Thanks everyone. I have already tried the full path:
(defn get-msms-pts-OSX
;; Finds the msms points for a density (optional DEFAULT = 1.0) and
radius (optional DEFAULT = 1.5)
[pdb-file density radius]
(execute (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/
pdb_to_xyzr " pdb-file
" > /Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr")))
Here it seemed to run (the above error isn't shown) but nothing
happened and the REPL become unresponsive again. The call above only
takes a few seconds if I run it in a terminal using the output of (str
"...").
When I try:
(ns msms
(:gen-class)
(:use [clojure.contrib.duck-streams :only (read-lines)]
[clojure.contrib.shell-out :only (sh)]))
(defn get-msms-pts-OSX
;; Finds the msms points for a density (optional DEFAULT = 1.0) and
radius (optional DEFAULT = 1.5)
[pdb-file density radius]
(sh :in (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/pdb_to_xyzr
" pdb-file
" > /Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr")))
I get the following:
No matching method found: exec for class java.lang.Runtime
[Thrown class java.lang.IllegalArgumentException]
so I'll need to look at that a bit more.
Does anyone know why this doesn't seem to work:
(defn test-execute [ls-arg1 ls-arg2]
(execute (str "ls -" ls-arg1))
(execute (str "ls -" ls-arg2)))
Thanks again.
-Dave
On Aug 6, 11:06 pm, j-g-faustus <johannes.fries...@gmail.com> wrote:
> On Aug 6, 11:50 pm, Dave <david.dreisigme...@gmail.com> wrote:
>
> > I get the error:
>
> > Cannot run program "pdb_to_xyzr": error=2, No such file or directory
> > [Thrown class java.io.IOException]
>
> You may have a path problem.
> Try running "env" in the same fashion - I get a very basic path (just
> "/bin" and "/usr/bin") and none of my settings from .bashrc
> or .profile.
>
> Workarounds I know of:
>
> - Use clojure.contrib.shell-out and supply a map of the environment
> variables you need, including the
> path:http://richhickey.github.com/clojure-contrib/shell-out-api.html
>
> - Put the "pdb_to_xyzr" call into a shell script that sets the path
> for you, and call the shell script from your program.
>
> - Use the full path to the executable rather than relying on
> environment variables.
>
> - Use one of the Java Runtime.exec variants that takes a String array
> of environment variables. (Although I would recommend one of the other
> options - I don't think there's a direct way to create a String array
> in Clojure, but you could do it indirectly through String.split or
> similar.):http://download-llnw.oracle.com/javase/1.5.0/docs/api/java/lang/Runti...
>
> Regards
> jf
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