Hi Dave,
There are really 2 functions, -> and ->>
First ->
Sometimes you need to perform several functions on after another. You can
write something like
(func1 (func2 (func3 value)))
But you also can write like:
(-> value
(func3)
(func2)
(func1))
It takes value, insert it into (func1) form as second element, so it will
become (func3 value), evaluates it. Result of evaluation insert into
(func2), evaluates it and etc.
-> function inserts value as second element, e.g. (form3 a b c) becomes
(form3 value a b c)
->> function inserts value as last element, e.g. (form3 a b c) becomes
(form3 a b c value)
(->> (read-lines pdb-file)
(map #(parse-line % chains))
(apply concat)))
First it evaluates (read-lines pdb-file), let's name the result seq1
Then it evaluates (map #(parse-line % chains) seq1) and we get seq2
And finally it evaluates (apply concat seq2)
Regards,
Nikita Beloglazov
On Fri, Aug 6, 2010 at 7:26 PM, Dave <david.dreisigme...@gmail.com> wrote:
> Hi Nikita,
>
> Your function works! Could you explain the "->>" a bit? Thanks, -
> 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
> >
> > > > > --
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