Image Generation Using Marvin Beans

Table of Contents

Introduction

The examples below demonstrate how to integrate the Marvin Beans API into JSP pages to generate images from molecule sources. We provide only tryout for each example (see "online" link by the example). If you would like to install them to your server, see the "Installation" section.

System Requirement

Since the examples are JSP examples, you need a web server that implements Java Server Pages technology. We recommend Apache Tomcat to use. Tomcat needs a Sun's JDK to compile and run JSP code. Since Marvin Beans API requires at least Java 1.5, the JDK that Tomcat uses has to be 1.5 or later version.

On client side, you need only a web browser to access the web server and open the JSP pages. In a few examples, MarvinSketch or MarvinView applets are also referred to draw query or display result. To be able to run applet, you need a Java capable browser (most of the browser support it) and a Java Plugin. Read more about it in the System requirement of MarvinView/Sketch applet: System requirements.

Examples load the applet from the ChemAxon site. Of course, you can modify your local copy of JSP examples to get applet from your own site.

Installation

  1. Install Apache Tomcat. (Of course the examples also run under other servlet servers. In this document we demonstrates installation with a 4.1 version of Apache Tomcat under Linux that we placed into the /opt/apache-tomcat directory.) Refers to its manual how to do it.
  2. Download the Marvin Beans package and extract it somewhere. (You can use also the JChem package since it also includes the Marvin Beans API.)
  3. Copy all jar files (files with .jar extension) of the lib directory of Marvin Beans (or JChem) package into the shared/lib directory of Tomcat. 
    cd $HOME/marvinbeans/lib
cp *.jar /opt/apache-tomcat/shared/lib/
  4. Create the marvin directory where default JSP examples are situated under your Tomcat: webapps/examples/jsp/marvin. 
    cd /opt/apache-tomcat/webapps/examples/jsp
mkdir marvin
  5. Copy all files from the examples/beans/image-generation directory of Marvin Beans to previously created directory (webapps/examples/jsp/marvin/). 
    cp $HOME/marvinbeans/examples/beans/image-generation/* /opt/apache-tomcat/webapps/examples/jsp/marvin/
  6. Modify show_image3.jsp and show_image4.jsp to refer to that directory in the path to caffeine.smi. In this case the new path is /opt/apache-tomcat/webapps/examples/jsp/marvin/caffeine.smi.
  7. Start Tomcat (or restart it if it is already running).

The installation is completed. To test everything works fine, open the following URL in your web browser. 

http://localhost:8080/examples/jsp/marvin/show_image1.html
If you would like to access it from a different machine, substitute the localhost domain with the IP address or domain name of the web server.

Troubleshoot

If the example does not display when you open the above URL in the browser, the problem may be in the configuration. Probably, you have copied jars into the wrong directory. Check the error log of Tomcat: logs/catalina.out. In this case, you will find the following error message there: 

Error compiling file: /opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java     [javac] Compiling 1 source file

/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:9: package chemaxon.formats does not exist
import chemaxon.formats.MolImporter;
                        ^
/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:10: package chemaxon.struc does not exist
import chemaxon.struc.Molecule;
                      ^
/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:67: cannot find symbol
symbol  : class Molecule
location: class org.apache.jsp.generate_image_jsp
    Molecule mol = null;
    ^
/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:71: cannot find symbol
symbol  : class MolImporter
location: class org.apache.jsp.generate_image_jsp
        MolImporter mi = new MolImporter(f,"");
        ^
/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:71: cannot find symbol
symbol  : class MolImporter
location: class org.apache.jsp.generate_image_jsp
        MolImporter mi = new MolImporter(f,"");
                             ^
/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java:75: cannot find symbol
symbol  : variable MolImporter
location: class org.apache.jsp.generate_image_jsp
        mol = MolImporter.importMol(molstring);
              ^
6 errors

Info: Compile: javaFileName=/opt/apache-tomcat/work/Standalone/localhost/examples/jsp/marvin/generate_image_jsp.java
    classpath=/opt/apache-tomcat/webapps/examples/WEB-INF/classes/:/opt/apache-tomcat/webapps/examples/WEB-INF/classes/:/opt/apache-tomcat/shared/classes/:/opt/apache-tomcat/common/classes/:/opt/apache-tomcat/common/lib/ant-launcher.jar:/opt/apache-tomcat/common/lib/jasper-runtime.jar:/opt/apache-tomcat/common/lib/commons-collections-3.2.jar:/opt/apache-tomcat/common/lib/jasper-compiler.jar:/opt/apache-tomcat/common/lib/ant.jar:/opt/apache-tomcat/common/lib/naming-factory.jar:/opt/apache-tomcat/common/lib/commons-logging-api-1.1.1.jar:/opt/apache-tomcat/common/lib/servlet.jar:/opt/apache-tomcat/common/lib/naming-resources.jar:/opt/apache-tomcat/common/lib/naming-common.jar
     cp=/opt/apache-tomcat/webapps/examples/WEB-INF/classes
     cp=/opt/apache-tomcat/webapps/examples/WEB-INF/classes
     cp=/opt/apache-tomcat/shared/classes
     cp=/opt/apache-tomcat/common/classes
     cp=/opt/apache-tomcat/common/lib/ant-launcher.jar
     cp=/opt/apache-tomcat/common/lib/jasper-runtime.jar
     cp=/opt/apache-tomcat/common/lib/commons-collections-3.2.jar
     cp=/opt/apache-tomcat/common/lib/jasper-compiler.jar
     cp=/opt/apache-tomcat/common/lib/ant.jar
     cp=/opt/apache-tomcat/common/lib/naming-factory.jar
     cp=/opt/apache-tomcat/common/lib/commons-logging-api-1.1.1.jar
     cp=/opt/apache-tomcat/common/lib/servlet.jar
     cp=/opt/apache-tomcat/common/lib/naming-resources.jar
     cp=/opt/apache-tomcat/common/lib/naming-common.jar
     work dir=/opt/apache-tomcat/work/Standalone/localhost/examples
    srcDir=/opt/apache-tomcat/work/Standalone/localhost/examples
    include=jsp/marvin/generate_image_jsp.java
Exception compiling Compile failed; see the compiler error output for details.

Check the shared/lib folder of your Tomcat whether Marvin Beans jars are available there. If not, complete it. If yes, please consult with the manual of the Tomcat why it can not load classes from these jar.

Examples

The following examples send a structure to a JSP script that generates an image and displays it in the web browser.

  • Using the POST method for sending a SMILES string and the image format.
    http://localhost:8080/examples/jsp/marvin/show_image1.html
    (source | online version)
  • Using the GET method and URL encoding for sending a SMILES string and the image format.
    http://localhost:8080/examples/jsp/marvin/show_image2.jsp
    (source | online version)
  • Using the GET method and URL encoding for sending the name of the file (containing the structure) and the image format.
    http://localhost:8080/examples/jsp/marvin/show_image3.jsp
    (source) | online version)
  • Modification of the previous example: By clicking the image, the linking molecule will be displayed in a viewer applet.
    http://localhost:8080/example/jsp/marvin/show_image4.jsp
    (source | online version)
  • Several images on one page. By clicking on an image, the choosen structure will be displayed in a viewer applet. 
    http://localhost:8080/examples/jsp/marvin/show_image5.jsp
    (source | online version)
  • MarvinSketch Ajax example 1: Edit a structure in MarvinSketch and displays its image on the same page.
  • MarvinSketch Ajax example 2: Select an image and edit the linking molecule, the image will be refreshed automatically by updating the molecule.
    • Please also see: