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Full Discussion: Please help to fix awk script
Top Forums UNIX for Dummies Questions & Answers Please help to fix awk script Post 302794901 by snysmumrik on Wednesday 17th of April 2013 02:47:18 AM
Old 04-17-2013
Please help to fix awk script
Good morning, fellows. I would need to ask for your help in editing my awk script. Here is the original version:

BEGIN { printf ("CRYST1 200.000 200.000 200.000 90.00 90.00 90.00 P 1 1\n")
maxatoms=1000
natom=0
found_struct = 0
found_bond = 0
}
{
if( NF == 5 )
{
foundff=0
natom++
fftype[natom]="UNKNOWN"
if ($1 ~ /CT/)
{
fftype[natom] = "C"
foundff=1
}
else if ($1 ~ /OH/)
{
fftype[natom] = "O"
foundff=1
}
else if ($1 ~ /HC/)
{
fftype[natom] = "H"
foundff=1
}
else if ($1 ~ /N/)
{
fftype[natom] = "N"
foundff=1
}

else if ($1 ~ /H1/)
{
fftype[natom] = "H"
foundff=1
}
else if ($1 ~ /HO/)
{
fftype[natom] = "H"
foundff=1
}
else if ($1 = "C")
{
fftype[natom] = "C"
foundff=1
}
else if ($1 = "O")
{
fftype[natom] = "O"
foundff=1
}

next

x[natom] = $1
y[natom] = $2
z[natom] = $3


if (foundff == 0)
printf("PROBLEM : Atom ff type %s not known\n", $6)
}

}

END {
for (iatom=1; iatom <= natom; iatom++)
{
printf("HETATM %d %2s %d %14.9f %14.9f %14.9f\n" ,
iatom, fftype[iatom], iatom, x[iatom], y[iatom], z[iatom])
}
printf ("END\n")
}


And this is type of file I am working with.

0 3 186 200 75202
timestep 500 186 0 3 0.002000 1.000000
40.0000000000 0.0000000000 0.0000000000
-0.0000000034 40.0000000000 0.0000000000
-0.0000000034 -0.0000000034 40.0000000000
CT_1 1 12.011000 0.061000 1.087513
-1.961325738 1.828501682 -8.933652557
CT_1 2 12.011000 0.061000 0.789711
-3.851025437 3.495427316 -10.05849230
CT_1 3 12.011000 0.061000 0.581330
-5.804493575 4.589489777 -8.369482861

ect

I would like to get this as an output:

CRYST1 200.000 200.000 200.000 90.00 90.00 90.00 P 1 1
HETATM 1 C 1 -1.961325738 1.828501682 -8.933652557
HETATM 2 C 2 -3.851025437 3.495427316 -10.05849230
HETATM 3 C 3 -5.804493575 4.589489777 -8.369482861

ect

But coordinates are not really picking up well (next line after CT_1 1 12.011000 0.061000 1.087513). Can you please have a look and suggest any solutions. Thanks.
 

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LEARN ABOUT CENTOS

igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)
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