Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Failed to load latest commit information.|
A collection of mod_python based REST services. Many of these services are actually simple front ends to other SOAP based web services. While the code can be downloaded and run from any machine (with mod_python and Apache) they will be dependent on remote SOAP services. * format ------ Requires that OpenBabel and its Python bindings be installed * substruct --------- Requires that OpenBabel and its Python bindings be installed Supports GET or POST requests. If the former then the URL should be of the form /substruct/TARGET/QUERY where TARGET is a SMILES string for the target molecule and QUERY is a SMARTS (or SMILES) pattern. Both arguments should be appropriately escaped. The return value is either the string "true" or "false" if the query matches the pattern respectively. If a POST request is recieved then the service expects two form variables: - query - a single string containing the SMARTS pattern - target - a comma separated string of one or more SMILES strings The return value will be a multiline plain text document. The number of lines equals the number of input SMILES. Each line is either "true", "false" or "fail". Thus if the i'th row is "true", the i'th target molecule contained the query. The string "fail" implies that there was an error parsing the SMILES string. * predict ------- Requrements: Python 2.4 or better R 2.7.2 or better rpy2 Dependency : descriptor service Services that will use R via rpy2 to obtain predictions from previously built statisticalk models. These services are oriented to QSAR models, so the input to these services is usually a Base64 encoded SMILES string. The entry point to this service is dispatch.py which investigates the URL to identify which model is to be used to obtain predictions. To obtain a list of models visit the URL (return type is text/plain) /predict To get the details of a model (return type is text/xml), visit /predict/ModelName To obtain a prediction from a model, visit /predict/ModelName/SMILES where SMILES should be the Base64 encoded SMILES string. If an invalid model name is specified, a HTTP 404 error is returned. Each model should be stored in a Rda file (use "save" in R). Currently, only models that have an associated "predict" method are considered. Furthermore, the file should have a single model object called "model". This is currently a bit restrictive and future versions will probably encode the name of the model object in the manifest. The service can handle multiple models via a model manifest. This is an XML document, listing the details of one or more models and is shown schematically below: <modelManifest> <model title="A model title" name="ModelName" rda="theModel.Rda"> <author>The Modeler</author> <date>01-13-2009</date> <description>A description of the model</description> <descriptors> <descriptor class="xxx" value="xxx" /> <descriptor class="xxx" value="xxx" /> <descriptor class="xxx" value="xxx" /> </descriptors> <model> <model ... > ... </model> </modelManifest> Essentially the manifest describes the descriptors required for the model, along with other details such as the Rda file containing the model. Right now only CDK descriptors are supported and are accessed via the descriptor REST service. The _class_ attribute should be the fully qualified class name of the descriptor and _value_ should be the name of the specific descriptor value employed in the model. See http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly-1.2.x/dnames.html#molecule for a list of descriptors and their individual values.