Re: [Joelib-devel] JOELib installation problem

[Joerg K. W. <we...@in...>]

Hi Alexandre,

1. re-using avilable classes is highly recommended.
2. I recommend always the src-distribution, because there are a lot of 
text definition files, e.g. protonation model, joelib.properties and so 
on. With using apache-ant you can build a distribution and a jar-file on 
your own, easily. Please install Apache-Ant (and Cygwin).
3. For the 2D depiction and especially for the 2D layout you will need a 
2D layout algorithm, which is only available in the CDK and you must use 
the CDK interface and the old JOELib release or you must activate it in 
the JOELib2 release. So, visualization means not automatically to have a 
good 2D layout.
4. Please start with the examples in
joelib2/src/joelib2/example
If you are able to call them from your project you are done. If not, 
send specific error codes to this list. Please mention classpath 
environment. Here I recommend to use Ant also. You can use it to resolve 
the dependencies much easier than dos-scripting or shell-scripting, see 
example scripts in joelib2.
Especially under DOS you must explicitely define the complete classpath. 
  Even for the development with IDEs i recommend strongly to use Ant, 
because it is platform independent, and works also on servers (only 
command line) and linux machines.

Kind regards, Joerg

> Hi,
> 
> I am working on a Windows XP environment planning to use some of the JOELib classes (avoiding to re-invent the wheel). Actually, I am developping a virtual screening manager in Java and one of the things I found interesting in the JOELib is the 2D depiction for mol MDL files or SMILES for example. It really deals with an object taking a molecular file as input and drawing into a JPanel the 2D molecular structure of the selected file.
> What I really wanted to know is how to import/call JOELib class in my Java project in order to 'play' with the JOELib's objects: do I have to put the JOELib .jar in my JRE directory? Do I need to compile all the JOELib package for using a little bit of it? Which JOELib archive I better have to download: binaries or src? 
> Hoping I was clear enough, thank you very much in advance.
> 
> Best regards.
> 
> 
>  Alexandre BEAUTRAIT, bio-infomatic student
>  eDAM group, UHP Nancy1, FRANCE
> 
> 
> 
> 
> 
> *********** REPLY SEPARATOR  ***********
> 
> On 11/04/2005 at 14:57 Joerg K. Wegner wrote:
> 
> 
>>Hi,
>>
>>please explain me explicitely what you are planning and what your 
>>environment is. Your request is too unspecific to go into details, so 
>>'why' are there problems ?
>>
>>Environment:
>>E.g. linux(ant?), windows(cygwin?,ant?)
>>
>>Implementation:
>>Have you derived your examples from the examples in 
>>joelib2/src/joelib2/examples
>>Do you need a 2D layout, or have all your structures valid 2D coordinates?
>>
>>Which similarity measure are you planning to use?
>>
>>Kind regards, Joerg
>>
>>>Hi,
>>>
>>>I am currently developping an open standalone application in Java for
>>
>>virtual screening studies, and I would like to use just a part of the
>>JOELib library for the 2D depiction of structures present in .mol and .sdf
>>files. I tried several times to use the binaries directly, and also to
>>compile the srcs but I never succeed to use them. In fact, would it be
>>possible for you to give me a simple roadmap explaining me how to
>>integrate the few (but very useful) classes I need into my java project.
>>Do I have to install all the JOELib directory in my Java project or simply
>>install JOELib on the PC and call it in my project?
>>
>>>Thank you very much.
>>>
>>>Alexandre BEAUTRAIT, bio-infomatic student
>>>eDAM group, UHP Nancy1, FRANCE
>>>
>>>
>>
>>
>>-- 
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW:    http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>>                                    (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>>                               (Hugo Kubinyi,2004)
> 
> 
> 
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)