME format support.

Is there any function to reset the applet?

No. there is not any method in JMSketch/JMView API to reset all setting of the applet (or reinitalize it).

But you can reset the canvas. Call JMSketch.setMol(String) or JMView.setM(int,String) method to update the molecule in Marvin. If the new molecule is an empty one, actually it clear the canvas.

Dear support,

 

I have this warning in the apache log :

 

File does not exist: /www-data-dev/abonne/JMViewLaunch

 

the php code calling marvin :

 

<script LANGUAGE="JavaScript1.1" SRC="marvin/marvin.js"></script>

<script LANGUAGE="JavaScript1.1">

<!--

// marvin_jvm = "builtin"; // "builtin" or "plugin"

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

// you could also use the mview_begin("../../..", 200, 200, true ); function call to load the applet without splash screen.

<?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();

//-->

</script>

 

This warning appears only when i use google chrome .

It would help a lot if we can see what string has been transfered exactly by mview_param("mol",...) when this issue occured.

Please attach the proper part of the generated html source.

I assume that the structure string is not encoded well and that causes problem to Chrome when evaluate the expression.

mview_param("mol", "\n"+" -IDBS- 042120101113\n"+"\n"+" 5 4 0 0 0 0 0 0 0 0999 V2000\n"+" 3.1000 -5.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 2.3833 -5.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 0.9625 -5.9167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 0.2500 -6.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 1.6750 -6.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 2 1 3 0 0 0\n"+" 3 5 1 0 0 0\n"+" 4 3 2 0 0 0\n"+" 5 2 1 0 0 0\n"+"M END\n"+"");

 

mview_param("mol", "\n"+" -IDBS- 042720091552\n"+"\n"+" 5 4 0 0 0 0 0 0 0 0999 V2000\n"+" -0.9083 -2.2125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+" -1.6208 -1.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" -0.9083 -3.0375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+" -1.6208 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" -2.3333 -2.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+" 2 1 2 0 0 0\n"+" 3 1 1 0 0 0\n"+" 4 2 1 0 0 0\n"+" 5 2 1 0 0 0\n"+"M END\n"+"");

Thanks for sharing your example.

We will check how it works under the reported platform.

Hi,

I have checked the example you gave to us with Windows 7, Google Chrome5.0.375.70, and Java1.6.0_u20, on an Apache web server, with Marvin 5.3.3, and it is working for me, and loads the molecule.

I can assume the following: you are using different marvin.js and applet versions, or a customized marvin.js. Marvin 5.3.0 and newer versions are containing the JMViewLaunch class in the appletlaunch.jar file, under chemaxon.marvin.applet package, if you are using a customized marvin.js file, then it may use a wrong CODE and/or ARCHIVE parameter for the applet. The correct code parameter is chemaxon.marvin.applet.JMViewLaunch, and the correct ARCHIVE parameter is appletlaunch.jar unfortunatelly there is a mistake in our documentation in relation to this, but i'll fix it. But it is very interesting why it causes this issue only with Chrome, could it be a cache problem, or you have tried to clean the browser and java cache?

If i am wrong, and/or you have further informations, or the solution, then don't hasitate to share your experiences with us. If the problem persists, then the version of the operating system, the used java, Chrome and Marvin, would be also useful for further debugging.

Regards,
Istvan