RE: [Joelib-help] aromatize a molecule

[Sun, Hongmei* <HS...@nc...>]

Hello, there,

How could I remove all H atoms in a JOEMol? 

Happy Thanksgiving.


Thanks.

Hongmei 


-----Original Message-----
From: Joerg K. Wegner [mailto:we...@in...] 
Sent: Thursday, November 13, 2003 2:20 AM
To: Sun, Hongmei*
Cc: 'joe...@li...'
Subject: Re: [Joelib-help] aromatize a molecule

Hi all,

if you have loaded a molecule and then call, e.g.
JOEAtom atom=mol.getAtom();
boolean isAromatic=atom.isAromatic();

JOELib will determine the aromaticity on it's own; only once if you will 
not change atoms or bonds for beeing faster. That's one reason for the 
beginModify and endModify flags when working on molecules.

When you want to check the state on your own you can call:
boolean assignedAlready=molecule.hasAromaticPerceived();

or you can assign the flags on your own:
JOEAromaticTyper.instance().assignAromaticFlags(molecule);

For a short description see:
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper
.html
and all TEXT DEFINITION files in joelib/src/joelib/data/plain or online at:
http://cvs.sourceforge.net/viewcvs.py/joelib/joelib/src/joelib/data/plain/
which are based on SMARTS, so if you want to change things in the expert 
system models feel free to do so.

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:we...@in...
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