On Fri, 2010-04-30 at 13:35 +0100, Nicholas Keep wrote:
> If anyone has a piece of software that would do this it would be
> great.
>
How about this (this is a single line)
---
grep 'ATOM\|HETATM' file1.pdb file2.pdb |grep -v REMARK | cut -d: -f 2 |
cut -c 13-54 | sort | awk 'BEGIN {FIELDWIDTHS = "14 28"; pt=""} {if(pt==
$1) print pr,$2; pt=$1; pr=$0;}' | awk 'BEGIN {FIELDWIDTHS = "14 4 8 8 8
5 8 8 8"} {printf "%s %8.4f\n",$1,sqrt(($3-$7)^2+($4-$8)^2+($5-$9)^2);}'
| awk 'BEGIN {FIELDWIDTHS = "4 1 3 1 1 5 9"} {printf "%s %s %s %s %s\n",
$3,$5,$6,$1,$7;}'
---
The output is not sorted (sort isn't friendly to the idea of sorting
alphabetically and numerically at the same time). And "awk" means
"gawk" - "mawk" (Ubuntu default) doesn't allow fixed field selection
which is key to dealing with files that have alternate conformers).
HTH,
Ed.
--
"I'd sacrifice myself, but I'm too good at whistling."
Julian, King of Lemurs
