One can apply the Surface Diver to study similarities within a group of biomolecules. This can be done automatically (i.e. using a single BASH script) as in the example presented below:
Let us assume we have N proteins that we would like to group according to their physicochemical properties.
For simiplicity we will name the corresponding pqr and DX files using subsequent numbers (i.e. 1.pqr, 2.pqr … 1.dx, 2.dx … etc.).
All pqr and DX files are located in the same directory; an input file for Surface Diver is also present:
[edge] 129 [edge]
[irad] 0.0 [irad]
[rmax] 30 [rmax]
[spho] 64 [spho]
[nsph] 30 [nsph]
[grid] potential.dx [grid]
Now we can use the following script:
# BASH script for automatic Surface Diver computations: control.bash
#!/bin/bash
for i in $(seq N);do
ln -s $i.dx potential.dx
./surf_diver $i.pqr input
mv -f matrix_HB.dat $i.matrix_HB.dat
mv -f matrix_Qm.dat $i.matrix_Qm.dat
mv -f matrix_Qp.dat $i.matrix_Qp.dat
mv -f matrix_Vm.dat $i.matrix_Vm.dat
mv -f matrix_Vp.dat $i.matrix_Vp.dat
mv -f matrix_shape.dat $i.matrix_shape.dat
rm -f potential.dx
# we want to save DX files, the rest of created files will be overwritten
mv -f srfc.dx $i.srfc.dx
mv -f hb.dx $i.hb.dx
mv -f chrg.dx $i.chrg.dx
mv -f phi.dx $i.phi.dx
done
# Now we compute SI values, using small utility program
# called si_creator
for k in $(seq N);do
for l in $(seq N);do
./si_creator $k.matrix_HB.dat $l.matrix_HB.dat 30 64 >> si_HB.dat
./si_creator $k.matrix_HB.dat $l.matrix_Qm.dat 30 64 >> si_Qm.dat
./si_creator $k.matrix_HB.dat $l.matrix_Qp.dat 30 64 >> si_Qp.dat
./si_creator $k.matrix_HB.dat $l.matrix_Vm.dat 30 64 >> si_Vm.dat
./si_creator $k.matrix_HB.dat $l.matrix_Vp.dat 30 64 >> si_Vp.dat
./si_creator $k.matrix_HB.dat $l.matrix_shape.dat 30 64 >> si_shape.dat
done
done
To execute this script, the user should issue the following command:
bash ./control.bash
As a result, files si_property.dat will be created. Each file contains SI values computed for given property. Files are formatted as:
SI(1,1)
SI(1,2)
…
SI(1,N)
SI(2,1)
SI(2,2)
…
SI(2,N)
…
SI(N,N)