Hey,
I am currentyl working on a project using CDK, where I want to generate
aromatic fragment SMARTS from an initial molecule.
In further course of the project I want to relocate these fragments in
their inital molecules.
For the fragment SMARTS generation I aromatize the inital molecules using
the Aromaticity class:
Aromaticity aromaticity = new Aromaticity(ElectronDonation.cdk(),
Cycles.all())
For the relocation I use the SMARTSQueryTool class:
SMARTSQueryTool sqt = new SMARTSQueryTool(fragmentSmarts,
DefaultChemObjectBuilder.getInstance());
System.out.println(sqt.matches(molecule));
By doing this, I discovered the following problem.
Example:
* inital molecules SMILES: CCNC1=NC(=O)N=C(NC(C)(C)C)N1
* fragment SMARTS: C(=NC=O)N, CCNC=N
When I am aromatizing the molecule as described above, I get a non-aromatic
ring within the molecule, what is reflected by the found fragments.
When I try to find the the fragment CCNC=N in the inital molecule via the
SMARTSQueryTool, the method returns false for not finding it.
If I change the the fragment SMARTS to CCNcn, the method returns true.
I reproduced this problem by using this online tool, too:
http://www.simolecule.com/cdkdepict/depict.html
This leads me to the question, if the
SMARTSQueryTool internally aromatizes the molecule. The Aromaticity class
seems to aromatize the molecule correct by flagging the ring as
non-aromatic, because this molecule is not an aromatic compound. The ring
features a SP2-
hybridised double bond charateristic, but the molecule is not planar and
its electrons are not delocalized. On request, I can provide further
examples.
Now i am wondering why the
SMARTSQueryTool is make an own aromaticity on the molecule and under which
conditions?
I hope you can help me with this issue.
Kind regards
,
Iris
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