R: Self Organising Maps for the Analysis of Molecular Dynamics Data

# Self Organising Maps for the Analysis of Molecular Dynamics Data

## Documentation for package ‘SOMMD’ version 0.1.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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