# Stupid 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 ack script

passing variable from csh scrip to a nested ack script

#! /bin/csh

set stringval = "text"

# the following two line perduce the same thing
ack '{print "text"\$2}'
ack '{print "' \$stringval '"\$2}'

If you want to use a variable defined in the shell you must brack the string pased to awk

ack '{print "' \$stringval '"\$2}'
ack string1     string2    string3

The combination of the strings are executed in awk. string 2 is uses the variable contained in the string.