Gaussian Cube

Code name: cube

Marvin imports and exports Gaussian Cube molecule files that have the following format:

comment line          (always written, ignored at import)

comment line          (always written, ignored at import)

N vx vy vz          number of atoms,
         followed by the position of the origin
         of the volumetric data (the latter is ignored at import, set to 0 0 0 at export)

M1 vx1 vy1 vz1          number of voxels along the first axis,
         followed by the first axis vector (ignored at import, set to 1 1 0 0 at export)

M2 vx2 vy2 vz2          number of voxels along the second axis,
         followed by the second axis vector (ignored at import, set to 1 0 1 0 at export))

M3 vx3 vy3 vz3          number of voxels along the third axis,
         followed by the third axis vector (ignored at import, set to 1 0 0 1 at export))

atom1 x y z

atom2 x y z

...

atomN x y z

volumetric data lines          (ignored at import, set to 0 at export)

Restrictions of the Gaussian Cube format import/export in Marvin:

Bonds are not stored.
As a consequence, all the hydrogens must be explicit, otherwise the bond types can not be guessed reliably by the importing program.
Charges are not stored.
Query properties and other extra features are not stored.
Volumetric data is ignored at import, filled with defaults (a single voxel with zero volumetric value).

The default behavior is to use the "any" bond type for all bonds, 0 charge for each atom, no implicit hydrogens.

Import options can be specified by writing "{options}" after the filename.

{f...}      Bond length cut-off. Two atoms can be connected if they are closer than the sum of their covalent radii times the cut-off value. Default: "{f1.12}"

{Z#}      Set maximum number of connections for element Z.
Example: "{f1.4,C4,H1}". This setting increases the cut-off value, but does not let Carbons to have more than 4 connections, and Hydrogens to have more than 1 connection.

{b}      Try to guess bond types, atom charges and implicit hydrogens from atom distances and valence rules.
Warning: This is an experimental feature. Since Gaussian Cube files do not contain bond information, these "guesses" can be different from the actual bond orders, especially in case of

-   radicals

-   missing Hydrogen atoms

-   complexes

The user should check the calculated bonds after import.

Limitations:

Volumetric data is ignored at import
Volumetric data is filled with defaults (a single voxel with zero volumetric value) at export

comment line	(always written, ignored at import)
comment line	(always written, ignored at import)
N vx vy vz	number of atoms, followed by the position of the origin of the volumetric data (the latter is ignored at import, set to `0 0 0` at export)
M1 vx1 vy1 vz1	number of voxels along the first axis, followed by the first axis vector (ignored at import, set to `1 1 0 0` at export)
M2 vx2 vy2 vz2	number of voxels along the second axis, followed by the second axis vector (ignored at import, set to `1 0 1 0` at export))
M3 vx3 vy3 vz3	number of voxels along the third axis, followed by the third axis vector (ignored at import, set to `1 0 0 1` at export))
atom1 x y z
atom2 x y z
...
atomN x y z
volumetric data lines	(ignored at import, set to `0` at export)