ChemMine Web Tools is an online service for analyzing and clustering small molecules. It provides numerous cheminformatics tools which can be used directly on the website, or called remotely from within R. When called within R jobs are sent remotely to a queue on a compute cluster at UC Riverside, which is a free service offered to
The website is free and open to all users and is available at http://chemmine.ucr.edu. When new tools are added to the service, they automatically become availiable within
ChemmineR without updating your local R package.
List all available tools:
Show options and description for a tool. This also provides an example function call which can be copied
verbatim, and changed as necessary:
Launch a Job
When a job is launched it returns a job token which refers to the running job on the UC Riverside cluster. You can check the status of a job or obtain the results as follows. If
result is called on a job that is still running, it will loop internally until the job is completed, and then return the result.
Launch the tool
pubchemID2SDF to obtain the structure for PubChem cid 2244:
Use the previous result to search PubChem for similar compounds:
Compute OpenBabel descriptors for these search results:
View Job Result in Browser
browseJob launches a web browser to view the results of a job online, just as if they
had been run from the ChemMine Tools website itself. If you also want the result data within R, you must first call
result object from within R before calling
browseJob has been called on a job token,
the results are no longer accessible within R.
If you have an account on ChemMine Tools and would like to save the web results from your job, you must first login to your account within the default web browser on your system before you launch
browseJob. The job will then be assigned automatically to the currently logged in account.
View OpenBabel descriptors online:
Perform binning clustering and visualize result online: