Hi,
I don't understand why this doesn't work:
(ns dpa
(:gen-class)
(:use [incanter.core :only ( matrix )]
[clojure.core :only ( defn doseq line-seq println with-open )]
[clojure.contrib.string :only ( blank? substring? )]
(:import (java.io BufferedReader FileReader)))
(defn process-dpa-file
"This makes the matrix of CA coordinates from a pdb file."
[pdb-file chains]
(def hold-coords [])
((with-open [rdr (BufferedReader. (FileReader. pdb-file))]
(doseq [^String line (line-seq rdr)]
;; Make sure the file line is the correct length
;; We only want the atom entries
;; We don't want any repeated measurements for an atom
;; Is it a CA?
;; Are we using this chain?
(if (and (= (.length line) 80)
(= (str (.substring line 0 4) (.substring line 26 27)
(.substring line 13 15)) "ATOM CA")
(substring? (.substring line 21 22) chains))
;; This are the CA coordinates
(def hold-coords (into hold-coords [ (Double. (.substring line
30 37))
(Double. (.substring line 38 45))
(Double. (.substring line 46 53)) ]
)))))
(matrix hold-coords 3)))
dpa> (def my-mat (process-dpa-file "/Users/daviddreisigmeyer/MyStuff/
DPA_release_12-JUL-2010/1RD8.pdb" "A") )
No message.
[Thrown class java.lang.NullPointerException]
Restarts:
0: [QUIT] Quit to the SLIME top level
Backtrace:
0: dpa$process_dpa_file.invoke(NO_SOURCE_FILE:1)
1: clojure.lang.AFn.applyToHelper(AFn.java:165)
2: clojure.lang.AFn.applyTo(AFn.java:151)
3: clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:2901)
4: clojure.lang.Compiler$DefExpr.eval(Compiler.java:361)
5: clojure.lang.Compiler.eval(Compiler.java:5424)
6: clojure.lang.Compiler.eval(Compiler.java:5386)
7: clojure.core$eval.invoke(core.clj:2382)
8: swank.commands.basic$eval_region.invoke(basic.clj:47)
9: swank.commands.basic$eval_region.invoke(basic.clj:37)
10: swank.commands.basic$eval799$listener_eval__800.invoke(basic.clj:
71)
11: clojure.lang.Var.invoke(Var.java:365)
12: dpa$eval9236.invoke(NO_SOURCE_FILE)
13: clojure.lang.Compiler.eval(Compiler.java:5419)
14: clojure.lang.Compiler.eval(Compiler.java:5386)
15: clojure.core$eval.invoke(core.clj:2382)
16: swank.core$eval_in_emacs_package.invoke(core.clj:90)
17: swank.core$eval_for_emacs.invoke(core.clj:237)
18: clojure.lang.Var.invoke(Var.java:373)
19: clojure.lang.AFn.applyToHelper(AFn.java:169)
20: clojure.lang.Var.applyTo(Var.java:482)
21: clojure.core$apply.invoke(core.clj:540)
22: swank.core$eval_from_control.invoke(core.clj:97)
23: swank.core$eval_loop.invoke(core.clj:102)
24: swank.core$spawn_repl_thread$fn__484$fn__485.invoke(core.clj:307)
25: clojure.lang.AFn.applyToHelper(AFn.java:159)
26: clojure.lang.AFn.applyTo(AFn.java:151)
27: clojure.core$apply.invoke(core.clj:540)
28: swank.core$spawn_repl_thread$fn__484.doInvoke(core.clj:304)
29: clojure.lang.RestFn.invoke(RestFn.java:398)
30: clojure.lang.AFn.run(AFn.java:24)
31: java.lang.Thread.run(Thread.java:637)
But, this does work:
(defn process-dpa-file
"This makes the matrix of CA coordinates from a pdb file."
[pdb-file chains]
(def hold-coords [])
(doseq [^String line (read-lines pdb-file)]
;; Make sure the file line is the correct length
;; We only want the atom entries
;; We don't want any repeated measurements for an atom
;; Is it a CA?
;; Are we using this chain?
(if (and (= (.length line) 80)
(= (str (.substring line 0 4) (.substring line 26 27)
(.substring line 13 15)) "ATOM CA")
(substring? (.substring line 21 22) chains))
;; This are the CA coordinates
(def hold-coords (into hold-coords [ (Double. (.substring line
30 37))
(Double. (.substring line 38 45))
(Double. (.substring line 46 53)) ]
))))
(matrix hold-coords 3))
dpa> (def my-mat (process-dpa-file "/Users/daviddreisigmeyer/MyStuff/
DPA_release_12-JUL-2010/1RD8.pdb" "A") )
#'dpa/my-mat
I'd certainly appreciate any comments on the code in general. I only
have a Matlab/R/Fortran 95 background.
Thanks,
-Dave
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