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Retrieve a feature similarity matrix from the mmo

GetSimMat.Rd

Looks up a similarity matrix stored in the mmo by name. Works with the three built-in matrices added by AddChemSim() as well as any custom matrix added via AddCustomSim(). Returns the matrix as-is (dense numeric or sparse dgCMatrix); downstream functions are responsible for converting to distance when needed.

Usage

GetSimMat(mmo, distance = "dreams")

Arguments

mmo

The mmo

distance

Name of the similarity matrix to retrieve. Built-in options are 'dreams', 'cosine', and 'm2ds'. Any name passed to AddCustomSim(mmo, name = ...) is also valid.

Value

The similarity matrix (numeric matrix or sparse dgCMatrix with feature ID row/col names).

Examples

if (FALSE) {
sim_matrix <- GetSimMat(mmo, distance = 'dreams')
sim_matrix <- GetSimMat(mmo, distance = 'tanimoto')  # custom
}