I calculated a set of physicochemical descriptors using cxcalc. I wish to use this list to use the Jarvis-Patrick Algorithm (Jarp) using this data and hopefully the command line.
Is there a way to do this, or do I need to load all my data through JChem Base?
there's no need to use the JChemBase, jarp can access the data from file. Use -f 0 option in the command-line to indicate that the length of the fingerprint to be used is 0 (i.e. no fingerprints are used in clustering), and the -m option to specify the dimension of your data. In your input each row represents one data item, and each data value is a decimal value separated by one or ore whites-space character.
Does this help at all?