Recursive insertion of a line

Henry henry.robinson at
Tue Nov 20 01:15:16 CET 2007

On 19/11/2007, Francesco Pietra <chiendarret at> wrote:
> New to the list and just beginning with Python (Linux B console). Urgent
> problem before I can correctly program:
> How to insert "TER" records recursively, i.e. some thousand fold,  in a
> file
> like in the following example? "H2 WAT" is the only constant
> characteristic of
> the line after which to insert "TER"; that distinguishes also for lines
> for
> other atoms. Just to illustrate what I want to do - for those unfamiliar
> with
> this type of file - a three-line set between two "TER" defines a water
> molecule, with a set of xyz coordinates for each atom.

If every molecule is water, and therefore 3 atoms, you can use this fact to
insert TER in the right place. You don't need recursion:

f = open( "atoms.txt", "rt" )
lineCount = 0
for line in f.xreadlines( ):
    lineCount = lineCount + 1
    print line
    if lineCount == 3:
        lineCount = 0
        print "TER"
f.close( )

You could do the above in fewer lines with a regex (this would also work
even if all molecules weren't water), which would probably be neater, but is
left as an exercise for the reader :) There are probably much better
idiomatic ways to do this, and I defer to much more experienced Python
programmers to show you them.


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