CML

Codename: cml

Contents

• CML format
• Export options
• References

CML format

Import. The following CML2 standard tags are recognized:

• <cml>
  Children:
  • <molecule>
  • <reaction>
• <molecule>
  Attributes:
  • title
  Children:
  • <propertyList>
    • <property dictRef="name" title="name"> - A property.
      
      • <scalar [dataType="dataType"]> value</scalar> - Supported data types: "string" (default), "boolean", "integer", "double", "ENTITY" (for special property classes).
      • <array dataType="dataType" [delimiter="delimiter"]>list of values</array> - 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</bondStereo>
        - 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

Export options

cml:...	Basic options for aromatization and H atom adding/removal.
cml:A	Atom attributes are stored in arrays. For 2D molecules, only the x, y coordinates are stored. This is a more compact form of storage than the default (using <atom> tags).

Example CML file exported without options:

<?xml version="1.0" ?>
<cml>
<molecule title="Ethane" id="m1">
  <atomArray>
    <atom id="a1" elementType="C"
          x2="0.0" y2="0.0" />
    <atom id="a2" elementType="C"
          x2="0.0" y2="1.54" />
  </atomArray>
  <bondArray>
    <bond atomRefs2="a1 a2" order="1" />
  </bondArray>
</molecule>
</cml>

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

• cml.sourceforge.net — OpenSource Site for CML
• cml.sourceforge.net/schema/ — Schemas and documentation