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CML (.cml)

Background & Context

    • MIME type: chemical/x-cml
    • Chemical Markup Language, for interchange of chemical information.
    • Represents an arbitrary number of chemical compounds.
    • XML format.
    • Stores atomic coordinates, chemical bond information and metadata.

Import & Export

  • Import["file.cml"] imports a list of molecules from a CML file.
  • Export["file.cml",expr] exports a molecule or list of molecules to a CML file.
  • Import["file.cml",elem] imports the specified element from a CML file.
  • The import format can be specified with Import["file","CML"] or Import["file",{"CML",elem,…}].
  • Export["file.cml",mol] creates a CML file from a molecule.
  • Export["file.cml",{mol1,mol2,…}] creates a CML file from a list of molecules.
  • See the following reference pages for full general information:
  • Import, Exportimport from or export to a file
    CloudImport, CloudExportimport from or export to a cloud object
    ImportString, ExportStringimport from or export to a string
    ImportByteArray, ExportByteArrayimport from or export to a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Data elements:
  • "Molecule"a symbolic representation of the molecule model
    "Molecule", na symbolic representation of the n^(th) molecule
    "Metadata"an Association containing the metadata from the file
    "Metadata", nthe metadata for the n^(th) molecule

Options

Examples

open allclose all

Basic Examples  (2)Summary of the most common use cases

Show the Import elements available in a CML file:

In[3]:=3
✖
https://wolfram.com/xid/0bfrki0j-oag3vt
Out[3]=3

Import all molecules from the file:

In[4]:=4
✖
https://wolfram.com/xid/0bfrki0j-vukf6q
Out[4]=4

Import the second and fifth molecules from the file:

In[6]:=6
✖
https://wolfram.com/xid/0bfrki0j-xf0elg
Out[6]=6

Import metainformation for the first compound in this file:

In[8]:=8
✖
https://wolfram.com/xid/0bfrki0j-xl8crt
Out[8]=8

Export a molecule to a CML file:

In[1]:=1
✖
https://wolfram.com/xid/0bfrki0j-7bdo93
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0bfrki0j-1iel08
Out[2]=2

Export Options  (2)

IncludeHydrogens  (1)

With the default setting of IncludeHydrogensAutomatic, hydrogen atoms are included in the output file if they are explicitly present in the molecule:

In[1]:=1
✖
https://wolfram.com/xid/0bfrki0j-u6960j
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0bfrki0j-o2upsh
Out[2]=2

Specify that explicit hydrogens should be added before export:

In[3]:=3
✖
https://wolfram.com/xid/0bfrki0j-0xs5h3
Out[3]=3

"CoordinateDimension"  (1)

The option "CoordinateDimension" can take values of Automatic, 2 or 3.

In[1]:=1
✖
https://wolfram.com/xid/0bfrki0j-7pa3b2

Export a molecule to CML with two-dimensional coordinates:

In[2]:=2
✖
https://wolfram.com/xid/0bfrki0j-19gxgn
Out[2]=2

Export a molecule to CML with three-dimensional coordinates:

In[3]:=3
✖
https://wolfram.com/xid/0bfrki0j-wkzl4b
Out[3]=3