Only allow adding real molcules

Hi Szilard,





How can I prevent adding of smarts to the structures table.


Currently I check whether smiles include '$['. Which is not sufficient.


I guess you know a better way.





Sincerely,





Niels.

Hi Niels,





You should import the structure into a Molecule object.


The you can determine the file format of the structure, but there are file formats which can describe both query and "real" structures.


Therefore I recommend to check for other query features, such as R-groups, atom lists, any atoms and so on.





The following code demonstrates the inspection of some of these properties:


(see the Molecule API for more information)

Code:

Molecule mol=MolImporter.importMol(molstring);         if (mol.getInputFormat().equals("smarts")) {             System.out.println("SMARTS !");         }         if (mol instanceof RgMolecule) {             if (((RgMolecule) mol).getRgroupCount()>0) {                 System.out.println("R-group query !");             }         }         for (int x=0; x<mol.getAtomCount() ; x++) {             MolAtom atom=mol.getAtom(x);             if (atom.getAtno()>MolAtom.ELEMENT_COUNT) {                 System.out.println("Special atom type !");             }             if (atom.getQuerystr()!=null) {                 System.out.println("Query properties on atom !");             }             if (atom.isQuery()) {                 System.out.println("Query !");             }             if (atom.isQProp()) {                 System.out.println("Query property !");             }             if (atom.getList()!=null) {                 System.out.println("Atom list !");             }         }

Thanks. That is what I need. Sincerely, Niels.

Hi!





Don't forget the query bonds:

Code:

for (int x = 0; x < mol.getBondCount(); x++) {         MolBond bond = mol.getBond(x);         if (bond.isQuery() || // Query bond type             ((bond.getFlags() & MolBond.TOPOLOGY_MASK)!=0) || // chain/ring bond             (bond.getQuerystr() != null ) // (smarts bond)         ) {             System.out.println("   QUERY BOND!");         }     }//end for(x)

Additionally, from the next release (Marvin 3.5?) toFormat("smiles") will throw an exception if there is a feature in the molecule which cannot be represented as smiles, i.e. in all the above cases, except ANY atom.





Szabolcs