Thanks for the extra parentheses catch. I just noticed that while
working on a different function (after hours of trying to figure it
out).
The program is reading in a pdb file line-by-line. I only want the
xyz-coordinates of carbon atoms, avoiding any repeats when the
coordinate of an atom is uncertain. Also, a protein may have multiple
sub-units, and the chains parameter can pick out the desired sub-
unit(s). So I need to:
1) make sure the line is long enough
2) make sure I have an atom
3) make sure it's not a repeated measurement
4) make sure it's a C_{alpha} atom
If the current pdb-file line matches those criteria, I'll then put its
xyz-coordinates into the output matrix.
I tried this using let:
(defn process-dpa-file2
"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))
;; These are the CA coordinates
(let [coords (into hold-coords [ (Double. (.substring line 30
37))
(Double. (.substring line 38 45))
(Double. (.substring line 46 53))])
hold-coords coords]))
(matrix hold-coords 3)))
but the output gives:
dpa> (def my-mat (process-dpa-file2 "/Users/daviddreisigmeyer/MyStuff/
DPA_release_12-JUL-2010/1RD8.pdb" "A") )
#'dpa/my-mat
dpa> my-mat
nil
A simpler example:
dpa> (def y [5 6 7]) (let [x (into y [2 3 4]) y x ] y)
[5 6 7 2 3 4]
dpa> y
[5 6 7]
So it seems that in process-dpa-file2 I have the coordinates of the
1st carbon atom in hold-coords, and then the 2nd, the 3rd ... After
finding the 3rd carbon, I'd want:
hold-coords = [x1 y1 z1 x2 y2 z2 x3 y3 z3] (**)
but instead I get
hold-coords = [x3 y3 z3]. Any idea about how I could get (**)
instead? Thanks! -Dave
On Aug 5, 2:46 pm, Nikita Beloglazov <[email protected]> wrote:
> Hi, Dave
> Why do you use 2 parenthesis before "with-open" in the first variant?
> And, as I know, it's not good practice to use def inside functions. Use let
> instead.
> I also advice you to split your program to smaller functions.
> Can you describe, what your program must do? Because don't understand :(
>
>
>
> On Thu, Aug 5, 2010 at 9:28 PM, Dave <[email protected]> wrote:
> > 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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