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File Date Author Commit
data 2003-10-17 steinbeck steinbeck [640f37] new test cases for SSSR search
doc 2004-01-27 egonw egonw [3556cd] Linked with local DocBook DTD
dtd 2001-07-21 egonw egonw [a5d4b3] Commited Java CML Filter Library (JCFL) library...
gcj 2004-01-27 egonw egonw [afc661] Removed some old obsolete stuff
jar 2004-01-24 egonw egonw [275549] Removed obsolete JARLIBDIR definition
org 2002-06-24 steinbeck steinbeck [d3c3c8] removing old src files
packages 2004-01-25 egonw egonw [a6d335] Fixed creation of correct directory
src 2004-01-27 egonw egonw [97d254] Applied patch by Ricardo Stefani: fixed renderi...
.cvsignore 2003-02-21 egonw egonw [5acec1] Added autogenerated reports dir to ingnore list
BUGS 2002-01-03 egonw egonw [04105e] These bugs are fixed some time ago. The doc now...
CHANGELOG 2004-01-27 egonw egonw [4c075d] Added Ant doc.xml build file for converting doc...
README 2004-01-07 egonw egonw [45f30a] Updated copyright year
agenda.txt 2002-08-20 egonw egonw [24b338] Updated agenda, and made 1 instance.
build.xml 2004-01-27 egonw egonw [24af77] Delete autogenerated .javafiles in clean target
doc.xml 2004-01-27 egonw egonw [4c075d] Added Ant doc.xml build file for converting doc...
javadoc.xml 2004-01-26 egonw egonw [2fd0b9] Added HTML output for @cdkPackage tag
jmol.xml 2004-01-14 egonw egonw [b9e4e2] Applied lazyCreation patch to source code, no l...
test.bat 2003-09-10 egonw egonw [47af66] Removed all last bits of JSX stuff (except for ...
test.sh 2003-09-10 egonw egonw [47af66] Removed all last bits of JSX stuff (except for ...

Read Me

CDK The Chemical Development Kit

Copyright 1997-2004 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://jmol.sourceforge.net) 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/):

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

2.1 Applying patches

A list of available patches is given by the command

cdk/$ ant info

In brackets the names of the patches are given. To apply a patch when compiling, type:

cdk/$ ant -Ddo.lazy.creation=yes clean dist-all

3. Running tests

After you compiled the code, you can do "ant test" to run the test suite of non-interactive, automated
tests. You should see something like:

test:
Running org.openscience.cdk.test.CDKTests
Tests run: 15, Failures: 0, Errors: 0, Time elapsed: 1.192 sec

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 about 350 test, of which a large part tests the core classes,
of which 3 are known to fail. This is expected behaviour.