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 2020.09

Changes in the chemistry model

We’ve added additional allowed valences for Cl (now 1, 3, 5), Br (now 1, 3, 5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now 2, 4, 6). Molecules with atoms in the new valence states will no longer generate sanitization errors. Note that this has an impact on the chemistry of molecules containing 3-valent I and at least one implicit H (present 24 times in ChEMBL 27): previously this was incorrectly assigned two implicit Hs, now it has no implicit Hs.

Aromaticity perception of molecules like Cc1nnc2n1c1ccccc1n1c(C)nnc12 now correctly recognizes the full outer envelope, i.e. the bonds joining the rings are now also aromatic. In 2020.03 the three rings were connected by single bonds.

FindMCS can now return single atom MCSs

FindMCS() may return single atom MCSs, whereas previously it returned an empty MCS unless there was at least one commond bond across the input structures. So the MCS between molecules CC and CO is now [#6] rather than being null.

New return type for tautomer enumeration

Due to improvements in the tautomer enumeration code, the method TautomerEnumerator::enumerate now returns a TautomerEnumeratorResult object instead of a vector of molecules. Note that if you are iterating over the results of a call to enumerate() you shouldn’t need to change your code. If you want to invoke the old (and deprecated, see below) form from C++, call TautomerNumerator::enumerate(mol, nullptr) or explicitly pass a boost::dynamic_bitset* to capture the modified atoms.

Default precision for coordgen

The default precision setting for coordgen has been changed. The new default was selected to greatly reduce the number of molecules for which it takes a very long time to generate coordinates while still producing nice looking structures. We may continue to tweak this default value if/when problems with it are reported. If you would like to go back to the previous setting, set CoordgenParams.minimizerPrecision to CoordgenParams.sketcherStandardPrecision when you invoke rdCoordGen.AddCoords()

Change in uncharge() behavior for inorganic acids

Uncharger::uncharge() will now neutralize [Cl,Br,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O)[O-], [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-], S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-]. Previously not all of these inorganic acid counterions were consistently neutralized.

Release 2020.03

Use of chirality with @= in PostgreSQL cartridge

Searches for equal molecules (i.e. mol1 @= mol2) in the PostgreSQL cartridge now use the do_chiral_sss option. So if do_chiral_sss is false (the default), the molecules CC(F)Cl and C[C@H](F)Cl will be considered to be equal. Previously these molecules were always considered to be different.

Handling of empty/invalid files in MolSuppliers

Attempting to create a MolSupplier from a filename pointing to an empty file, a file that does not exist or sometihing that is not a standard file (i.e. something like a directory) now generates an exception.

Renaming a cmake option

The cmake option RDK_OPTIMIZE_NATIVE has been renamed to RDK_OPTIMIZE_POPCNT

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.”