- changed status to resolved
Bug: mktrj.nma()
Issue #107
resolved
Got following errors in R CMD check on feature_pdb_dataframe. Possibly came from mktrj.nma.R:
* checking examples ... ERROR
Running examples in ‘bio3d-Ex.R’ failed
The error most likely occurred in:
> ### Name: geostas
> ### Title: GeoStaS Domain Finder
> ### Aliases: geostas amsm.xyz
> ### Keywords: analysis
>
> ### ** Examples
>
> ## Fetch stucture
> pdb <- read.pdb("1hel")
Note: Accessing on-line PDB file
HEADER HYDROLASE(O-GLYCOSYL) 10-JAN-92 1HEL
>
> ## Calculate (vibrational) normal modes
> modes <- nma(pdb)
Building Hessian... Done in 0.052 seconds.
Diagonalizing Hessian... Done in 0.132 seconds.
>
> ## Mode trajectories
> trj <- rbind(mktrj(modes, mode=7),
+ mktrj(modes, mode=8),
+ mktrj(modes, mode=9))
Error in cbind(x$xyz, plus, plus[, rev(1:ncol(plus))], x$xyz, minus, minus[, :
number of rows of matrices must match (see arg 2)
Calls: rbind -> mktrj -> mktrj.nma -> t -> cbind
Execution halted
Comments (1)
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jupp- due to xyz being a matrix. fixed now