Print the shifts in individual atom positions - Revision history

Pozharski at 15:06, 16 December 2010

2010-12-16T15:06:00Z

← Older revision		Revision as of 17:06, 16 December 2010
Line 1:		Line 1:
	This can be done with one command line (albeit a rather long one). It also implies a rather recent version of awk, some older versions won't support the fixed width argument splitting. Below is the code with (remove backslashes if pasting as a single line)		This can be done with one command line (albeit a rather long one). It also implies a rather recent version of awk, some older versions won't support the fixed width argument splitting. Below is the code with (remove backslashes if pasting as a single line)

	grep 'ATOM\\|HETATM' file1.pdb file2.pdb \| \		grep 'ATOM\\|HETATM' file1.pdb file2.pdb \| \
			grep -v REMARK \| \
	grep -v REMARK \| \		cut -d: -f 2 \| \
			cut -c 13-54 \| \
	cut -d: -f 2 \| \		sort \| \
			awk 'BEGIN {FIELDWIDTHS = "14 28"; pt=""} {if(pt==$1) print pr,$2; pt=$1; pr=$0;}' \| \
	cut -c 13-54 \| \		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;}'
	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;}'


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Pozharski at 14:49, 14 December 2010

2010-12-14T14:49:44Z

← Older revision		Revision as of 16:49, 14 December 2010
Line 1:		Line 1:
	This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as a single line)		This can be done with one command line (albeit a rather long one). It also implies a rather recent version of awk, some older versions won't support the fixed width argument splitting. Below is the code with (remove backslashes if pasting as a single line)

	grep 'ATOM\\|HETATM' file1.pdb file2.pdb \| \		grep 'ATOM\\|HETATM' file1.pdb file2.pdb \| \

Pozharski at 15:30, 10 December 2010

2010-12-10T15:30:40Z

← Older revision		Revision as of 17:30, 10 December 2010
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	awk 'BEGIN {FIELDWIDTHS = "4 1 3 1 1 5 9"} {printf "%s %s %s %s %s\n", $3,$5,$6,$1,$7;}'		awk 'BEGIN {FIELDWIDTHS = "4 1 3 1 1 5 9"} {printf "%s %s %s %s %s\n", $3,$5,$6,$1,$7;}'


			Back to [[Useful scripts (aka smart piece of code)]]

Pozharski: Created page with 'This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as a single line) grep 'ATOM\|HETATM' file1.pdb file2.p…'

2010-07-03T16:33:49Z

Created page with 'This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as a single line) grep 'ATOM\|HETATM' file1.pdb file2.p…'

New page

This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as 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;}'