PQR file format

This format resembles the PDB format, however the PQR files are rather loosely formated. Surface Diver reads PQR files on a per-line basis using the following format:

Field_name Atom_number Atom_name Residue_name Residue_number X Y Z Charge Radius

with the whitespace being the delimiter. The fields are:

Field_name – a string which specifies the type of PQR entry; only ATOM entries are currently parsed by Surface Diver

Atom_number – an integer which provides the atom index

Atom_name – a string which provides the atom name

Residue_name – a string which provides the residue name

Residue_number – an integer which provides the residue index

X Y Z – 3 floats which provide the atomic coordinates

Charge – a float which provides the atomic charge

Radius – a float which provides the atomic radius

DX file format

Surface Diver reads electrostatic potentials, given as discretized scalar data, using the OpenDX format. It also outputs discretized data using this format:

# Comments
object 1 class gridpositions counts nx ny nz
origin xmin ymin zmin
delta hx 0.0 0.0
delta 0.0 hy 0.0
delta 0.0 0.0 hz
object 2 class gridconnections counts nx ny nz
object 3 class array type double rank 0 times n data follows
u(0,0,0) u(0,0,1) u(0,0,2)
…
u(0,0,nz-3) u(0,0,nz-2) u(0,0,nz-1)
u(0,1,0) u(0,1,1) u(0,1,2)
…
u(0,1,nz-3) u(0,1,nz-2) u(0,1,nz-1)
…
u(0,ny-1,nz-3) u(0,ny-1,nz-2) u(0,ny-1,nz-1)
u(1,0,0) u(1,0,1) u(1,0,2)
…
attribute “dep” string “positions”
object “regular positions regular connections” class field
component “positions” value 1
component “connections” value 2
component “data” value 3

where the variables are:

Comments – any number of comment lines, each line starting with the # symbol
nx ny nz – the number of grid points in the x-, y-, and z-directions
xmin ymin zmin – the coordinates of the grid lower corner
hx hy hz – the grid spacings in the x-, y-, and z-directions
n – the total number of grid points; n = nx * ny * nz
u(*,*,*) – the data values, ordered with the z-index increasing most quickly, followed by the y-index, and then the x-index.

Currently only cubic grids are supported with nx=ny=nz and hx=hy=hz