The output produced by Surface Diver consists of a number of files:

### DX scalar data

**srfc.dx** – DX-formatted file describing the volume of a molecule (optional, –grids option)

**hb.dx** – DX-formatted file with hydrophobicity assigned to grid points (optional, –grids option)

**chrg.dx** – DX-formatted file with charges assigned to grid points (optional, –grids option)

**phi.dx** – DX-formatted file describing the electrostatic potential in the whole space (input DX-file translated to the geometric centre of the molecule) (optional, –grids option)

### Data files

(**i** enumerates spherical surfaces)

**i.radius.dat** – this file contains the values of physicochemical parameters of the studied protein mapped onto spherical surface of a given radius:

radius=2.000000 order=32

x=0.049082 y=0.000000 z=1.999398 theta=0.024544 phi=0.000000 density=6.725776 hydrophobicity=4.489162 charge=-0.243362 potential=-11.960450

x=0.048846 y=0.004811 z=1.999398 theta=0.024544 phi=0.098175 density=6.722406 hydrophobicity=4.486836 charge=-0.244764 potential=-11.960450

x=0.048139 y=0.009576 z=1.999398 theta=0.024544 phi=0.196350 density=6.718655 hydrophobicity=4.484260 charge=-0.245980 potential=-11.960450

x=0.046969 y=0.014248 z=1.999398 theta=0.024544 phi=0.294524 density=6.714560 hydrophobicity=4.481459 charge=-0.246996 potential=-11.960450

……………..

**i.radius.HB.dat** – hydrophobicity at points of the spherical surface of a given radius

**i.radius.Qp.dat** – positive charge at points of the spherical surface of a given radius

**i.radius.Qm.dat** – negative charge at points of the spherical surface of a given radius

**i.radius.Vp.dat** – positive values of the electrostatic potential at points of the spherical surface of a given radius

**i.radius.Vm.dat** – negative values of the electrostatic potential at points of the spherical surface of a given radius

**i.radius.shape.dat** – shape of the molecule mapped onto the spherical surface of a given radius

The last six from files described above contain complex data. These files are formatted as follows:

Real(0)

Imaginary(0)

Real(1)

Imaginary(1)

Real(k)

Imaginary(k)

……………..

where k enumerates points of the spherical surface.

Next six files contain coefficients of the spherical harmonic decomposition for each property:

**i.SHD_HB.dat**

**i.SHD_Qm.dat**

**i.SHD_Qp.dat**

**i.SHD_Vm.dat**

**i.SHD_Vp.dat**

**i.SHD_shape.dat**

These files are formatted as follows:

L -L Real Imaginary

L -L+1 Real Imaginary

……………..

L 0 Real Imaginary

……………..

L +L-1 Real Imaginary

L +L Real Imaginary

with L enumerating frequencies.

### Descriptor files

Descriptors of shapes and physicochemical properties are written to the following files:

**matrix_HB.dat**

**matrix_Qm.dat**

**matrix_Qp.dat**

**matrix_Vm.dat**

**matrix_Vp.dat**

**matrix_shape.dat**

using the following format:

dsc(1,1) dsc(1,2) dsc(1,3) …

dsc(2,1) dsc(2,2) dsc(2,3) …

dsc(3,1) dsc(3,2) dsc(3,3) …

dsc(4,1) dsc(4,2) dsc(4,3) …

……………..

where columns are enumerated by the frequency and rows by the radius.