Backwards incompatible changes

Though we really try to maintain backwards compatibility across releases, there are rare instances when we need to break compatibility. The purpose of this document is to capture information about backwards incompatible changes that have been made in the RDKit. It’s broken down by release cycle and does not generally include changes in results that arise due to bug fixes; we try to call those out in the release notes. The release notes, in general, contain a more comprehensive version of this list.

Release 2019.09

Updated van der Waals radii

The atomic van der Waals radii used by the RDKit were corrected/updated in #2154. This leads to different results when generating conformations, molecular volumes, and molecular shapes.

“R” atoms in mol blocks are now converted into * queries

When reading Mol blocks, atoms with the symbol “R” are now converted into queries that match any atom when doing a substructure search (analogous to “*” in SMARTS). The previous behavior was to only match other dummy atoms.

PandasTools.LoadSDF() uses isomeric SMILES

When loading SDF files using PandasTools.LoadSDF(), we now default to producing isomeric smiles in pandas tables. To reproduce the original behavior, use isomericSmiles=False in the call to the function.

New fingerprinter defaults changed

The default values for some of the new fingerprint generators have been changed so that they more closely resemble the original fingerprinting code. In particular most fingerprinters no longer do count simulation by default and the RDKit fingerprint now sets two bits per feature by default.

Release 2019.03

As of this realease (2019.03.1) the RDKit no longer supports Python 2.

Release 2018.09

GetAtomSmiles() generates isomeric SMILES by default

In earlier releases, if you wanted to include information about stereochemistry or isotopic labels in the output SMILES it was necessary to set the optional isomericSmiles argument to true. The default value of this is now true. If you want to go back to the old behavior and get SMILES without stereochemistry information you can just set isomericSmiles to false.

Changes to ringMatchesRingOnly option in the MCS code

The ringMatchesRingOnly option to the FindMCS() function now applies to atom-atom matches as well as bond-bond matches.

The conformation generation code now uses ETKDG by default when called from Python

The Python functions EmbedMolecule() and EmbedMultipleConfs() now use the ETKDG algorithm by default instead of standard distance geometry.

Release 2018.03

MolToSmiles() generates isomeric SMILES by default

In earlier releases, if you wanted to include information about stereochemistry or isotopic labels in the output SMILES it was necessary to set the optional isomericSmiles argument to true. The default value of this is now true. If you want to go back to the old behavior and get SMILES without stereochemistry information you can just set isomericSmiles to false.

MolToMolBlock() generates a 2D conformation when the includeStereo flag is set

If you want to capture stereochemistry in Mol blocks, it’s necessary to have coordinates in the output. Earlier versions of the RDKit required you to remember to generate coordinates yourself. This is now done by default for molecules that don’t have a conformation when includeStereo is set.

The conformation generation code now uses ETKDG by default

Earlier RDKit releases would, by default, generate conformations using standard distance geometry. The new default is to use Sereina Riniker’s ETKDG algorithm, which is a bit slower but which has been shown to generate much better results.

License

This document is copyright (C) 2017-2019 by Greg Landrum

This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.

The intent of this license is similar to that of the RDKit itself. In simple words: “Do whatever you want with it, but please give us some credit.”