CML

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

    Import

    The following CML2 standard tags are recognized:

    • <cml>

      Children:

      • <molecule>

      • <reaction>

    • <molecule>

      Attributes:

      • title

      Children:

      Code : cml

      Extension : .cml See also CML Export Options

      • <propertyList>

        • <property dictRef=" name " title=" name " > - A property.

          • <scalar [dataType=" dataType "] > value - Supported data types: "string" (default), "boolean", "integer", "double", "ENTITY" (for special property classes).

          • <array dataType=" dataType " [delimiter=" delimiter "] > list of values - Currently, only the "integer" data type is supported. The default delimiter is the space character.

        • <property>

        • <atomArray>

        Attributes:

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

        Children:

        • <atom>

          Attributes:

          • id , elementType , x2 , y2 , x3 , y3 , z3 , formalCharge , hydrogenCount , isotope
        • <bondArray>

        Attributes:

        • atomRefs1 , atomRefs2 , order

        Children:

        • <bond atomRefs2=" a1 a2 " order=" order " >

          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:

          • <bondStereo > value

            • Value can be "W" (wedge - up), "H" (hatch - down), "C" (cis) or "T" (trans)

          • <bondStereo convention=" convention " conventionValue=" value " />

            convention conventionValue meaning
            MDL 1 up
            MDL 6 down
            MDL 4 either
            MDL 3 cis or trans
            ChemAxon CTUnspec cis/trans or unspecified

          A <bond> tag is recognized at import even if the bondArray container is not present.

    • <reaction>

      Attributes:

      • title

      Children:

      • <reactantList>

        • <molecule>

      • <productList>

        • <molecule>

      • <propertyList> - 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.

    References