I have a a.pdb file as,
ATOM 1 N ARG 1 0.000 0.000 0.000 1.00 0.00 N ATOM 2 H1 ARG 1 0.000 0.000 0.000 1.00 0.00 H ATOM 3 H2 ARG 1 0.000 0.000 0.000 1.00 0.00 H ATOM 4 H3 ARG 1 0.000 0.000 0.000 1.00 0.00 H
and a.xyz file as
16.388 -5.760 -23.332 17.226 -5.608 -23.768 15.760 -5.238 -23.831 17.921 -5.926 -26.697
I want to replace 6,7 and 8th column of a.pdb with a.xyz. Once replaced, I need to maintain tabs/space/columns of a.pdb.
I have tried
awk 'NR==FNR {fld1[NR]=$1; fld2[NR]=$2; fld3[NR]=$3; next} {$6=fld1[FNR]; $7=fld2[FNR]; $8=fld3[FNR]}1' a.xyz a.pdb
But it doesn't keep the format.
This is exactly what the 4th arg for split() in GNU awk was invented to facilitate:
gawk ' NR==FNR { pdb[NR]=$0; next } { split(pdb[FNR],flds,FS,seps) flds[6]=$1 flds[7]=$2 flds[8]=$3 for (i=1;i in flds;i++) printf "%s%s", flds[i], seps[i] print "" } ' a.pdb a.xyz ATOM 1 N ARG 1 16.388 -5.760 -23.332 1.00 0.00 N ATOM 2 H1 ARG 1 17.226 -5.608 -23.768 1.00 0.00 H ATOM 3 H2 ARG 1 15.760 -5.238 -23.831 1.00 0.00 H ATOM 4 H3 ARG 1 17.921 -5.926 -26.697 1.00 0.00 H
Not a general solution, but this might work with in this particular case:
awk 'NR==FNR{for(i=6; i<=8; i++) A[FNR,i]=$(i-5); next} {for(i=6; i<=8; i++) sub($i,A[FNR,i])}1' file2 file1
or
awk '{for(i=6; i<=8; i++) if(NR==FNR) A[FNR,i]=$(i-5); else sub($i,A[FNR,i])} NR>FNR' file2 file1
There is a bit of a shift, though. We would need to know the fields widths to prevent this.
-- Or perhaps with substrings:
awk 'NR==FNR{A[FNR]=$0; next} {print substr($0,1,p) FS A[FNR] substr($0,p+length(A[FNR]))}' p=33 file2 file1
-- changing it in the OP's original solution:
awk 'NR==FNR {fld1[NR]=$1; fld2[NR]=$2; fld3[NR]=$3; next} {sub($6,fld1[FNR]); sub($7,fld2[FNR]); sub($8,fld3[FNR])}1' file file1
with the same restrictions as the first 2 suggestions.
So 1, 2, and 4 use sub to replace, which is not a water proof solution, since earlier fields might interfere and it uses regex rather than strings (and so the regex dot happens to match the actual dot), but with this particular input, it might pan out..
Probably nr. 3 would be a more fool-proof method..
--edit-- I think this would work with the given input:
awk 'NR==FNR{A[FNR]=$1 " " $2 " " $3; next} {print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR]))}' p=32 file2 file1
but I think something like printf or sprint formatting would be required to make it fool-proof. So, perhaps something like this:
awk 'NR==FNR{A[FNR]=sprintf("%7.3f %7.3f %8.4f", $1, $2, $3); next} {print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR]))}' p=31 file2 file1
or not on one line:
awk ' NR==FNR { A[FNR]=sprintf("%7.3f %7.3f %8.4f", $1, $2, $3) next } { print substr($0,1,p) A[FNR] substr($0,p+length(A[FNR])) } ' p=31 file2 file1
You can try this one
paste -d' ' test4 test5 |awk '{print $1,$2,$3,$4,$5,$12,$13,$14,$9,$10,$11}'
