[Joelib-devel] Re: [Open Babel] Re: [Joelib-help] Simple ChemTransformation Question

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

There's really no reason it can't add atoms, IMHO. The class itself is
exposed mostly through adding hydrogens.

I do have some ideas about how that would be implemented in Open Babel,
but things are a bit busy here with an oral exam coming up soon.

And I'd certainly be interested to know about LISP uses of Open Babel!

--
-Geoff Hutchison=09=09<hut...@ch...>
Marks/Ratner Groups=09=09(847) 491-3295
Northwestern Chemistry=09=09<http://www.chem.northwestern.edu>

On 6 Feb 2003, Daniel Charles McShan wrote:

> Hmm, it does seem that while the ChemTransformation class was perhaps
> unintended as a general transformation mechanism we could us it as such.
>
> Consider:
>
> sh-2.05a$ ./transform CO [C:1][O:2] [C:1]=3D[O:2]
> CO - [C:1][O:2] + [C:1]=3D[O:2] =3D> C=3DO
>
> (This is using openbabel - I just exposed their transformation class to
> the command line - the first argument is the smiles for the starting
> molecule, the second is the "search" and the third is the "replace")
>
> So the example above works great. But, as we've noted, you can't just
> add atoms.  But I wonder if we can add this capability to the transform
> class?  The other solutions you offer might work if I was working in
> java, but I program in lisp, so I'm really looking for a general API
> that I can either access from the command line or a library call...
>
> Ultimately, though, I suppose all I'm really looking for is regular
> expression search/replace for graphs (in particular chemical graphs).
>
> I'll give this some more thought and keep you posted on what I come up
> with...
>
> Thanks!
>
> Dan
>
> On Thu, 2003-02-06 at 04:42, "J=F6rg K. Wegner" wrote:
> > Hello Daniel,
> >
> >  > [C:1]=3D[O:2]>>[C:1](O)=3D[O:2]
> > no, adding atoms isn't implemented. Additionally this looks weird !;-)
> > because the transformation is based on two SMARTS substructure
> > searches
> > and the second pattern implies already the product which you want to
> > generate !
> >
> > Have a look at the examples at
> > http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/func=
tionalities/mol-smarts.html
> >
> > For what is this facility used --> (de)protonation model !
> > joelib/src/joelib/data/JOEChemTransformation
> > loading transformations:lines 161-180
> > doing transformations:lines 330-344
> > the problem is, that the transformation informations (vector bindings)
> > must be stored in joelib/src/joelib/smarts/JOESmartsPattern
> > It's not designed to apply all kind of chemical transformations !
> >
> > If you want to do that, i would recommend a Patty search:
> > 1. see example joelib/src/joelib/test/TestPatty
> > 2. i would recommend the pattern (only BO=3D2):
> > [CQ2(=3DO)C] carbonylC
> > see
> > http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/func=
tionalities/mol-smarts.html
> > 3. now you can add the following things in
> >     joelib/src/joelib/test/TestPatty:line 144
> > if(typeString.equals("carbonylC"))
> > {
> >    JOEAtom add2atom =3D mol.getAtom(i1);
> >    JOEAtom addAtom  =3D new JOEAtom();
> >    addAtom.setAtomicNum(JOEElementTable.instance().getAtomicNum("O"));
> >    addAtom.setType("O");
> >    if (!mol.addAtom(addAtom))
> >    {
> >
> >      throw new MoleculeIOException("Atom could not be added.");
> >    }
> >    if (!mol.addBond(add2atom.getIdx(), addAtom.getIdx(), 1, 0))
> >    {
> >      throw new MoleculeIOException("Bond could not be added.");
> >    }
> > }
> >
> > or alternative (better) solution, because it's no good idea to use
> > a hard coding of such tasks. One error and you can invest a lot of
> > time
> > to search such errors. A flexible and transparent text based soulution
> > would be recommended (as in OpenBabel and JOELib shown for simpler
> > tasks).
> >
> > If you want to do this for a lot of different patterns you could also
> > use SMILES patterns which could be added automatically (if you have a
> > method for that !;-), e.g.
> > BO1 SMILES1 B2 S2 ...||reaction      ||transformation t2 t3 ...
> > 1   O                ||ox_acetobacter||
> > 1   H                ||reduction     ||C:1]=3D[O:2]>>[C:1]-[H:2]
> > ...
> > The first number gives the bond order for the new connection and the
> > SMILES pattern the pattern to be added starting at the first atom of
> > this pattern.
> > The JOEChemTransformation (or a modified version) class can be used
> > with
> > another input file to take standard atom,charge and bond modifications
> > into account.
> > It's possible to add your own ReactTransformation class to
> > joelib/data and
> > the data for this task to
> > joelib/data/plain
> >
> > By the way, do you known the atom property descriptors in JOELib ?
> > Eventually you can use these descriptors for reactivity prediction.
> > Additionally you can use the Petra descriptors (Prof. Gasteiger,
> > Erlangen, Germany) with more atom/bond properties in JOELib
> > (CTX import) ! They used these descriptors also for this task
> > (CACTVS program).
> >
> > I hope that will help you !
> > I would be pleased if you will adapt JOELib for your needs. I would
> > help you to join your classes into JOELib (if you're interested), but
> > i
> > can not implement AND test them, because i've other main tasks in my
> > project.
> >
> > Best regards, Joerg
> >
> >
> > > Hello, I'm currently an OpenBabel user, but am interested in
> > > "converting"
> > >
> > > I'm mostly interested in SMILES/SMARTS transformations capabilities.
> > >
> > > In particular, Can I represent the following transformation:
> > >
> > > CC=3DO =3D> CC(O)=3DO
> > >
> > > I tried this (in OpenBabel)
> > >
> > > [C:1]=3D[O:2]>>[C:1](O)=3D[O:2]
> > >
> > > But it didn't work.
> > >
> > > I'd actually hoped it could be as simple as C=3DO>>C(O)=3DO, but this
> > was
> > > not to be, so I'm looking around for other options.
> > >
> > > Can JOElib do this sort of thing?
> > >
> > > Of course, t is quite likely this is due to my lack of SMARTS
> > knowledge
> > > rather than the software ;)
> > >
> >
> >
> > --
> > Dipl. Chem. Joerg K. Wegner
> > Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen,
> > Germany
> > Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
> > E-Mail: mailto:we...@in...
> > WWW:    http://www-ra.informatik.uni-tuebingen.de
> --
> Daniel Charles McShan <Dan...@uc...>
> University of Colorado Health Science Center
>
>
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld http://www.vasoftware.c=
om
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>