[Joelib-devel] Delete Hydrogens

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

Hi Hongmei,

> How could I remove all H atoms in a JOEMol? 
JOEMol mol;
mol=YourGetMolecule();
mol.deletetHydrogens();

BTW, I've found a dead-loop-bug  in
mol.deletetHydrogen();
which works independantly from
mol.deletetHydrogens();
so all will be fine for you. I will check in the bug fixes with some 
code cleanup (hopefully) this week.

Regards, Joerg

> 
> 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...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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