Also, this only shows the 2nd call (with ls-arg2):
(defn test-execute [ls-arg1 ls-arg2]
(execute (str "ls -" ls-arg1))
(execute (str "ls -" ls-arg2)))
so maybe the difficulty above is some problem with how the multiple
system calls are performed. If I only use this:
(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 "pdb_to_xyzr " pdb-file
" > /Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr")))
I get the error:
Cannot run program "pdb_to_xyzr": error=2, No such file or directory
[Thrown class java.io.IOException]
I've put pdb_to_xyzr on my path, and I can call it from a terminal,
i.e., putting this output in a terminal works:
(str "pdb_to_xyzr " "/Users/daviddreisigmeyer/lisps/clojure/dpa/src/
1RD8.pdb"
" > /Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr")
********* I use this in a terminal: *********
"pdb_to_xyzr /Users/daviddreisigmeyer/lisps/clojure/dpa/src/1RD8.pdb
> /Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"
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