Self Organising Maps for the Analysis of Molecular Dynamics Data

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Documentation for package ‘SOMMD’ version 0.1.2

• DESCRIPTION file.
• Package NEWS.

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