The primary change in the 16.1 series is the addition of the JME 2-D Editor tool:

• drag-drop CDX and CDXML files for 2D rendering using legacy JME
• convert to/from 3D
• automatically cleans ill-positioned fragments and "nicknames", such as Ph, OTs, etc.
• cleans fragments using NCI/CADD development server (cirx) with =smiles2D and =smiles3D
• leverages JNIInChI to check structures
• allows creation of 2D MOL and 2D CDXML files from any 2D or 3D model

Another new feature is =smiles2d and =smiles3d:

• implements NCI/CADD development server
• guaranteed 2D and 3D MOL file return
• uses
  • =smiles2d as "https://cirx.chemicalcreatures.com/chemical/structure/%FILE/file?format=sdf&get3d=false"
  • =smiles3d as "https://cirx.chemicalcreatures.com/chemical/structure/%FILE/file?format=sdf&get3d=true"
• allows for future modification of that pathway back to NCI/CADD home

There are numerous bug fixes in this version as well.