I am clustering a number of molecules from Smiles files. I read them, convert them to mols and then convert them to Morgan Fingerprints, which I use to compute similarity and then clustering.
However I would like to output the clustering result to a file. Ideally this is done in Smiles format such that it can then be read again for evaluation.
How can this be done please?
The only way I found was by getting the list Smiles, convert them to Mols and then to Fingerprints. The list of fingerprints and molecules are of the same size and order therefore
Fingerprints[0] == Mols[0]
in terms of the molecule they are representing. Clustering fingerprints returns the index of the fingerprint in the list, thus the indexes may be used to retrieve the molecule from the Mol list.
I do not think that it is the cleanest solution, but works.