Execution of awk script gives error message for invalid character

[tanggo81]

Hi,

I have installed cygwin in a vista platform and tried to run an awk script from the shell but I got an error message pointing that the single qoute as invalid character. Here is the codes I used:

#! /bin/sh
#
awk 'BEGIN {
xmin = 100000.
xmax = -100000.
ymin = 100000.
ymax = -100000.
zmin = 100000.
zmax = -100000.
xsum = 0.
ysum = 0.
zsum = 0.
xpoints = 0
ypoints = 0
zpoints = 0
atom_total = 0
add = 5.0
passo = 0.375
}
$1 ~ /ATOM|HETATM|atom|hetatm/ {
x[atom_total] = substr($0,31,8) + 0.
y[atom_total] = substr($0,39,8) + 0.
z[atom_total] = substr($0,47,8) + 0.

xsum += x[atom_total]
ysum += y[atom_total]
zsum += z[atom_total]

atom_total++
}
END {
if ( atom_total != 0 ) {
xmean = xsum / atom_total
ymean = ysum / atom_total
zmean = zsum / atom_total
#
# Loop over atoms in molecule to find the xyz-coordinates of
# the atom nearest the mean xyz-coordinates of the whole
# molecule...
#
dmin = 100000.
for (i=0; i<atom_total; i++) {
dx = x - xmean
dy = y - ymean
dz = z - zmean
d2 = dx*dx + dy*dy + dz*dz
if (d2 < dmin) {
dmin = d2
centralatom = i
}
if (x < xmin) {
xmin = x
}
if (x > xmax) {
xmax = x
}
if (y < ymin) {
ymin = y
}
if (y > ymax) {
ymax = y
}
if (z < zmin) {
zmin = z
}
if (z > zmax) {
zmax = z
}
}

dx_max = xmax - xmin
dy_max = ymax - ymin
dz_max = zmax - zmin

max = -100000
if (dx_max > max) {
max = dx_max
}
if (dy_max > max) {
max = dy_max
}
if (dz_max > max) {
max = dz_max
}

xmin -= max/2
ymin -= max/2
zmin -= max/2
xmax += max/2
ymax += max/2
zmax += max/2
#xmin -= add
#ymin -= add
#zmin -= add
#xmax += add
#ymax += add
#zmax += add

xpoints = (xmax-xmin)/passo
ypoints = (ymax-ymin)/passo
zpoints = (zmax-zmin)/passo

printf("=========================== Cut from the line below ========================\n")
printf("REMARK Box file to be displayed in any molecule visualizer\n")
printf("REMARK Atoms 1-8 are the vertex of the box\n")
printf("REMARK Atom 9 is the center of the box\n")
printf("REMARK gridcenter %.3f %.3f %.3f\t#xyz-coordinates or \"auto\"\n", xmean, ymean, zmean)
printf("REMARK npts %d %d %d\t\t\t# num.grid points in xyz\n", xpoints, ypoints, zpoints)
printf("REMARK\n")
printf("HETATM 1 C BOX 1 %7.3f %7.3f %7.3f\n", xmin,ymax,zmax)
printf("HETATM 2 C BOX 1 %7.3f %7.3f %7.3f\n", xmax,ymax,zmax)
printf("HETATM 3 C BOX 1 %7.3f %7.3f %7.3f\n", xmin,ymin,zmax)
printf("HETATM 4 C BOX 1 %7.3f %7.3f %7.3f\n", xmax,ymin,zmax)
printf("HETATM 5 C BOX 1 %7.3f %7.3f %7.3f\n", xmin,ymax,zmin)
printf("HETATM 6 C BOX 1 %7.3f %7.3f %7.3f\n", xmax,ymax,zmin)
printf("HETATM 7 C BOX 1 %7.3f %7.3f %7.3f\n", xmin,ymin,zmin)
printf("HETATM 8 C BOX 1 %7.3f %7.3f %7.3f\n", xmax,ymin,zmin)
printf("HETATM 9 C BOX 1 %7.3f %7.3f %7.3f\n", xmean, ymean, zmean)
printf("CONECT 1 5 3 2\n")
printf("CONECT 2 1 4 6\n")
printf("CONECT 3 1 4 7\n")
printf("CONECT 4 3 2 8\n")
printf("CONECT 5 1 6 7\n")
printf("CONECT 6 5 2 8\n")
printf("CONECT 7 5 3 8\n")
printf("CONECT 8 4 6 7\n")
printf("END\n")
printf("=========================== to the line previous this one ========================\n")
printf("\n")
printf("\n")
printf("\n")
printf("\t\t ... and paste into a text file named box.pdb\n")

}
}' $1




and here is the error message that I recieved:
awk: awk 'BEGIN {
awk: awk ^ invalid char ''' in expression

I tried to change the single qoute to double qoute at the beginning and the end of the script but it ended up with an error like this:
awk: awk "BEGIN {
awk: awk ^ unterminated string

Am I missing something or done anything wrong in the code?
Thanks.

 

[p5wizard]

if you use double quotes around the awk program, you'll need to escape all double quotes used in printf or other awk statements...

Give it a try on a simpler awk program.

awk "{printf \"%s\", $1}" testfile

HTH,

p5wizard

 

[Annihilannic]

I just ran it in Cygwin under XP and it seems to pass syntax checks fine.

How exactly are you running the script? Are you running it from the Cygwin bash prompt?

Do you have other Win32 awks on your system that might be running instead of Cygwin's /usr/bin/awk? What's the output of which awk and awk --version?

Annihilannic.