Daylight Web Services Demonstration Application

This application provides a simple interface to the Daylight Web Services. The Core page allows you to enter (or draw) a SMILES and to try out the getDepiction, canonicalizeSmiles, desaltSmiles and normalizeSmiles web services. The Daylight Web Services will, in general, allow multiple structures to be entered per request although this page only allows one SMILES to be entered at a time. After entering the SMILES, simply press each of the appropriate buttons to submit a web services request and see the results.

For the getDepiction request, you can enter various parameters to modify the depiction in the appropriate text box, one per line (for example, colormode COW).

The isomeric smiles check box controls whether or not the canonicalizeSmiles web service generates an isomeric smiles.

The Properties page demonstrates the Daylight properties calculations via the getProperties web service. You should enter a SMILES and then select any combination of the properties to compute from the list selection box. To make multiple selections, use control-click on Windows or command-click on Macintosh. If you select the match_count property you need to input a SMARTS pattern in the pattern text box. If the SMILES has multiple components (even starting materials and products in a reaction), selecting the single molecule check box will compute the sum for all the parts for each property. If the SMILES is a reaction SMILES, then selecting the "Calculate difference" checkbox will compute the differences in property values between the reactants and products.

The Conversion page uses the convertStructure web service to convert to and from SMILES and MDL formats. You can enter a SMILES to convert to either SDF or RDF format or you can upload or paste an MDL RDF or SDF file to convert to SMILES. For this demonstration, the conversions are limited to a single structure although the convertStructure web service can convert multiple structures in a single request.

The Scaffolds page demonstrates the deriveScaffold web service. You can type in multiple SMILES, one per line, in the appropriate text box or you can upload a file containing SMILES (one per line) using the choose file and upload buttons. Optional parameters to modify the request can be entered in the appropriate text box, one per line. Pressing the deriveScaffold button submits a request and displays the resulting scaffold (if one can be derived for the set of structures submitted). Note that the request, in this demonstration, is limited to a maximum of 100 structures although this is not a limitation on the deriveScaffold web service. Rolling the cursor over the structures in the scaffold display will show larger depictions. Note that the depictions are generated using the getDepiction web service.

The RTable page illustrates the computation of a table of scaffold structures and substituents. The input required is a set of SMILES (via a file or by entering SMILES in the text box) and a SMARTS pattern which defines the scaffold shared by the structures. Again, this demonstration is limited to 100 structures although that is not a limitation on the underlying web service. Note that the Clustering page can also use the generateRTable web service to display computed clusters.

The Clustering page demonstrates the deriveSDClusters web service and is used in the same way as the Scaffolds page. Again there is a 100 structure limit although this is not a limitation of the deriveSDClusters web service. The clusters can be displayed either as structure drawings with the shared scaffolds highlighted or as R Tables by selecting the check box appropriately.

Further information on the Daylight Web Services, including details on the parameters for each service, can be found in the Daylight Web Services users manual.