Issue
EDIT BELOW
I'm new to bash scripting, sorry if this has been answered elsewhere, couldn't find it in any searches I've done.
I'm using sed -i to add a line above an argument, for example.
for EFP in *.inp; do
sed -i "/^O */i FRAGNAME=H2ODFT" $EFP
done
and it works as expected. but I would like it to only add the line when the argument is true across multiple lines, like so:
O
C
O
C
FRAGNAME=H2ODFT
O
H
H
FRAGNAME=H2ODFT
O
H
H
Notice there's no added line above the two O's that are followed by C's.
I tried the following:
for FILE in *.inp; do
sed -i "/^O*\nH*\nH */i FRAGNAME=H2ODFT" $EFP
done
and I was expecting it to show up above the 3 lines that went O - H - H, but nothing happened, it passed through the file thinking that that argument was nowhere in the document.
I've looked elsewhere and thought of using awk, but I can't wrap my head around it.
Any help would be greatly appreciated! L
EDIT
Thanks for the help. And sorry for being a bit unclear. I've tried a ton of things, too many to put in this post. I've tried awk, perl and sed solutions, but they're not working.
My input has a series of O's C's and H's, with cartesian coordinates assigned to them:
C 36.116 34.950 34.657
C 35.638 34.681 35.883
C 36.134 33.569 36.703
C 34.379 34.567 37.522
N 34.579 35.375 36.476
N 35.234 33.518 37.706
O 37.045 32.745 36.559
H 36.892 34.226 34.415
O 35.234 38.803 30.513
H 34.303 39.079 30.567
C 33.490 35.015 38.608
H 34.002 35.390 39.503
H 32.894 34.170 38.974
H 32.832 35.813 38.245
C 35.342 32.708 38.920
H 35.920 33.237 39.688
H 35.942 31.802 38.772
H 34.356 32.475 39.340
O 30.226 35.908 36.744
H 30.557 36.408 37.490
H 30.642 36.311 35.982
O 37.356 40.420 29.232
H 36.473 40.786 29.286
H 37.220 39.474 29.189
O 40.889 37.054 35.401
H 40.304 36.361 35.706
H 41.620 36.587 34.995
I'm trying to input a new line above a specific set of three lines, the OHH lines.
The awk solution posted didn't work, because it would add extra lines where there shouldn't be when the stage gets reset. I'm looking for the following output:
C 36.116 34.950 34.657
C 35.638 34.681 35.883
C 36.134 33.569 36.703
C 34.379 34.567 37.522
N 34.579 35.375 36.476
N 35.234 33.518 37.706
O 37.045 32.745 36.559
H 36.892 34.226 34.415
O 35.234 38.803 30.513
H 34.303 39.079 30.567
C 33.490 35.015 38.608
H 34.002 35.390 39.503
H 32.894 34.170 38.974
H 32.832 35.813 38.245
C 35.342 32.708 38.920
H 35.920 33.237 39.688
H 35.942 31.802 38.772
H 34.356 32.475 39.340
FRAGNAME=H2ODFT
O 30.226 35.908 36.744
H 30.557 36.408 37.490
H 30.642 36.311 35.982
FRAGNAME=H2ODFT
O 37.356 40.420 29.232
H 36.473 40.786 29.286
H 37.220 39.474 29.189
FRAGNAME=H2ODFT
O 40.889 37.054 35.401
H 40.304 36.361 35.706
H 41.620 36.587 34.995
The ^tsed was a typo and should've been an indent instead of ^t
Solution
Here is a ruby to do that:
ruby -e 'lines=$<.read.split(/\R/)
lines.each_with_index{|line,i|
three_line_tag=lines[i..i+2].map{|sl| sl.split[0] }.join
puts "FRAGNAME=H2ODFT" if three_line_tag == "OHH"
puts line
}
' file
Or any awk, same kind of method:
awk '{lines[NR]=$0}
END{
for(i=1;i<=NR;i++) {
tag=""
for(j=0;j<=2;j++) {
split(lines[i+j],arr)
tag=tag arr[1]
}
if (tag=="OHH")
print "FRAGNAME=H2ODFT"
print lines[i]
}
}
' file
Or Perl:
perl -0777 -pe 's/(^\h*O\h.*\R^\h*H\h.*\R^\h*H\h.*\R?)/FRAGNAME=H2ODFT\n\1/gm' file
Any print:
C 36.116 34.950 34.657
C 35.638 34.681 35.883
C 36.134 33.569 36.703
C 34.379 34.567 37.522
N 34.579 35.375 36.476
N 35.234 33.518 37.706
O 37.045 32.745 36.559
H 36.892 34.226 34.415
O 35.234 38.803 30.513
H 34.303 39.079 30.567
C 33.490 35.015 38.608
H 34.002 35.390 39.503
H 32.894 34.170 38.974
H 32.832 35.813 38.245
C 35.342 32.708 38.920
H 35.920 33.237 39.688
H 35.942 31.802 38.772
H 34.356 32.475 39.340
FRAGNAME=H2ODFT
O 30.226 35.908 36.744
H 30.557 36.408 37.490
H 30.642 36.311 35.982
FRAGNAME=H2ODFT
O 37.356 40.420 29.232
H 36.473 40.786 29.286
H 37.220 39.474 29.189
FRAGNAME=H2ODFT
O 40.889 37.054 35.401
H 40.304 36.361 35.706
H 41.620 36.587 34.995
===
Edit in place:
Read THIS about awk and that is generally applicable.
Any of these scripts as written write to stdout.
You can redirect the output to a new file:
someutility input_file >new_file
Or some (like perl, ruby, GNU awk, GNU sed) have the ability to do in-place file replacement. If you don't have that option, you cannot do:
someutil 'prints to STDOUT' file >file
since file will be destroyed before fully read.
Instead you would do:
someutil 'prints to STDOUT' file > tmp && mv tmp file
Answered By - dawg Answer Checked By - Senaida (WPSolving Volunteer)