GNM model issue

[Mamta Mohan]

Hello,

I am trying to generate Normal Modes via Gaussian Network Model.

It does not seem to generate the NMs.

I will appreciate your response.

I am listing the commands and their results below:

> # Calculate NMs via GNM
> modes.gnm <- gnm(pdb)
> # Print modes
> print(modes.gnm)
$fun
function (n, m, directed = FALSE, loops = FALSE) 
{
    type <- "gnm"
    type1 <- switch(type, gnp = 0, gnm = 1)
    on.exit(.Call("R_igraph_finalizer", PACKAGE = "igraph"))
    res <- .Call("R_igraph_erdos_renyi_game", as.numeric(n), 
        as.numeric(type1), as.numeric(m), as.logical(directed), 
        as.logical(loops), PACKAGE = "igraph")
    if (igraph_opt("add.params")) {
        res$name <- sprintf("Erdos renyi (%s) graph", type)
        res$type <- type
        res$loops <- loops
        res$m <- m
    }
    res
}
<environment: namespace:igraph>

$args
[[1]]
$expr
pdb

$env
<environment: R_GlobalEnv>

attr(,"class")
[1] "lazy"

attr(,"class")
[1] "lazy_dots"

$lazy
[1] FALSE

attr(,"class")
[1] "igraph_constructor_spec"

[Xinqiu Yao]

Hi,

It seems that the 'igraph' package also has a function named gnm, which was the one you actually called above. It is an unfortunate conflict and we may think solving it in future. Currently, you need to specifically call gnm.pdb() or bio3d::gnm(). Alternatively, you could change the order of search path by

detach(package:bio3d)
library(bio3d)

[Mamta Mohan]

Thank you.

I will do that.