Man pages for SOMMD
Self Organising Maps for the Analysis of Molecular Dynamics Data
| 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 |
