CMLConvert

A package for importing and exporting Chemical Markup Language files.

CMLConvert extends the Import[]/Export[] functionality of Mathematica to handle Chemical Markup Language (CML) files.

Download the paclet from the releases page, and install it by evaluating the following in Mathematica:

Needs["PacletManager`"]
PacletInstall["/path/to/paclet/CMLConvert-1.0.paclet"];
Get[FileNameJoin[{$UserBaseDirectory, "Paclets", "Repository", "CMLConvert-1.0", "CMLConvert.m"}]];

where "/path/to/paclet/CMLConvert-1.0.paclet" should be replaced with the actual path to the downloaded paclet file, and "CMLConvert-1.0" should be replaced with the actual version to be installed.

After installation, try it out:

(* for version 12 *)
m = Import["http://chem-file.sourceforge.net/data/polycyclic_alkanes/abietic_acid.cml", "CML"];
MoleculePlot3D[m]

Export["abietic.cml", m, "CML"]

(* for version 11 and earlier *)
Import["http://chem-file.sourceforge.net/data/polycyclic_alkanes/abietic_acid.cml", "CML"]

asp = Import["ExampleData/aspirin.mol",
             {"MOL", {"EdgeRules", "EdgeTypes", "FormalCharges",
                      "MassNumbers", "VertexCoordinates", "VertexTypes"}}];
Export["aspirin.cml", asp, {"CML", {"EdgeRules", "EdgeTypes", "FormalCharges",
                                    "MassNumbers", "VertexCoordinates", "VertexTypes"}}]