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 E                ]     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 (" ") 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.

    {warning} Do not export 2D structures in XYZ!

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