Hi,
I am trying to use CDK to generate structure data for SMILES codes and write it
to a MDL file. However, I have a problem with aromatic rings.
If I write the file using the property WriteAromaticBondTypes set to true, the
aromatic bonds are correctly stored as aromatic-type.
If I write the file with the property not set (or set to false), I get only
single bonds instead.
Applying DeduceBondSystemTool::fixAromaticBondOrders doesn't change anything,
apparently. In fact, DeduceBondSystemTool::isOK returns false both before and
after the call to fixAromaticBondOrders.
My actual code is written in R with rcdk and direct calls with rJava, but for
convenience the "java-translated" untested version of what I do:
String s = "C1(=Nc2c(Nc3c1cccc3)ccc(c2)Cl)N1CCN(CC1)C";
SmilesParser p = new SmilesParser(builder);
IMolecule m = p.parseSmiles(s);
// Here follows, in this or any other order:
CDKHueckelAromaticityDetector::detectAromaticity(m);
AtomContainerManipulator::percieveAtomTypesAndConfigureAtoms(m);
i.configureAtoms(m); // i is an IsotopeFactory
AtomContainerManipulator::convertImplicitToExplicitHydrogens(m);
StructureDiagramGenerator g = new StructureDiagramGenerator();
g.setMolecule(m);
g.generateCoordinates();
m = g.getMolecule();
DeduceBondSystemTool d = new DeduceBondSystemTool();
bool beforeOK = d.isOK(m); // false
m = d.fixAromaticBondOrder(m);
bool afterOK = d.isOK(m); // still false!!!!
// And finally le write:
// (I don't use the built-in Rcdk writing function)
MDLV2000Writer w = new MDLV2000Writer(new FileWriter("blablubfilename"));
Property aromatic = new Property();
aromatic.setProperty("WriteAromaticBondTypes", "true"); // or alternatively,
"false"
PropertiesListener pl = new PropertiesListener(aromatic);
w.addChemObjectListener(pl);
w.customizeJob();
w.write(m);
w.close();
If WriteAromaticBondTypes is set to "true", the bonds are written with type 4
as expected.
However, with "false", all aromatic bonds are of order 1; common double bonds
are 2, of course.
Am I using fixAromaticBondOrder() in a wrong way? All steps above have been
tried in various order.
Best regards
-Michael
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