Re: [Jmol-developers] Jmol <-> JOELib connection

Joerg K. Wegner Tue, 24 Feb 2004 22:26:10 -0800

Hi Miguel,

Unfortunately, I know absolutely nothing about JOELib ... the only thing I
know anything about is Jmol.
If you could give me a very simple paragraph that describes JOELib for a
non-chemist that would be very helpful.

So are you a computer scientist :-) So here is the comp. sci. desc.: It's a graph based representation of chemical compounds. It includes some expert systems to tell the graph the chemical labels of it's nodes and edges. A regular expression syntax for subgraph searching known as SMARTS is included. Transformation rules on the graph calculation values (e.g. weight, or more biological relevant properties) and fragmentation and generation base classes are available. A data mining connection to Matlab and Weka is available. For energy minimization and more theoretical chemistry stuff you can use the Ghemical interface or use other external interfaces. Please read for more informations: http://www-ra.informatik.uni-tuebingen.de/software/joelib/index.html

You said 'draw a structure'. Jmol is a visualization program, not an
editor. Therefore, 'drawing' is not something that Jmol can do. Nor are
there any plans to add this functionality any time within the forseeable
future.
The JChemPaint project is for 2D drawing ...

O.k., then i hope the PlugIn will work there also !!! That's important ! A basic visualization is also available in JOELib (slightly enhanced CDK parts), test e.g. the PDF export.

- JMol molecule <--> Getting force-filed minimized structure from the
JOELib-Ghemical interface (only Linux using IBM's virtual machine).

I don't understand this.
Nor do I understand your reference to the IBM virtual machine.

The implemented Ghemical interfaces uses the JNI interface C/C++. Problem: SUN's virtual machine causes a segmentation fault ? IBM's virtual machine works correctly for this interface, so i assume that there is a JVM internal bug in this very special case. Plain C/C++ works fine, so it's not a problem of the implementation.

Checking operation system and installation is not too difficult.
1. - JMol molecule <--> Getting descriptors, e.g. MR, PSA, LogP, MW, ...
for complex transformation rules i recommend to use the JOELib command
line, e.g. for RDF and the rest.
2. - JMol molecule and SMARTS expression <--> JOELib return atom indixes of
unique or not unique SMARTS matching
3. - JMol molecule SET <--> JOELib data mining connection to Weka ? can be
possible only if multiple molecules can transferred to JOELib

Sorry, I don't understand any of these things either :-(

1. Get values for molecule, some are complexity measures, some other are solubility relevant ones, or are related to desribe the absorption rate of leads in humans. 2. Get index list after requesting a regular expression on molecular graph 3. Data mining and all it's possibilities. Please try 'machine learning java' under Google :-)

1. draw molecule
No

Hmmm, that's not good. I hope CDK will work.

   3. get result set (format ?, e.g. using JOELib GenericData
framework)

Don't understand

Return type of the interface connection ! There is a huge amount of possible return values ! So there must be a default definition to transfer such results (CDK plugin interface definition ?)

It does not look like Jmol is in very good shape to support your needs.

Critic is always recommended ... let's see ... at the moment i think your right ...

Let me know what you think. And talk to Egon.

I think Egon will read this mail also ...

Regards, Joerg

--
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:[EMAIL PROTECTED]
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                    (E. Hemingway)

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

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Re: [Jmol-developers] Jmol <-> JOELib connection

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