Dear Ed,
Welcome to the CDK :-)
First off, what do you use to write java programs? A lot of the difficulties
of Java dependency management just vanish if you use a good programmer's
editor (Integrated Development Environment, IDE) that can handle stuff like
that for you. Java is especially 'annoying' in this case, because it demands
a very specific filename/directory structure, which is just a pain to
maintain by hand. (I too started my first java programming with windows
explorer, notepad and a terminal to type in "javac ......". I NEVER want to
go back there..)
I myself (and a few other CDK-users/developers too) use the free, open
source Eclipse, available from http://eclipse.org/downloads/. If you are
just writing a java program for on your computer, you will want the "Eclipse
IDE for Java Developers".
Eclipse (or any other IDE) helps you to organize your code, warns you about
common problems, and can often suggest fixes for things.
It may seem a bit daunting at first, but after a month you will wonder how
you ever did without it.
To help you a bit on your first steps, you can try Lars Vogel's Eclipse
Tutorial <http://www.vogella.de/articles/Eclipse/article.html>, which
includes creating your first program, and has a special chapter on including
external libraries.
once you get some eclipse experience, this list of useful key
shortcuts<http://theshyam.com/2009/07/eclipse-productivity-shortcuts/>can
be very handy to keep somewhere nearby.
Then, for your first steps in Java itself, I recommend a good, physical,
paper book. (I liked O'Reilly's "Headfirst Java" by Sierra & Bates myself,
it's different in a good way, and good in teaching you the basics of
programming, and programming in Java specifically.)
Failing good paper books, there's the Java Trail
tutorials<http://download.oracle.com/javase/tutorial/java/index.html>.
They are a bit lengthy/wordy in my taste, but they take you through all the
small steps. Another resource that seems useful (haven't used it myself) is
www.javabeginner.com, aimed at absolute newcomers to Java.
Having set up the ultimate programmers environment, it is now time to get
the CDK. Don't trouble yourself with "ant", "building" etc. just yet, and
just get the pre-baked, ready made JAR-libraries. For the stable, production
version, get
cdk-1.2.8.jar<http://sourceforge.net/projects/cdk/files/cdk/1.2.8/cdk-1.2.8.jar/download>,
for the more cutting edge version, with more features, but slightly more
likely to change out under you, get
cdk-1.3.8.jar<http://sourceforge.net/projects/cdk/files/cdk/1.2.8/cdk-1.2.8.jar/download>
.
A ".jar" is a complete java package, containing everything you need. Best of
all, you don't even need to unpack it, just tell your eclipse project where
it is (Lars's tutorial will have told you how to do that), and it works!
Once you have made it through all these steps, you should be able to start
writing your first CDK code, and you will be able to fiddle around with the
examples.
Let us know how you fare, and if you run into anything, don't hesitate to
ask!
Best regards,
Jules Kerssemakers
bioinformatics PhD student,
Vriend Group,
CMBI, Nijmegen
On 6 April 2011 09:53, Ed Barker <mredbar...@yahoo.co.uk> wrote:
> Hi
>
> I am a chemist in desperate need of some of the algorithms in cdk for
> research purposes. However, I am brand new to java. I learn best by example
> but I am having a difficult time trying to get a simple program which
> imports the cdk packages working. I have been trying this for some weeks but
> getting nowhere. The problem seems to be a classpath problem - when
> compiling the "package does not exist".
>
> I know this is very basic and most here are developers but I was wondering
> if it is not possible for someone to describe in detail, with examples, the
> full process of going from installation (which I have done with ant) through
> to compiling and running a simple java cdk program. The support material
> available is aimed at expert java users, so I can find nothing that helps
> chemists like me new to this language keen to get started. Once I know how
> to compile a java cdk program I should be fine with learning how to use the
> cdk and learning java. I would be happy, once I understand this, to share
> this knowledge by writing it up as a tutorial for others in a similar
> situation.
>
> Thanks
>
>
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>
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