From: Computational toxicology using the OpenTox application programming interface and Bioclipse
Command(parameters) | Description |
---|---|
Querying | |
listModels(service) | Lists the predictive models available from the given service. |
getFeatureInfo(ontologyServer, feature) | Returns information about a particular molecular feature (property). |
getFeatureInfo(ontologyServer, features) | Returns information about a set of molecular features. |
getModelInfo(ontologyServer, model) | Returns information for a computational model. |
getModelInfo(ontologyServer, models) | Returns information for a list of computational models. |
getAlgorithmInfo(ontologyServer, algorithm) | Returns information for a computational algorithm. |
getAlgorithmInfo(ontologyServer, algorithms) | Returns information for a list of computational algorithms. |
listAlgorithms(ontologyServer) | Returns a list of algorithms. |
listDescriptors(ontologyServer) | Returns a list of descriptor algorithms. |
listDataSets(service) | Returns the data sets available at the given OpenTox server. |
searchDataSets(ontologyServer, query) | Returns matching data sets using a free text search. |
search(service, inchi) | Returns matching structures based on the InChI given. |
search(service, molecule) | Returns matching structures based on the molecule given. |
Computation | |
calculateDescriptor(service, descriptor, molecules) | Calculates a descriptor value for a set of molecules. |
calculateDescriptor(service, descriptor, molecule) | Calculates a descriptor value for a single molecule. |
predictWithModel(service, model, molecules) | Predicts modeled properties for the given list of molecules. |
predictWithModel(service, model, molecule) | Predicts modeled properties for the given molecule. |
Data exchange | |
createDataset(service) | Creates a new data set on an OpenTox server. |
createDataset(service, molecules) | Creates a new data set on an OpenTox server and adds the given molecules. |
createDataset(service, molecule) | Creates a new data set on an OpenTox server and adds a single molecule. |
addMolecule(dataset, mol) | Adds a molecule to an existing data set. |
addMolecules(dataset, molecules) | Adds a list of molecules to an existing data set. |
deleteDataset(dataset) | Deletes a data set. |
downloadCompoundAsMDLMolfile(service, dataset, molecule) | Downloads a molecule from a data set as a MDL molfile. |
downloadDataSetAsMDLSDfile(service, dataset, file-name) | Download a complete data set as MDL SD file and saves it to a local file in the Bioclipse workspace. |
listCompounds(service, dataset) | Lists the molecules in a data set. |
Authentication | |
login(accountname, password) | Authenticate the user with OpenSSO and login on the OpenTox network. |
logout() | Logout from the OpenTox network. |
getToken() | Returns a security token when Bioclipse is logged in on the OpenTox network. |