Difficulty resolving "can not find channel number" error in my code 1

[scottjn]

Hi there all,

I have the below code, which is to be interpreted in the software package VMD, and I am having some basic Tcl problems with it. Basically what I want to do is to open a file, discard the first line of that file, and then store the numerical value of the 4th column of the file in a variable called trpshift, which I will use in VMD to color individual molecules.

I know that the coloring part of the script works, because I was able to use a similar script successfully, but now my input files are a bit different and I need to discard the first line (this wasn't an issue before, because I had specially formatted files to access). I found an example of how to discard a line in Tcl on a webpage somewhere, but I keep getting the error "can not find channel number <file contents>" when the script reaches the first nested while loop, the one that is supposed to process the file data. It appears that the entire contents of $file_data are being expanded within the while evaluation, but I can't get this behavior to stop.

Can anyone offer any help with this issue? This is probably a very basic Tcl screw up on my part, but I can't seem to figure it out and would sincerely appreciate any help you can offer!

while {$i >= $first && $i <= $last} {
        set fp [open "/data/1stn/$mut/pd5/1stn_$mut_$i.pd5" r]
        set file_data [read $fp]
        close $fp

        while {[gets $file_data line] >= -1 } {
        set data [split $file_data "\n"]
        foreach {one} $data {
                lappend trpshift [lindex $one 3]
        }
	}

	set prot [atomselect $mol_ID protein frame $j]
        $prot frame $j
        set user_list {}
        for {set a 0} {$a < 136} {incr a} {
                set u [lindex $trpshift $a]
                lappend user_list $u $u $u
        }
	$prot set user $user_list
        $prot delete

        set wat [atomselect $mol_ID waters frame $j]
        $wat frame $j
        set user_list {}
        for {set a 136} {$a < 10233} {incr a} {
                set u [lindex $trpshift $a]
                lappend user_list $u $u $u
        }
	$wat set user $user_list
        $wat delete

        set ions [atomselect $mol_ID ions frame $j]
        $ions frame $j
        set user_list {}
        for {set a 10233} {$a < 10244} {incr a} {
                set u [lindex $trpshift $a]
                lappend user_list $u $u $u
        }
	$ions set user $user_list
        $ions delete

        unset trpshift
        incr j 1
        incr i 2
}

 

[scottjn]

By the way, here are the first few lines of one of the sorts of files I need to read, so you can see the format I am dealing with. The column I want to store in the trpshift list is the 4th one, the pdif column.

#0 pdifc4: indx,amino,rave,pdif,runsum,segid,resid
1 LYS 32.66 1.16985 1.16985 LYS 6
2 LEU 26.73 0.03381 1.20365 LEU 7
3 HIS 31.00 -0.00297 1.20069 HIS 8
4 LYS 27.72 0.13354 1.33423 LYS 9
5 GLU 31.13 -0.56292 0.77131 GLU 10
6 PRO 32.50 -0.04138 0.72992 PRO 11
7 ALA 29.89 0.03035 0.76028 ALA 12
8 THR 31.89 -0.05019 0.71009 THR 13
9 LEU 28.16 -0.01579 0.69430 LEU 14
10 ILE 31.11 0.03815 0.73245 ILE 15
11 LYS 28.13 0.34762 1.08007 LYS 16

 

[Bong]

I think you may have made this too complicated.

while {$i >= $first && $i <= $last} {
set fp [open "/data/1stn/$mut/pd5/1stn_$mut_$i.pd5" r]
set file_data [read $fp]
close $fp

while {[gets $file_data line] >= -1 } {
set data [split $file_data "\n"]
foreach {one} $data {
lappend trpshift [lindex $one 3]
}
}

The outer while loop seems to be determining which files you open. Is that a) correct, and b) working right for you? I suggest you make a list of lines in the erstwhile "read" step:

while {$i >= $first && $i <= $last} {
        set fp [open "/data/1stn/$mut/pd5/1stn_$mut_$i.pd5" r]
        set data [split [read $fp] \n]
        close $fp
 ...............
    }

Now if all you're interested in doing is to discard the first line of the file (now the first element of the list, data:

set data [lrange $data 1 end]

Now you seem to be doing something peculiar:

while {[gets $file_data line] >= -1 }

In your original code, "file_data" is a string, having been returned from "[read...]" so that's the problem you're seeing: "gets" is trying to interpret the string, file_data, as an open channel number. Anyway, my way you're already working with a list so without evaluating what you're doing inside the loop:

while {$i >= $first && $i <= $last} {
        set fp [open "/data/1stn/$mut/pd5/1stn_$mut_$i.pd5" r]
        set data [split [read $fp] \n]
        close $fp
        foreach line [lrange $data 1 end] {
                lappend trpshift [lindex $line 3]
        }
    }

_________________
Bob Rashkin

 

[scottjn]

Bob, thank you so much for your help, your method is so much simpler and more straightforward than what I was trying to do. My outer while loop *was* in fact working to read in the correct file data, but my clunky attempt to start creating the data list at the 2nd line wasn't working at all (as you could tell). I've only done a very small amount of Tcl programming (and not that much programming at all!) and I had completely forgotten about the extensive list modification methods in Tcl.

Thank you again very much for your help, your time and expertise are sincerely appreciated!

Best,
Nathan