Thanks Nikita, I really appreciate your help. -Dave On Aug 5, 5:53 pm, Nikita Beloglazov <nikelandj...@gmail.com> wrote: > See my variant of your > application:https://gist.github.com/efdb66487e899446332f > I don't know if it works, because I can't test :( > > My thoughts about your example > You shouldn't think about this procedure as about procedure where you use > loop, like in other imperative languages with mutable data. As I understand > you tried something like: > > for every line in file do > if line matches then > convert line to coords > add coords to global variable hold-coords > end if > end for > > But it's not the clojure way, I think clojure way is: > > get all lines as sequence > convert every element of this sequence to vector of coords > concat all vectors to one > > And in your 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] > > When you use y in let, it introduce new local variable y, which "hides" > global y > It you want to use mutable data (I don't think it's good), you can use atoms > - it's special mmm... mechanism for mutable data: > > user> (def y (atom [1 2 3])) > #'user/y > > user> @y > [1 2 > 3] > > user> (swap! y into [4 5 6]) > [1 2 3 4 5 > 6] > > user> @y > [1 2 3 4 5 > 6] > > Here you bind to variable y an atom with initial value - vector [1 2 3]. To > get value of atom you use @ before the variable name: @y > To change value you call (swap! atom func x y z). First it calculates new > value like this: (func @atom x y z), in our example it will calculate (into > @y [4 5 6]). It returns vector [1 2 3 4 5 6], and this vector is set as new > value of y. > > Regards, > Nikita Beloglazov > > > > On Thu, Aug 5, 2010 at 11:49 PM, Dave <david.dreisigme...@gmail.com> wrote: > > 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 > > > > > > > <clojure%2bunsubscr...@googlegroups.com<clojure%252bunsubscr...@googlegroup > > s.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... > > read more »
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