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
--
Never mistake motion for action.
E. Hemingway
|
