formatted reading using awk - scripting

Question

I am trying to read in a formatted file using awk. The content looks like the following:
1PS1 A1 1 11.197 5.497 7.783
1PS1 A1 1 11.189 5.846 7.700
.
.
.
Following c format, these lines are in following format
"%5d%5s%5s%5d%8.3f%.3f%8.3f"
where, first 5 positions are integer (1), next 5 positions are characters (PS1), next 5 positions are characters (A1), next 5 positions are integer (1), next 24 positions are divided into 3 columns of 8 positions with 3 decimal point floating numbers.
What I've been using is just calling these lines separated by columns using "$1, $2, $3". For example,
cat test.gro | awk 'BEGIN{i=0} {MolID[i]=$1; id[i]=$2; num[i]=$3; x[i]=$4;
y[i]=$5; z[i]=$6; i++} END { ...} >test1.gro
But I ran into some problems with this, and now I am trying to read these files in a formatted way as discussed above.
Any idea how I do this?

Answer 1

Looking at your sample input, it seems the format string is actually "%5d%-5s%5s%5d%8.3f%.3f%8.3f" with the first string field being left-justified. It's too bad awk doesn't have a scanf() function, but you can get your data with a few substr() calls
awk -v OFS=: '
{
a=substr($0,1,5)
b=substr($0,6,5)
c=substr($0,11,5)
d=substr($0,16,5)
e=substr($0,21,8)
f=substr($0,29,8)
g=substr($0,37,8)
print a,b,c,d,e,f,g
}
'
outputs
1:PS1 : A1: 1: 11.197: 5.497: 7.783
1:PS1 : A1: 1: 11.189: 5.846: 7.700
If you have GNU awk, you can use the FIELDWIDTHS variable like this:
gawk -v FIELDWIDTHS="5 5 5 5 8 8 8" -v OFS=: '{print $1, $2, $3, $4, $5, $6, $7}'
also outputs
1:PS1 : A1: 1: 11.197: 5.497: 7.783
1:PS1 : A1: 1: 11.189: 5.846: 7.700

Answer 2

You never said exactly which fields you think should have what number, so I'd like to be clear about how awk thinks that works (Your choice to be explicit about calling the whitespace in your output format string fields makes me worry a little. You might have a different idea about this than awk.).
From the manpage:
An input line is normally made up of fields separated by white space,
or by regular expression FS. The fields are denoted $1, $2, ..., while
$0 refers to the entire line. If FS is null, the input line is split
into one field per character.
Take note that the whitespace in the input line does not get assigned a field number and that sequential whitespace is treated as a single field separator.
You can test this with something like:
echo "1 2 3 4" | awk '{print "1:" $1 "\t2:" $2 "\t3:" $3 "\t4:" $4}'
at the command line.
All of this assumes that you have not diddles the FS variable, of course.