Self Organising Maps for the Analysis of Molecular Dynamics Data


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Documentation for package ‘SOMMD’ version 0.1.2

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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