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

[<we...@in...>]

Hello Daniel,

 > [C:1]=[O:2]>>[C:1](O)=[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/functionalities/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=2):
[CQ2(=O)C] carbonylC
see
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/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 = mol.getAtom(i1);
   JOEAtom addAtom  = 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]=[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=O => CC(O)=O
> 
> I tried this (in OpenBabel)
> 
> [C:1]=[O:2]>>[C:1](O)=[O:2]
> 
> But it didn't work.
> 
> I'd actually hoped it could be as simple as C=O>>C(O)=O, 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