Hi!
I have a question concerning the rcdk package:
I generated a test sdf-file with 3 molecules in it and tried to perform
clustering by fingerprints and plot the results in a dendogramm.
This is what I did:
mols <- load.molecules ("molecules.sdf")
fp.list <- lapply (mols, get.fingerprint, 'maccs')
fp.dist <- fp.sim.matrix (fp.list, method='tanimoto')
fp.dist <- as.dist(1-fp.dist=
clus.hier <- hclust (fp.dist, method='ward')
plot (clus.hier, label=FALSE)
When I did so, plot generated a dendogramm, but the "lines" were not labeled -
so I could not see which molecule clusters with the other. When I checked the
outcome of get.fingerprint, I noticed that the name field was empty.
The sdf file I generated contained names for the molecules (as seperate field,
but also as chain name).
How can I get these names into the mols variable and how can this be included
into the fingerprint output?
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