CML

Code name: cml

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

Import. The following tags are recognized:

• <molecule>
  Standard (CML2) attributes:
  • title
  Children:
  • <atomArray>
    Standard (CML2) array attributes:
    • atomID, elementType, x2, y2, x3, y3, z3, formalCharge, isotope
    Nonstandard (Marvin only) array attributes:
    • residueType, residueId - residue type/ID value or zero
    • residueAtomName - PDB atom name or zero.
    • radical - Radical center value or zero.
    • reactionStereo - Reaction stereo value or zero.
    • rgroupRef - R-group reference value or zero.
    • sgroupRef - S-group reference value or zero.
    • attachmentPoint - R-group attachment point value or zero.
    • mrvQueryProps - Query atom properties or zero.
      
    • mrvStereoGroup, mrvMap
    Children:
    • <atom>
      Standard CML2 attributes:
      • id, elementType, x2, y2, x3, y3, z3, formalCharge, isotope
      Nonstandard (Marvin only) attributes:
      • residueType, residueId - They were present in CML1 but removed later.
      • residueAtomName - PDB atom name.
      • radical - Radical center: "monovalent" (doublet), "divalent", "divalent1" (singlet), "divalent3" (triplet) or "trivalent".
      • reactionStereo - Reaction stereo: "Inv" (inversion) or "Ret" (retention).
      • rgroupRef - R-group reference. Currently, only positive integer values are accepted.
      • sgroupRef - S-group reference.
      • attachmentPoint - R-group attachment point: "1", (on first site) "2" (on second site) or "both" (on both sites).
      • mrvQueryProps - Query atom properties.
        Format: [atom Type:][SMARTS properties], where atom type can be "A" (any atom), "Q" (heteroatom), "L,element1,..." (inclusive atom list) or "L!element1!..." (exclusive atom list). SMARTS properties is a semicolon separated list. An element of the list starts with character `H', `X', `v', `R', `r' or `a', the following characters are digits representing an integer value. Examples: "A:" (any atom), "L!O!S:H1,R1" (atom is not oxygene, not sulfur, 1 hydrogen is connected to it and it is inside a ring).
      • mrvStereoGroup, mrvMap
      An <atom> tag is recognized at import even if the atomArray container is not present.
      
  • <bondArray>
    • <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).
      Non-standard (Marvin only) attributes:
      • queryType - Query bond type: "SD" (single or double), "SA" (single or aromatic), "DA" (double or aromatic) or "Any".
      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.
      
  • <molecule id="sg1" role="SuperatomSgroup"> - contracted Superatom S-group
    • <atomArray>
    • <atom>
    • <bondArray>
    • <bond>
  • <molecule id="sg2" role="SuperatomSgroup" /> - expanded Superatom S-group
  • <molecule id="sg3" role="MultipleSgroup" atomRefs="a1 a2 ... "/> - Multiple S-group
  • <propertyList>
    • <property dictRef="name"> - Molecule property. It is recognized at import even if the propertyList container is not present.
      
      • <scalar>value</scalar>
• <reaction>
  • <reactantList>
    • <molecule>
  • <agentList> - Marvin extension
    • <molecule>
  • <productList>
    • <molecule>

Export options and defaults. 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 option which affects the compactness of the storage.

"cml" (default):	Atoms are stored in <atom> tags, with the specification of three coordinates (x, y, z) and the element type.
"cml:A" (array option):	Atom attributes are stored in arrays instead of atom tags. For 2D molecules, only the x, y coordinates are stored. This is a more compact form of storage.
"cml:a" or "cml:+a":	Aromatize.
"cml:-a":	Dearomatize.

cml

<?xml version="1.0"?>
<molecule title="ethane">
  <atomArray>
    <atom id="a1" elementType="C"
          x2="0.0" y2="0.0"
          x3="0.0" y3="0.0" z3="0.0" />
    <atom id="a2" elementType="C"
          x2="0.0" y2="1.54"
          x3="0.0" y3="1.54" z3="0.0" />
  </atomArray>
  <bondArray>
    <bond atomRefs2="a1 a2" order="1" />
  </bondArray>
</molecule>

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

• www.xml-cml.org
• www.xml-cml.org/dtdschema/cmlCore/HTMLDOCS/cmlCore.pdf
• cml.sourceforge.net/schema/cmlReact/HTMLDOCS/cmlreact.pdf