cml

When to Use This Skill

Use this skill when:

Exchanging molecular data between different chemistry software
Encoding chemical reactions with stoichiometry and conditions
Representing spectroscopic data (NMR, IR, MS)
Building interoperable chemistry workflows
Archiving computational chemistry results
Creating machine-readable chemical documents

Overview

Chemical Markup Language (CML) is an XML-based standard for representing molecules, compounds, reactions, spectra, and crystals. It provides a flexible, extensible framework for chemical data exchange.

Format Specification

Encoding: XML with namespaces
Namespace: http://www.xml-cml.org/schema
Schema: Modular XSD definitions
Conventions: Standard attribute sets for coordinates, bonding
Validation: XSD schema validation supported

Key Elements

Element	Description
`<molecule>`	Root for molecular data
`<atomArray>`	Container for atoms
`<atom>`	Individual atom with id, elementType, x3, y3, z3
`<bondArray>`	Container for bonds
`<bond>`	Bond with atomRefs2, order
`<crystal>`	Unit cell and symmetry
`<spectrum>`	Spectroscopic data
`<reaction>`	Chemical reaction data
`<property>`	Observable properties

Example Snippet

<molecule xmlns="http://www.xml-cml.org/schema" id="water">
  <atomArray>
    <atom id="O1" elementType="O" x3="0.0" y3="0.0" z3="0.117"/>
    <atom id="H1" elementType="H" x3="0.0" y3="0.757" z3="-0.469"/>
    <atom id="H2" elementType="H" x3="0.0" y3="-0.757" z3="-0.469"/>
  </atomArray>
  <bondArray>
    <bond atomRefs2="O1 H1" order="1"/>
    <bond atomRefs2="O1 H2" order="1"/>
  </bondArray>
</molecule>

Tools Using CML

Tool	Purpose
OpenBabel	Conversion to/from CML, format interoperability
CDK (Chemistry Development Kit)	Java chemistry toolkit with CML support
CMLDOM	DOM-based CML parser
JUMBO	Java CML toolkit
JChemPaint	Chemical structure editor (CML-native)
JSpecView	Spectroscopy viewer (CML spectra)
Bioclipse	Integrated bio/chem platform
ODDT	Open drug discovery toolkit
PyBEL	OpenBabel Python interface

Usage Examples

Create CML Molecule

from openbabel import openbabel as ob

# Create molecule
mol = ob.OBMol()
mol.NewAtom()
mol.NewAtom()
mol.GetAtom(1).SetAtomicNum(8)  # Oxygen
mol.GetAtom(2).SetAtomicNum(1)  # Hydrogen

# Convert to CML
conv = ob.OBConversion()
conv.SetOutFormat("cml")
cml_output = conv.WriteString(mol)
print(cml_output)

Parse CML with CDK (Java)

import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.CMLReader;

CMLReader reader = new CMLReader(new FileReader("molecule.cml"));
IChemFile chemFile = reader.read(new ChemFile());
IAtomContainer molecule = chemFile.getChemSequence(0)
                                 .getChemModel(0)
                                 .getMoleculeSet()
                                 .getAtomContainer(0);

CML Reaction

<cml xmlns="http://www.xml-cml.org/schema">
  <reaction id="r1">
    <reactantList>
      <molecule id="H2">
        <atomArray>
          <atom id="H1" elementType="H"/>
          <atom id="H2" elementType="H"/>
        </atomArray>
        <bondArray>
          <bond atomRefs2="H1 H2" order="1"/>
        </bondArray>
      </molecule>
    </reactantList>
    <productList>
      <molecule id="H2O">
        <!-- water structure -->
      </molecule>
    </productList>
    <propertyList>
      <property dictRef="reaction:enthalpy">
        <scalar>-286 kJ/mol</scalar>
      </property>
    </propertyList>
  </reaction>
</cml>

Resources

Website: http://www.xml-cml.org

SKILL.mdskills/cml/SKILL.md