View source for Slick awk tricks

Grep out the wallclock time from the namd out files, convert to hours and adds them together. 
 grep "WallClock:" *.out | awk '{sum+=$2/3600} END {print "Hours="sum}'
Same thing, but now also does mean and sd
 awk '{sum+=$2/3600; n+=1; sumsq+=($2/3600)^2} END {print "SD="sqrt(sum^2-sumsq)/(n+1),"Mean="sum/n}'
correction
 awk -F, '{mean+=$94/5000; n+=1; meansq+=(($94^2)/5000)} END {print "SD="sqrt(meansq - mean^2),"Mean="mean}'

Theoretical success rate i.e. at least one pose in mol2 file with RMSD<=2
 awk '/RMSD:/{if($3<=2.0)ths=1}END{print ths}' scored.mol2 

Return lowest EMSD in mol2 file
 awk 'BEGIN{lrm=99}/RMSD:/{if($3<=lrm)lrm=$3}END{printf"%.2f",lrm}' mol2file

==Lowest DOCK RMSD in MOL2 output==
 grep RMSD mol_scored.mol2 | awk '{print $3}' | sort -n | head 

==Using a shell variable==
Here we use the shell variable rmsdcut to set a different RMSD cutoff for success rate when calculating the theoretical success rate in the multi-mol2 file of docked poses. This prints 1 if any of the poses in the mol2 file have an RMSD <= $rmsdcut.
 awk 'BEGIN{ths=0}/RMSD:/{if($3<='$rmsdcut')ths=1}END{print ths}' $mol2file

==Formal charge of a LIG mol2 file==
This will only work on lines where the residue name is LIG
 awk '/  LIG  /{sum+=$9}END{print sum}' lig.mol2  

==Average # of rotatable bonds from dock.out==
 awk 'BEGIN{tot=0;sum=0}/Number of rotatable bonds/{sum+=$6;tot+=1}END{print tot,sum/tot}' rot.out

==Average size of a whole bunch of files==
 du ????/003_grid/$spacing/????.rec.nrg | awk '{sum+=$1;n+=1}END{print sum/n,n}'

==csh variable in awk script==
Passing variable from a csh script to a nested awk script can be done as follows:

 #! /bin/csh
 
 set stringval = "text"
 
 # the following two lines produce the same thing
 awk '{print "text"$2}' 
 awk '{print "' $stringval '"$2}'

If you want to use a variable defined in the shell, you must break the string passed to awk in pieces
 awk '{print "' $stringval '"$2}'
 awk string1     string2    string3

The combination of the strings are executed in awk.
string2 uses the string contained in the variable.

==References==
[http://www.chemie.fu-berlin.de/chemnet/use/info/gawk/gawk_3.html awk Tutorial]