User cbef711ba6
24-03-2011 05:39:34
Hi,
I am developing a web application where I need to integrate JChembase for structural search similar to the following weblink
http://chem.sis.nlm.nih.gov/chemidplus/
Do I need to write extensive coding for this integration?
Could you please help me with some brief steps for this integration or if possible, with some sample code.
My entire project is in Java environment.
I am runnning on tight timelines. I am more than happy for a quick answer.
Thanks......
Peter
ChemAxon e274e1bada
24-03-2011 08:42:19
Hi Peter,
we have two advanced examples which show how is it possible to create web based chemical database search application with JChem Base. Both of them are open source, and free to use.
The first is a JSP example, it is part of the JChem distribution, you can fin it in the examples/db_search directory.
You can also find the online version on our website: http://www.chemaxon.com/jchem/examples/db_search/index.jsp
The second is a Web Service based AJAX example, it is part of the JChem Web Services product. Here is the online version: http://www.chemaxon.com/ajax/
Regards, Edvard
User cbef711ba6
24-03-2011 11:01:03
Hi Edvard,
Thanks for the swift reply.
I have seen your example on your site. But not sure how to integrate it with my web application similar to http://chem.sis.nlm.nih.gov/chemidplus/
Any help on this.
Thanks...
Peter
User c1ce6b3d19
24-03-2011 11:13:39
User cbef711ba6
24-03-2011 12:02:31
Hi Jon,
I would like to emulate the enclosed snappy of the site with search capability.
Thanks...
Peter
User c1ce6b3d19
24-03-2011 12:53:39
Peter,
Thanks for the further info.
It looks like you want to embed a marvin sketch applet for drawing a structure. Our searching API has many types of structure search (superstructure, substructure, exact, similarity, etc.) so be sure to research the types so that you match what you want to provide on your site. Structure search hits are returned in a number of structure or image formats. Displaying structures can be done with simple image output (jpg, png, etc.) or the marvin view applet can be used for simple and complex viewing.
The links provided below are great starting points in the documentation for using our software. As Edvard stated earlier, the examples are also a good place to grab some code and alter it to fit your site's design.
Jon
User cbef711ba6
14-04-2011 14:05:07
Hi Jon,
Thanks for the help I could able to integrate Jchem search with my
application. But one small issue, I get my results in mview applet. How do I
convert the resultset to an image format (jgp or png)?
Can you help me on this.
Peter
User c1ce6b3d19
14-04-2011 14:38:45
Peter,
I'm glad you could find a way to integrate with your application. There are many ways to create images of your molecules. Perhaps you can tell us what approach you ended up using and we can point you to further resources.
User cbef711ba6
15-04-2011 07:13:58
Jon,
I have included the same code of db_search example (from the link you have provided) in my code. I get the similar output in Mview applet as in the example. Now I want the output in image format rather than in a mview applet.
Could you help with a sample code for getting output (result) in image format.
Peter
ChemAxon a9ded07333
22-04-2011 14:27:25
Hi Peter,
If you know the cd_id of the structure in database you may use the following code excerpt:
<% String pictureString = "<img src=\"./img.jsp?cd_id=" + cd_id +"\">"; %>
<tr>
<td width="20%">
<%= pictureString%>
</td>
</tr>
Then you need to implement img.jsp that will return the images based on cd_id parameter (sorry for superfluous imports, it's just part of a bigger jsp).
<%@ page import="
java.sql.*,
java.util.Vector,
java.util.Arrays,
chemaxon.jchem.db.*,
chemaxon.util.*,
chemaxon.sss.search.JChemSearchOptions,
chemaxon.license.*,
chemaxon.formats.*,
javax.xml.parsers.DocumentBuilder,
javax.xml.parsers.DocumentBuilderFactory,
javax.xml.parsers.ParserConfigurationException,
java.io.*,
javax.servlet.*"
%><%@ include file="init.jsp" %><%
ConnectionHandler ch = (ConnectionHandler)session.getAttribute(sessionVarPrefix+"ch");
if((ch==null)||(!ch.isConnected())) {
ch = new ConnectionHandler();
ch.setDriver(driver);
ch.setUrl(url);
ch.setLoginName(username);
ch.setPassword(password);
ch.setPropertyTable(propertyTableName);
ch.connectToDatabase();
session.setAttribute(sessionVarPrefix+"ch",ch);
}
Connection con=ch.getConnection();
String sql =
"SELECT " +
structureTableName + ".cd_structure " +
"FROM "+ structureTableName +
" WHERE " +
structureTableName + ".cd_id = ?";
PreparedStatement pstmt = con.prepareStatement(sql);
try {
pstmt.setInt(1, Integer.valueOf(request.getParameter("cd_id")));
ResultSet rs = pstmt.executeQuery();
try {
if(rs.next()) {
byte[] molBytes = DatabaseTools.readBytes(rs, 1);
byte[] pictureBytes = MolImporter.importMol(molBytes).toBinFormat("jpeg:setcolors,w300,h200,Q90");
OutputStream outs = response.getOutputStream();
response.setHeader("Content-type", "image/jpg");
outs.flush();
outs.write(pictureBytes, 0, pictureBytes.length);
outs.close();
}
} finally {
rs.close();
}
} finally {
pstmt.close();
}
%>
Best regards,
Tamas
User cbef711ba6
05-05-2011 10:53:35
Hi Tamas,
Thank you.
I have already used generate image.jsp code & it worked well. Is it similar code to that? I will try this as well.
Peter
User cbef711ba6
06-05-2011 08:08:32
Hi Guys,
The given code works.
Thanks a lot for the help.
Peter