Dear David and Kaiser:
While the PDB format is (thankfully--to those used to it) around, it seems to
me it is certainly a rather poor deterrent to the enjoyment of AWK:
For fixed-field format input, the designers of AWK suggested a useful solution:
the function substr(s,p,n), i.e., "return substring of s of length n starting
at position p" (Aho et al. The AWK Programming Language. Addison-Wesley, 1988,
pp. 42, 43, 72).
The solution I've used, though, is to use gnu awk (gawk) with the format
definition as follows:
BEGIN {FIELDWIDTHS="6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 10 2 2";}
--hope you'd find that useful too.
As for Perl, somebody put it nicely that one should comment programs bearing in
mind that the person reading them later is always a different one from the one
who wrote them; that includes the programmer as she/he will always be in a
different state of mind her/himself.
Best regards,
Navdeep
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On Tue, Aug 06, 2013 at 08:07:22AM -0400, David A Case wrote:
>
> An awk script with /^ATOM/ as its selection is actually easier to write
> than the corresponding script for a PDB ATOM record, since the line can
> be split on white space.
On Mon, Aug 05, 2013 at 03:10:55AM -0700, kaiser wrote:
> Yes, using grep on mmcif files is "awk"ward (but petfectly possible); awk
> on the other hand works much better. It's actually more of a pain to use it
> on pdb files. And perl, well perl can handle anything and it will always look
> nice while you write it and never look nice when you look back at it...
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Navdeep Sidhu
University of Goettingen
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