Page tree
Skip to end of metadata
Go to start of metadata

Cube format

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 not read in case of import option 'M',
					 in which case it is set to 0 0 0 at export)

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

atom1 x y z
atom2 x y z
...
atomN x y z
volumetric data lines    (if volumetric data is ignored at import then this is set to a single 0 at export)

Restrictions

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

Limitation

  • No labels