Sirius-APIs

This repository contains the R package Rsirius. Rsirius is a SIRIUS API written in the programming language R. It enables the use of SIRIUS' REST service and its provided functions in R. It has to be considered that this API is currently not supporting any computations, e.g. the computation of fragmentation trees or the structure elucidation. At this moment the REST API enables the request of some informations that are already computed and stored in your local project space. For example, you can get all computed molecular formula candidates, fragmentation trees, structures and predicted fingerprints computed with SIRIUS.

Installing Rsirius directly from Github

To install Rsirius directly from Github you need the package remotes and its method install_github. The following code will install Rsirius from this Github repository:

require(remotes)
install_github(repo = "boecker-lab/sirius-apis", subdir = "Rsirius", ref = "master", build = TRUE)

Start SIRIUS' REST service using Rsirius

For using Rsirius you have to create an SiriusApi client object first. An object of this class SiriusApi handles the client-server communication and is necessary for starting the SIRIUS REST service as background service. The REST service has to be started in order to use Rsirius.

api_client <- SiriusApi$new(host = "http://localhost:", port = 8080)
api_client$start(pathToSirius, inputData)

There is also a method to shut down the REST service:

api_client$shutdown()

Example

comp_controller <- CompoundControllerApi$new(api_client)
resp <- comp_controller$get_compound_ids_using_get(pid = "mySiriusProjectSpace")
compound_ids <- resp$content

mf_controller <- FormulaResultController$new(api_client)
resp <- mf_controller$get_formula_ids_using_get(compoundId,projectSpaceId,includeFormulaScores = TRUE)
formula_ids <- resp$content