i will have a look.
- JMol molecule <--> Getting force-filed minimized structure from the JOELib-Ghemical interface (only Linux using IBM's virtual machine). Checking operation system and installation is not too difficult. - 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. - JMol molecule and SMARTS expression <--> JOELib return atom indixes of unique or not unique SMARTS matching - JMol molecule SET <--> JOELib data mining connection to Weka ? can be possible only if multiple molecules can transferred to JOELib
furthermore we can use
5. add/removeHydrogens
6. JOELib's protonation model for pH value correction if the user defines transformation rules for a preferred pH value.
7. supporting the PATTY (programmable atom typer) for molecules, when defining SMARTS rules (used to assign atom types for each of the four expert systems)
I can't really follow your questions... please elaborate...3. get result set (format ?, e.g. using JOELib GenericData framework) example ? Please use your preffered mechanism.
Descriptor results or all other results, like SSSR, aromaticity, atom typer, ... are stored in JOELib as generic data objects, some can occur multiple times, others are only allowed to have one entry, because a hash table is used to store them, e.g. plain descriptors, like MW which should occur only once.
For the interface it would be easier if we can use this functionality, or we must define for each result our own transformation rule.
This is easy for integer and double results.
But what's with arrays matrices and ... If we apply e.g. a SMARTS matching we get a Vector of int[]'s, where every integer array represents matching atom indices.
... converge iteration (running :-) ) ...Ok, let's email more and converge...Then i will be able to implement the functionality for your Jmol-JOELib interface definition !
Using the plugin API it has a very well defined interface, and it is reasonably straight forward... We'll work it out...I think so, ...
Regards, Joerg
Egon
- -- [EMAIL PROTECTED]
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6
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-- 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
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