XYZ format

Code: xyz

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

[ # optional comment line ] not written but allowed at import
[ N ] always written, but can be omitted in imported files
[ name\tE ] always written, but can be omitted in imported files
atom1 x y z
atom2 x y z
...
atomN x y z

where N is the number of atoms and E is the energy (optional). If energy is set for the molecule, then it is separated from the molecule name with a TAB ("\t") character.

Restrictions of the XYZ format:

  • 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. In Marvin, implicit hydrogens are automatically converted to explicit H atoms at XYZ export.

  • Charges are not stored.

  • Query properties and other extra features are not stored.

Do not export 2D structures in XYZ!

XYZ export in Marvin is only meaningful for 3D molecules with realistic atomic distances.