nma: check for correct ordering of trivial modes

[Lars Skjærven]

Unphysical structures (i.e. with C-alpha clashes) can yield negative eigenvalues. This messes up the ordering since I assume that the trivial modes come first, and not negative modes first. Possible solutions: Output a warning and reorder the eigenvalues (and vectors), or stop() function since the structure is anyway not meaningful.

Example: PDB-id 1GRU (chain H) contains c-alpha clashes: pdb=read.pdb("1gru", maxlines=700000) sele=atom.select(pdb, chain="H") m=nma(pdb, sele) head(m$L, n=8) [1] -2708.634577 0.000000 0.000000

[Lars Skjærven]

A warning is issued in case of negative eigenvalues.

[Barry Grant]

I like this warning() approach rather than the stop() option. Good job Lars!