SOMMD (version 0.1.2)

remap.data: map data to existing SOM

Description

Assign new data to a pre-trained SOM

Usage

remap.data(SOM, X, add = FALSE)

Value

An object of class "kohonen" with the new data mapped

Arguments

SOM

a trained SOM

X

a data set with the same number of features of the dataset used to train the SOM

add

whether to append the new data to the ones used to train the SOM

Author

Stefano Motta

Examples

#Read example SOM data
som_model <- readRDS(system.file("extdata", "SOM_HIFa.rds", package = "SOMMD"))
#Read a trajectory that was not used to train the som
trj_2 <- read.trj(trjfile = system.file("extdata", "HIF2a-MD-2.xtc", package = "SOMMD"),
  topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))
#Read reference structure file
gro <- read.struct(system.file("extdata", "HIF2a.gro", package = "SOMMD"))
#Selection of the same intermolecular distances used to train the SOM
protein.sele <- which(gro$atom$resid!="020")
ligand.sele <- which(gro$atom$resid=="020")
heavy.atoms <- which(startsWith(gro$atom$elety, "H")==FALSE)
sele.dists <- native.cont(struct=gro, distance=0.6, mol.2=ligand.sele, atoms=heavy.atoms)
# Compute distances on new simulations (the same used for SOM training)
dist_2 <- calc.distances(trj_2, mol.2=ligand.sele, sele=sele.dists, atoms=heavy.atoms)
# Map new data on the existing SOM
som_model_2 <- remap.data(SOM=som_model, X=dist_2)