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
