CML

Codename: cml

CML format

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:
- <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

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

Export options

The argument of MolConverter and the getMol/getM functions (of the applets and beans) is the format string. The format specification ("cml") and the option(s) are separated by a colon in the format string. CML export currently only has one special option which affects the compactness of the storage.

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.

CML

Contents:

CML format

Export options

References

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).