[Joelib-devel] Re: Question about JOELib

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

Hi Eakasit Pacharawongsakda,

i forward this message also to the developer and help mailing list.

> 		I 'm developing a web-based chemoinformatics system for searching 2D structure. I'm using JOELib library and JME Molecular Editor. I have some question , like belows
> 		-  I use JME Molecular Editor to create SMILES and using open babel to create SMILES from MOL file , but both didn't create the same SMILES. 
> 		  for example
> 			- In my database using open babel SMILES format, we have Cc1ccc(cc1)S(=O)(=O)N(CC(=O)O)c1cc(ccc1)Cl
> 			- A SMILES query from JME Molecular Editor is Cc2ccc(S(=O)(=O)N(CC(=O)O)c1cccc(Cl)c1)cc2
SMILES is a line notation, which says nothing about the uniqueness of 
such a notation. If you want to grant this you should use a molecule 
canonisation, like the morgan algorithm (available in JOELib with 
several tie resolvers), or any newer algorithm (see JCICS or now JCIM 
Journal).

> 			Can I use any functions of JOELib library to search the SMILES query in my database? If so, please explains .
This is too unspecific. What do you want if you are interested to 
compare only the SMILES entries, you must use a unique SMILES, but this 
will depend on the canonisation algorithm you will use.

You can also try a SMARTS matching (exact matching) or any other 
similarity matching (e.g. atom pair coding, feature subset coding, 
fingerprint coding, name it ...)

> 		   Can you explain or advise me how to deal with this for searching ?
Please contact the developer mailing list for further discussions, then 
i will go into details, this will reduce redundancy. The first thing i 
need is an exact problem definition.

> 		- For the method init( ) in JOESmartsPattern class. What SMILES or SMART pattern string is expected to be a parameter of method ?  
> 		  If it is SMART pattern  string, how can I generate it from SMILES pattern using JOELib ?
SMILES is in some parts a subset of SMARTS, but i'm not sure if you can 
always simply use a SMILES-String for the SMARTS initialization.

Kind regards, Joerg Kurt Wegner

-- 
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
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