Marvin applet

Hi,





Whenever the compound structure is displayed using marvin view, the applet is getting freezed and I have to kill the java_vm process and the browser. After I do it for a number of times, it ll work well . What is causing the java_vm to freeze? How can I prevent that. Please help me.





Bhargav

Can you show me an example to check this problem?


Please give me more info about your software environment.


- operating system


- browser type


- Java version


- Marvin version

Hi,


I am using





RedHat Enterprise linux AS 3


browser- mozilla


Java- j2sdk-1.4.2


Marvin version-3.3.2





to display the compound structure I am using the following code:





<script LANGUAGE="JavaScript1.1">


<!--


<% /* Intializing the applet */ %>


mview_name="mview";


mview_begin("/combichem/jchem/marvin",


"100",


"100");


mview_param("rows", "1");


mview_param("cols", "1");


mview_param("navmode", "rot3d");


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


mview_param("rendering", "ballstick");


mview_param("bgcolor", "#e0e0e0");


mview_param("border", "1");


mview_param("animate", "0");


mview_param("layout0", ":4:1:"+


"M:0:0:1:1:c:n:1:10"); <% /* Molecule */%>


mview_param("param0", ":"+


"M:100:100");


<%


try{


if(rs2.next())


{


String dbMolfile = new String(rs2.getBytes("cd_structure"),"ASCII");


%>


mview_param("cell0",


"|<%= HTMLTools.convertForJavaScript(


dbMolfile) %>");


<%


}


}





catch(Exception e)


{


out.print(e.getMessage());


}





%>





The web application that uses this code has been hosted on a server with the above configuration. The same thing works without much problems on my workstation.








Bhargav

Can you show me the JSP generated html page? I would like to check the molecule where the applet is getting freezed.


(You can do it by using the File-> Save (Page) As menu in the browser, after the JSP is loaded.)





By the way, you can try to update Marvin, Marvin 3.3.2 is an old version.

Hi,


This is the part of the html file for the displayed structure generated by the JSP .





<tr>


<td align="center"><h4>1</h4></td>





<td>


<center>


<script language="JavaScript1.1" src="information_data/marvin.txt">


</script>


<script language="JavaScript1.1">


<!--


mview_name="mview";





mview_begin("/combichem/jchem/marvin",


"100",


"100");





mview_param("rows", "1");


mview_param("cols", "1");


mview_param("navmode", "rot3d");


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


mview_param("rendering", "ballstick");


mview_param("bgcolor", "#e0e0e0");


mview_param("border", "1");


mview_param("animate", "0");


mview_param("layout0", ":4:1:"+




















"M:0:0:1:1:c:n:1:10");





mview_param("param0", ":"+








"M:100:100");











mview_param("cell0",














"|\n Marvin 02070515393D\n\n 27 27 0 0 0 0 999 V2000\nWKzVGVxVFv1W60\nTt-VF8xVpL4W60\nOG2Wz9zVrI5W60\nz+2W3Q0Wa64W60\nQQ6W5r0WXQ-V60\n+b7WuxzVBHzV60\nXC7WFvtVrayV60\nkm7WcewV73-V60\nR6BWS8wVhg0W60\n7rvVfL0WZw0W60\nFmsVRo+V3L-V60\nRlqV3dxVKYwV60\nf-sV3P+VTcxV60\nYzrV1X1WrpvV60\nr17W7+3WLtzV60\nKm5WDh4WlFxV80\nUB9WE26W7D-V80\nqe7WzV8WfA1W60\n5CvVaa1WxB4W60\nvsxVzG6W4q5W60\nquuVVo4WCh4W80\nDiuVqh-VIT6W80\nlv+VK74WkbzV80\n-o-VlS0WlX+VG0\ntG0WsY+V6BxV80\ngoyV0e+Vjb0W70\n7G3WzX0WYj0W70\nO0Q01\nR0O01\nQ0101\n10201\n20302\n30401\n40R01\nR0501\n50F01\n50601\n60801\n80701\n80901\nQ0A01\nA0J01\nA0B01\nB0D01\nD0C01\nD0E01\nF0G02\nF0H01\nH0I01\nJ0M02\nJ0L01\nL0K01\nO0N02\nO0P02\nM END\n");











mview_end();


//-->


</script><applet width="100" height="100" name="mview" codebase="/combichem/jchem/marvin" archive="jmarvin.jar" code="JMView">


<param name="rows" value="@javascript-escape-encoded@1">


<param name="cols" value="@javascript-escape-encoded@1">


<param name="navmode" value="@javascript-escape-encoded@rot3d">


<param name="molbg" value="@javascript-escape-encoded@%23ffffff">


<param name="rendering" value="@javascript-escape-encoded@ballstick">


<param name="bgcolor" value="@javascript-escape-encoded@%23e0e0e0">


<param name="border" value="@javascript-escape-encoded@1">


<param name="animate" value="@javascript-escape-encoded@0">


<param name="layout0" value="@javascript-escape-encoded@%3A4%3A1%3AM%3A0%3A0%3A1%3A1%3Ac%3An%3A1%3A10">





<param name="param0" value="@javascript-escape-encoded@%3AM%3A100%3A100">


<param name="cell0" value="@javascript-escape-encoded@%7C%0A%20%20Marvin%20%2002070515393D%0A%0A%2027%2027%20%200%20%200%20%200%20%200%20%20%20%20%20%20%20%20%20%20%20%20999%20V2000%0AWKzVGVxVFv1W60%0ATt-VF8xVpL4W60%0AOG2Wz9zVrI5W60%0Az+2W3Q0Wa64W60%0AQQ6W5r0WXQ-V60%0A+b7WuxzVBHzV60%0AXC7WFvtVrayV60%0Akm7WcewV73-V60%0AR6BWS8wVhg0W60%0A7rvVfL0WZw0W60%0AFmsVRo+V3L-V60%0ARlqV3dxVKYwV60%0Af-sV3P+VTcxV60%0AYzrV1X1WrpvV60%0Ar17W7+3WLtzV60%0AKm5WDh4WlFxV80%0AUB9WE26W7D-V80%0Aqe7WzV8WfA1W60%0A5CvVaa1WxB4W60%0AvsxVzG6W4q5W60%0AquuVVo4WCh4W80%0ADiuVqh-VIT6W80%0Alv+VK74WkbzV80%0A-o-VlS0WlX+VG0%0AtG0WsY+V6BxV80%0AgoyV0e+Vjb0W70%0A7G3WzX0WYj0W70%0AO0Q01%0AR0O01%0AQ0101%0A10201%0A20302%0A30401%0A40R01%0AR0501%0A50F01%0A50601%0A60801%0A80701%0A80901%0AQ0A01%0AA0J01%0AA0B01%0AB0D01%0AD0C01%0AD0E01%0AF0G02%0AF0H01%0AH0I01%0AJ0M02%0AJ0L01%0AL0K01%0AO0N02%0AO0P02%0AM%20%20END%0A">


<center><b>YOU CANNOT SEE A JAVA APPLET HERE</b></center>


</applet>





</center>





Bhargav

I have tested your code both with Marvin 3.3.2 and the current Marvin (3.5.5).


In both cases, I have not managed to reproduce the browser freezing.





Please try the attached applet example in your browser. Actually, it is the modificated version of your example. In this example, the applet's


codebase links to "http://www.chemaxon.com/marvin". It means that this example uses the latest Marvin.





Have you got browser freezing with this example?

Hi,


I am not able to see the attached applet that you have sent. Do I need special permissions to view attachments?








Bhargav

HI Bhargav,





We are checking this now. It may be an edit or permissions error as it was working earlier. We will post when it is corrected and you will receive a notification (as you are tracking this topic)

bhargav wrote:

Hi, I am not able to see the attached applet that you have sent. Do I need special permissions to view attachments?

It is not easy to find, but it is there. Just scroll to the right.





The forum engine made the discussion cell extra wide because there were some long lines in the messages above.





Regards,





Szabolcs

Hi,





i have tried linking to the codebase of the applet to http://www.chemaxon.hu/marvin/marvin.js and its working fine without freezing. I have observed that the applet has lot of other features that previous versions didnt have and also it is not asking for license while calculating logp, TPSA, etc any number of times. Can my application contiune use the chemaxon's codebase for the applet?? Our organization has acquired the academic license for jchem .





bhargav

HI bhargav,





Your academic package license covers the use of all tools in an unlimited manner (although you are limited to less than 3 searches/minute). Please note that the license is issued to you however not your organisation. For other researchers to use these tools they should also apply for the Academic Package license

Hi bhargav,





We have discussed your question and at this time we do not wish to make policy for this type of linking.





We can allow this, at this time, but with the proviso that if traffic on our site becomes prohibitive then we will ask you to site the applet on your server





Please note that the conditions of your academic package license should be linked to 'rules for use' of the applet as they will be relevant to all users accessing the applet through the link





Hope this help - come back if you have any comments