Re: [Joelib-help] aromaticity in SD files

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Hi Wayne,

you're right, added as support request as additional flag in 
joelib.properties:
https://sourceforge.net/tracker/index.php?func=detail&aid=862349&group_id=39708&atid=425970

Should not be too difficult :-)
If you've already implemented such a method in MDLSD i would be happy to 
  check this in. It's not necessary to implement things twice !

Regards, Joerg

> bondPairs is a HashMap.  The intent is to make sure that an aromatic
> atom is involved in at most one double-bond.  If an atom has not
> participated in a double-bond and an aromatic atom it is attached to
> also has not participated in a double-bond, then bondType is set to 2.
> Both atoms are then added to the bondPairs HashMap, with the target of
> one atom's HashMap pointing to the other atom.
> 
> If what I wrote it correct at all, though, it could just be a
> java.util.HashSet I guess.  Doesn't need to be a HashMap.
> 
> 
>>-----Original Message-----
>>From: Joerg K. Wegner [mailto:we...@in...]
>>Sent: Monday, December 15, 2003 8:12 AM
>>To: Wayne Volkmuth
>>Cc: Joe...@li...
>>Subject: Re: [Joelib-help] aromaticity in SD files
>>
>>Hi Wayne,
>>
>>what contains the 'bondPairs'-variable ? Seems to be a HashMap or
>>something related, but what's their content.
>>
>>Regards, Joerg
>>
>>
>>>Hi Joerg,
>>>
>>>A couple weeks ago I asked about the bond type "4" in the sd files
>>>produced by JOELib.  You said
>>>
>>>
>>>
>>>>ah, o.k., but that's not a bug that's a feature! These bonds are
>>>>aromatic and you will find this also in the SD-FILE definition of
> 
> MDL.
> 
>>>>That why you should use JOELib or OpenBabel, because they have a
>>>>really
>>>>great chemical expert system behind 'simple' file conversion. Only
> 
> if
> 
>>>>you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!
>>>
>>>
>>>I went and looked at the sd file definition on the mdl web site.  A
> 
> bond
> 
>>>type of "4" is only permitted (required?) for structures intended
> 
> for
> 
>>>use as queries (against, presumably, a database).  I'm sure you'll
> 
> find
> 
>>>that particular distinction as odd as I do but at any rate, that's
> 
> their
> 
>>>standard.
>>>
>>>>From what I've seen JOELib seems to be focused on representing
> 
> specific,
> 
>>>rather than generic (i.e. query), molecules so it seems as though
> 
> the sd
> 
>>>writer should put out alternating 1's and 2's.  Or perhaps it's
> 
> sensible
> 
>>>to have behavior depend on a flag, so you can ask the sd writer to
> 
> use
> 
>>>type "4" bonds if desired.
>>>
>>>Here's a fragment of code that I think will do the trick.  Let me
> 
> know
> 
>>>what you think.
>>>
>>>Wayne
>>>
>>>                    //check, if aromatic bond
>>>                    if (atom.isAromatic() && nbr.isAromatic() ||
>>>(bond.getBO() == JOEBond.JOE_AROMATIC_BOND_ORDER))
>>>                    {
>>>                        //  Non-query structures must use Kekule
>>>representation
>>>                        if (bondPairs.containsKey(new
>>>Integer(atom.getIdx())) || bondPairs.containsKey(new
>>>Integer(nbr.getIdx())))
>>>                        {
>>>                            bondType = 1; // single bond
>>>                        }
>>>                        else
>>>                        {
>>>                            bondType = 2; // double bond
>>>                            bondPairs.put(new
> 
> Integer(atom.getIdx()),
> 
>>>new Integer(nbr.getIdx()));
>>>                            bondPairs.put(new Integer(nbr.getIdx()),
> 
> new
> 
>>>Integer(atom.getIdx()));
>>>                        }
>>>                    }
>>>                    else
>>>                    {
>>>                        // 1 single
>>>                        // 2 double
>>>                        bondType = bond.getBO();
>>>                    }
>>>
>>>
> 
> ------------------------------------------------------------------------
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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:we...@in...
>>WWW:    http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>>                          E. Hemingway
>>
> 
> 
> 
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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:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                          E. Hemingway