# Difference between revisions of "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
```