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CML

Marvin is capable of importing and exporting files in the Chemical Markup Language. Special atom types are lost during export.

Code : cml

Extension : .cml

Import

The following CML2 standard tags are recognized:

  • Children:

  • Attributes:

    • title

      Children:

    • - A property.

      • value - Supported data types: "string" (default), "boolean", "integer", "double", "ENTITY" (for special property classes).
      • list of values - Currently, only the "integer" data type is supported. The default delimiter is the space character.

    • 1
      Attributes:
      • atomID , elementType , x2 , y2 , x3 , y3 , z3 , formalCharge , hydrogenCount , isotope

        Children:

      • 1
          Attributes:
        • id , elementType , x2 , y2 , x3 , y3 , z3 , formalCharge , hydrogenCount , isotope 

    • 1
      Attributes:
      • atomRefs1 , atomRefs2 , order

        Children:

      • 1
2
3
          The atom references  *a1*  and  *a2*  must be valid atom ids. The  *order*  value can be "1", "S" (single), "2", "D" (double), "3", "T" (triple) or "A" (aromatic).

  Children:

        • value **

          • Value can be "W" (wedge - up), "H" (hatch - down), "C" (cis) or "T" (trans)
convention conventionValue meaning
MDL 1 up
MDL 6 down
MDL 4 either
MDL 3 cis or trans
Chemaxon CTUnspec cis/trans or unspecified 
1
        A <bond> tag is recognized at import even if the bondArray container is not present.

  • Attributes:

    • title

      Children:

    • - Reaction properties

CML in other programs:

  • JChemPaint (last version tested: 1.9.8) and Marvin imports each other's CML files.
  • Jmol 8 imports CML files exported by Marvin that contain 3D structures. Jmol is a 3D viewer that does not import bonds but calculates them from atomic distances. This means that bonds are not imported correctly if the molecule is 2D.

See also
CML Export Options

References