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"}}]