No image for triple bonds when # is in smiles

Hi,


I'm using


chemaxon.formats.MolImporter,


chemaxon.struc.Molecule,chemaxon.formats.*,


chemaxon.util.*


for designing smiles in web.





But I not obtain any image when in my smiles I have "#".








This is my code:


....


// Setting content type


String type = format.indexOf(":") == -1 ?


format : format.substring(0, format.indexOf(":"));


response.setContentType("image/" + type);





Molecule mol = null;


if(molstring == null) {


File f = new File(filename);


MolImporter mi = new MolImporter(f,"");


mol = mi.read();


} else {





mol = MolImporter.importMol(molstring);


}





if(mol.getDim()==0) {


mol.clean(2, "O1");


}





byte[] b = mol.toBinFormat(format);


ServletOutputStream outs = response.getOutputStream();


outs.flush();


outs.write(b,0,b.length);


outs.close();


....





I'm using an old version of your jar?


Thanks,Cristina

Any information?


thanks,Cristina

Sorry for the late answer, could you please let me know what sort of SMILES is failing? Is it a particular structure or fails for any string containing # ? What is the value of the "format" string in the code? Marvin/MolConverter should read triple bonds without any problem.

Hi,


1)no work for smiles like 'C#C'(sorry but I can not post the smiles!)


2)all smiles with # in the string


3)it's a parameter, generally format=jpeg





Thanks, Cristina

Hello, I can see you are following the example we provided, still there must be some mix up of strings. I wrote a simple non-jsp example (see attachment) where you can see that the generated image has triple bonds. Is there a way to show the (stripped down but still working) JSP page as an attachment as we are not able to reproduce the error.

hi,


probably my code is terrible wrong! I have inserted your smiles:


C#CCC#Cc1ccccc1C#C" in my molstring parameter.


I don't obtain a structure but a sort of image ... see attachment ... probably I have to change jar? ?? Or I have not understood ... sorry


thanks,Cristina

Sorry again, I have copy your java class in my project... it's ok i see the trible bonds... probably I use wrong code in my jsp but I don't understand what is wrong!


Thanks,Cristina

Hello, I am happy it works now. There are JSP and applet samples bundled with the distribution and also on our site to help: http://www.chemaxon.com/marvin/examples/index.html


Still, if you have any questions please write it on the forum - usually we are faster in answering.

No... it's not worked now... it'ok in your class but not in my jsp...


Cristina

Hi,


I have find the problem in jsp:


if I write in my code:


myMol="C#CCC#Cc1ccccc1C#C" it's ok and I obtain my structure as jpeg.


If I send C#CCC#Cc1ccccc1C#C as a get parameter in web browser it doesnt' work .


es:


...viewstructure.jsp?mol=C#CCC#Cc1ccccc1C#C





Cristina

...you need to pass the SMILES string encoded. For example, in your JSP you might have a link like

Code:

<a href="viewstructure.jsp?mol=<%=SMILES%>">Click</a>"

(sorry if syntax is wrong)





The SMILES variable needs to be URL encoded, otherwise it will be chopped off before the first occurrence of the #, e.g. C#CCC#Cc1ccccc1C#C becomes C, i.e. methane as you saw!

Code:

<%@page import="java.net.URLEncoder"%> . . <% String encsmiles = java.net.URLEncoder.encode(SMILES); %> . . <a href="viewstructure.jsp?mol=<%=encsmiles%>">Click</a>

KR,





Gaspode

...and by the way, please say "Hello" to Cesare for me!