I know for a single case, this could be finished quickly with Excel. But if we have hundreds of files, we definitely want to do it with a script or a FORTRAN code. Since I have no knowledge of FORTRAN, I tried to work out a script to do it. The math is very simple. we chose one atom (in x, y, z, Cartesian coordinate), and we calculate the distance from other atom to the reference atom with the simple math sqrt((x(i)-x(1))^2+(y(i)-y(1))^2+(z(i)-z(1))^2)
Problem explanation: we have a list of numbers
Code:
P 1.219142 0.637315 -0.824280
N -0.265369 0.551699 -1.665314
P -1.232957 -0.291982 -0.536350
C 1.550001 2.370502 -0.242803
C 0.756639 2.983923 0.747041
C 1.003518 4.293274 1.173466
C 2.045233 5.026004 0.616725
C 2.835510 4.452541 -0.372444
C 2.587869 3.143957 -0.800209
C 2.645951 0.045340 -1.859172
assume we set the P1 as the center atom, now we need to calculate all the distance of other atoms from P, respectively.
and we print out the results as follows,
Thanks so much for the script. It works like a charm.
Would you please give me some explanation about this script? How does it works so fast. Since you use unformatted print inside awk, so the bond title and bond distance are not aligned with each other if there are hundreds of bond.
for instance, there are 19 bond titles and 24 distances
BEGIN {
CONVFMT="%.3f"
}
NR==1 {
split($0,F)
next
}
{
ht=sprintf("%-9s",$1 NR "-" F[1]1)
rt=sprintf("%-9s",sqrt(($2-F[2])^2+($3-F[3])^2+($4-F[4])^2))
h=(h)? h OFS ht:ht
r=(r)?r OFS rt:rt
}
END {
print h ORS r
}
Great! Now, these two rows are aligned within each column. The output is perfectly formatted.
Would you please explain a little bit on 'split', 'sprintf', 'OFS', 'h ORS r'?
How does it work? It's an advanced script with so many keywords I've never seen before.
Thanks you very much!
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