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XYZ format

Code : xyz

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

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[ # 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.

Do not export 2D structures in XYZ!

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