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If you need to download the tarball yourself to know how to help me here's the file. I'm running 12.10 if it is relevant.

I don't know where to go in installing CDK I know the README file says to run:

cdk/$ ls build.xml
build.xml
cdk/$ ant

in terminal. When I got to running build.xml from the extracted directory I received the error:

build.xml: command not found

The contents of the README file are:

CDK - The Chemical Development Kit

Copyright 1997-2012 The CDK Development Team
License: LGPL v2, see doc/lgpl.license

1. Introduction

You are currently reading the README file for the Chemistry Development Project (CDK).
This project is hosted under http://cdk.sourceforge.net/
Please refer to these pages for updated information and the latest version of the CDK.

The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in 
the programming language Java(tm). The library is published under terms of the the 
GNU Lesser General Public License v2. This has implications on what you can do with sources and
binaries of the CDK library. For details, please refer to the file LICENSE, which should have been
provided with this distribution.

PLEASE NOTE: This is a library of useful data structures and algorithms to manipulate them 
from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
programmers, who wish to save some effort by reusing code. It is not intended for the enduser. 
If you consider yourself to be more like user, you might not find what you wanted. 
Please refer to other projects like the JChemPaint project (http://jchempaint.github.com/)
or the Jmol project (http://www.jmol.org/) for programs that actually take advantage of the 
CDK library.

2. Compiling

Compiling and jar-ing the software is done with Jakarta's 
Ant (http://jakarta.apache.org/ant/) 1.7.1 or better and Java 1.6.0 or better:

cdk/$ ls build.xml
build.xml
cdk/$ ant

"ant -p" gives a list of possible compilation targets. The default target is 'dist-all', which
creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK
functionality. For convenience, one large .jar file containing everything can be created using the
target 'dist-large' (using the command "ant dist-large"). This is also created in dist/jar and is
typically named something like 'cdk-1.4.11.jar'.

2.1 Creating the JavaDoc documentation for the API

The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as
the user manual for the CDK, although you should also look at the list of examples and tutorials
below. This documentation is created by 'ant' from the Java source code for the CDK as follows:

cdk/$ ls javadoc.xml
javadoc.xml
cdk/$ ant -buildfile javadoc.xml html

The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read
the documentation using the following command:

cdk/$ firefox doc/api/index.html

3. Running tests

IMPORTANT: this requires the Git version of the sources, because the test files are not included in
the source code distribution.

After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated
tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib
directory or somewhere else in your classpath.
Upon "ant dist-all test-dist-all test-all", you should see something like:

test:
Running org.openscience.cdk.test.CDKTests
Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec

As you can see, the vast majority of tests ran successfully, but that there
are failures and errors. The $CDK_HOME/reports/results.txt file contains
information about the outcome of the tests.

There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run"
target in the build.xml file to look like this:

    <target name="run" depends="dist">
        <java classname="org.openscience.cdk.test.ControllerTest" fork="yes">
            <arg value=""/>
            <classpath>
                <pathelement location="${dist}/jar/cdk.jar"/>
                <pathelement path="${java.class.path}"/>
                <pathelement location="."/>
                <fileset dir="jar">
                <include name="*.jar"/>
                </fileset>
            </classpath>
        </java>  
    </target>

Then, a "ant run" should give you a window where you can add bonds to a given structure.
Currently, there are more than 2500 test, of which a large part tests the data, datadebug and 
nonotify classes.

You can run the tests for an individual module with (for the core module):

cdk/$ ant -Dmodule=core compile-module jarTestdata test-module

4. Using CDK

CDK is a class library intended to be used by other programs. It will not run 
as a stand-alone program, although it contains some GUI- and command
line applications. In order to use the CDK in your program, you need to build
the distribution jars by running "ant dist-all". They will end up in
$CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar
to the lib directory of the project for which you intend to have CDK support and
use them as you would use any other third party jar.

Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in
$CDK_HOME/dist/jar. This large jar contains all the CDK code and all third
party libraries that code depends on. 

5. Examples and tutorials

To get started using the CDK, you may be interested in the following websites which contain
examples and tutorials:

* http://pele.farmbio.uu.se/planetcdk/
* http://rguha.net/code/java/
* http://www.redbrick.dcu.ie/~noel/CDKJython.html

And for updates on CDK use cases:

* https://plus.google.com/103703750118158205464/posts
share|improve this question
    
Why are you trying to run build.xml? You only need to run ant. Or is the build.xml: command not found output from the ant command? –  iBelieve Feb 2 '13 at 3:19
    
It is not the output from ant. I am because that's what the README file told me to do. I ran it successfully, but now how do I run it? –  Brenton Horne Feb 2 '13 at 3:58
    
You are only supposed to run the commands prefixed with $ (which indicates you type it at a command prompt). The stuff under that is output from the command. So you would run ls build.xml, (because of the $), but not build.xml. You would also run ant for the same reason. –  iBelieve Feb 2 '13 at 4:03
    
There's a few different programs meant to be contained inside this package. How do I run them? By programs I mean GUI programs things like JChemPaint. –  Brenton Horne Feb 2 '13 at 4:07
    
Ah, OK I think I get it, I just downloaded the wrong file. –  Brenton Horne Feb 2 '13 at 4:11
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