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 <nikelandj...@gmail.com> 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 <david.dreisigme...@gmail.com> 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 > > > -- > > You received this message because you are subscribed to the Google > > Groups "Clojure" group. > > To post to this group, send email to clojure@googlegroups.com > > Note that posts from new members are moderated - please be patient with > > your first post. > > To unsubscribe from this group, send email to > > clojure+unsubscr...@googlegroups.com<clojure%2bunsubscr...@googlegroups.com > > > > > For more options, visit this group at > >http://groups.google.com/group/clojure?hl=en -- You received this message because you are subscribed to the Google Groups "Clojure" group. To post to this group, send email to clojure@googlegroups.com Note that posts from new members are moderated - please be patient with your first post. To unsubscribe from this group, send email to clojure+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/clojure?hl=en