assignment of bond type in SMARTS string

Hi,

When I make a molecule from SMARTS string "cn(=O)c", the aromatic bonds are assigned type 6 (SINGLE_OR_AROMATIC); however, when the SMARTS string is imported as a SMILES, then the aromatic bonds are assigned type 4 (AROMATIC).  Why are they not assigned to be just AROMATIC as a SMARTS string?  How can I get them to be assigned as just AROMATIC?

 

Thanks for any help

Andrew

 

 

This code generates SINGLE_OR_AROMATIC aromatic bonds:

MolHandler mhl = new MolHandler("cn(=O)c", true);

Molecule m = mhl.getMolecule();

MolBond[] mbs = mm.getBondArray();

for (int j=0; j<mbs.length; ++j) {

 

System.out.println(mbs[j].getType());

}

 

 

This code generates AROMATIC aromatic bonds:

MolHandler mhl = new MolHandler("cn(=O)c", false);

Molecule m = mhl.getMolecule();

MolBond[] mbs = mm.getBondArray();

for (int j=0; j<mbs.length; ++j) {

 

System.out.println(mbs[j].getType());

}

 

 

SMARTS language can describe substructures (queries) and if the bond between two aromatic atoms are not written explicitly it can be single or aromatic. So in the following SMARTS "cn(=O)c" the implicit bonds can be single or aromatic, so we assign single_or_aromatic bond type.

SMILES describes complete molecules. A molecule cannot have query bond type. So the importer should decide to assign single bond or aromatic bond for implicit bond between aromatic atoms. We assign aromatic bond in such cases.

I hope this helps

Andras

Hi,

Thanks for the quick response .. I didn't realize "cn(=O)n" was ambiguous .. using "c:n(=O):n" gets me my substructure with (only) aromatic c-n bonds.  Thanks again.