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File Date Author Commit
.externalToolBuilders 2008-01-29 egonw [r9967] Applied the mf/ branch to trunk/
META-INF 2008-09-24 egonw [r12456] Merged with branch cdk-1.2.x
develjar 2008-06-06 egonw [r11299] Upgraded to 4.2.2
doc 2008-10-16 shk3 [r12717] replaced some links to almost
jar 2008-09-24 egonw [r12456] Merged with branch cdk-1.2.x
perf 2006-12-28 egonw [r7588] Also output the number of structures generated ...
pmd 2008-09-07 egonw [r12216] Merge branch 'cdk-1.2.x'
src 2010-02-01 shk3 [r15363] reduces the number of duplicates generated
tools 2008-10-12 rajarshi [r12608] Updated nightly script to read config info from...
.classpath 2008-09-24 egonw [r12456] Merged with branch cdk-1.2.x
.cvsignore 2005-08-25 tohel [r4790] added undo/redo functionality to JChempaint
.gitignore 2008-10-01 egonw [r12508] Merged commits from cdk1.2.x
.project 2008-08-28 egonw [r12111] No, commiting a local git branch does not resul...
BUGS 2002-01-03 egonw [r322] These bugs are fixed some time ago. The doc now...
README 2008-07-03 egonw [r11487] Some minor updates.
build-eclipse.xml 2006-09-20 egonw [r7003] Added runDoclet, to get JUnit test working
build.properties 2008-09-24 egonw [r12456] Merged with branch cdk-1.2.x
build.props 2008-09-07 egonw [r12217] Should not have overwritten the version for trunk
build.xml 2008-10-01 egonw [r12508] Merged commits from cdk1.2.x
changelog.20060714.txt 2006-07-14 egonw [r6679] Applied Rajarshi's last-minute patches
changelog.xml 2006-07-14 egonw [r6675] Preparing for a release
changelog.xsd 2005-08-08 chhoppe [r4667] rename cho in chhoppe in changelog.*
doc.xml 2004-01-27 egonw [r2361] Added Ant doc.xml build file for converting doc...
javadoc.xml 2008-07-27 rajarshi [r11795] Removed refs to the experimental module
plugin.xml 2008-05-19 egonw [r11064] Reworked Eclipse settings, to define a org.open...
pmd-migrating.xml 2008-09-07 egonw [r12219] Merge branch 'my-local-1.2'
pmd-unused.xml 2008-08-20 egonw [r12075] Set up a new module, with the QM code
pmd.xml 2008-09-07 egonw [r12216] Merge branch 'cdk-1.2.x'
test.bat 2003-09-10 egonw [r1844] Removed all last bits of JSX stuff (except for ...
test.sh 2003-09-10 egonw [r1844] Removed all last bits of JSX stuff (except for ...

Read Me

CDK The Chemical Development Kit
 
Copyright 1997-2008 The CDK Development Team
License: LGPL, 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. 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 manipulated 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.sourceforge.net)
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/) and requires Java 1.5.0 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-cvs-20060303.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

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. Some tests might fail intentionally
to mark know issues in CDK.

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.

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://www.chemistry-development-kit.org
* http://blue.chem.psu.edu/~rajarshi/code/java
* http://www.redbrick.dcu.ie/~noel/CDKJython.html

Further examples can also be found in issues of the CDK News:
* http://cdknews.org/