average.neur.property   Compute average property
calc.distances          calc.distances
calc.dists              Calculation of Distances
cat.trj                 Concatenate simulations
cluster.pathways        Clustering of Pathways
cluster.representatives
                        Cluster Representatives
comp.trans.mat          Compute transition matrix
fit.trj                 Coordinate superposition
map.color               Map the property vector to colours
matrix2graph            Convert transition matrix to an igraph object
native.cont             Select native contact distances
neur.population         Get Neuron Population
neur.representatives    Neuron representative
print.struct            print.struct
print.trj               Print Trajectory
read.gro                Read gro file
read.struct             Read structure files
read.trj                Read trj file
remap.data              map data to existing SOM
rio_read_xtc            Read xtc trajectory file
rio_read_xtc2xyz        Read xtc trajectory file
rio_read_xtc_natoms     Read xtc trajectory file
rio_read_xtc_nframes    Read xtc trajectory file
rio_write_xtc           Write xtc trajectory file
silhouette.profile      Silhouette profile
silhouette.score        Silhouette score
som.add.circles         Add circles to SOM
som.add.clusters.legend
                        Add legend clusters
som.add.numbers         Add Neuron Numbering
stride.trj              Stride a trj
struct2pdb              Convert structure to pdb object
summary.struct          Summarizing a structure object
summary.trj             Summarizing a trajectory object
trace.path              Trace pathway
trj2pdb                 Extract frame to pdb
trj2xyz                 Convert Trajectory to xyz
