Backwards incompatible changes — The RDKit 2025.09.6 documentation

# 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 2023.09

### Changes in atomic stereochemistry perception

The algorithm for perception of atomic stereochemistry from 2D structures has been rewritten. The new algorithm is more accurate, which results in some differences in perceived stereo between this release and the previous ones.

### Changes in the MCS code

- The user-configurable `MCSParameters::FinalMatchChecker` function is now called after the built-in `FinalMatchChecker` function, rather as alternatively to the built-in `FinalMatchChecker` function. This was a design flaw which is worth correcting.

- Setting `MCSParameters::Timeout` to 0 means no timeout, rather than 0s timeout, which is rather pointless as it would cause MCS to be canceled immediately.

- Result SMARTS strings generated by `FindMCS` when `MCSParameters::MatchRingFusionStrict` is `true` now include ring membership queries where appropriate in order to ensure more specific substructure matches.

- In MCS Verbose statistics, `SingleBondExcluded` was renamed to `IndividualBondExcluded` to avoid confusion, since single bond has a different meaning in chemistry.

### Changes to canonicalization

Information about stereo groups is no longer used in the SMILES canonicalization process if CXSMILES are not being generated.

## Release 2023.03

### Changes to ring finding

- The ring-finding functions will now run even if the molecule already has ring information. Older versions of the RDKit would return whatever ring information was present, even if it had been generated using a different algorithm.

- The ring-finding functions now no longer consider dative bonds as possible ring bonds by default. All of the ring-finding functions have a new optional argument `includeDativeBonds` which can be used to change this behavior

### Changes to canonicalization

The canonical SMILES and CXSMILES generated for molecules with enhanced stereochemistry (stereo groups) is different than in previous releases. The enhanced stereochemistry information and the stereo groups themselves are now canonical. This does not affect molecules which do not have enhanced stereo and will not have any effect if you generate non-isomeric SMILES. This change also affects the output of the MolHash and RegistrationHash code when applied to molecules with enhanced stereo.

## Release 2022.09

### Changes in canonicalization

Changes to the way atomic chirality is used in the canonicalization algorithm mean that canonical atom ranking and canonical SMILES generated with this RDKit version can be different from those generated with previous versions

### Improvements to GetBestRMS() and CalcRMS()

`GetBestRMS() and CalcRMS()` by default now treat terminal conjugated functional groups like carboxylate and nitro symmetrically. For example, the group `C(=[O:1])[O-:2]` can match in either orientation. The SMARTS pattern which is used to recognize affected groups is: `[{atomP};$([{atomP}]-[*]=[{atomP}]),$([{atomP}]=[*]-[{atomP}])]~[*]` where `{atomP}` is `O,N;D1`. The previous behavior can be restored using by setting the `symmetrizeConjugatedTerminalGroups` argument to false when calling `GetBestRMS() and CalcRMS()`

## Release 2022.03

### Changes to the handling of dummy atoms and aromaticity

The rules for aromaticity in rings containing dummy atoms have been changed. The general intention of the new handling is that aromaticity will not be perceived for rings containing dummy atoms unless it’s clear that the dummies should be aromatic. As an example: the SMILES `C1=C*2=CC=CC=*2C=C1` is perceived to be aromatic while the SMILES `C1=C*2C=CC=C*2C=C1` (which does not have any double bonds to the dummy atoms) is not; in previous RDKit releases both of these structures were aromatic. There’s more information about this in the discussion of PR #4722 (https://github.com/rdkit/rdkit/pull/4722) and Issue #4721 (https://github.com/rdkit/rdkit/issues/4721).

### Tautomer enumeration improvements

The rules for tautomer enumeration in `MolStandardize` have been updated to more closely match the rules in the original publication. These changes primarily consist of making the rules more specific; the consequence is that less tautomers will be generated with this version. The previous rules can still be accessed via the function `GetV1TautomerEnumerator()` (Python) or `getV1TautomerEnumerator()` (C++)

## Release 2021.03

### Changes to conformer generation

In the interest of providing higher quality results by default, the conformer generator now uses symmetry when doing RMS pruning. The pure distance geometry based conformer generator also now generates trans(oid) conformations for amides, esters, and related structures.

### Changes to R-Group Decomposition results

There have been a large number of changes in the R-group decomposition code which we believe improve the quality of the results and the handling of the many strange edge cases which arise when doing RGD.

### Reactions now produce STEREONONE instead of STEREOANY for unspecified double bonds

Double bonds in the products of reactions which have unspecified stereochemistry are now set to be `STEREONONE` instead of `STEREOANY`. Using `STEREONONE` is consistent with the rest of the behavior of the RDKit with respect to double bonds.

### Moving MolToSVG()

The function `Chem.MolToSVG()` (or `Chem.rdmolops.MolToSVG()`) has been moved to the `Chem.Draw` package along with the other drawing code.

## Release 2020.09

### Changes in the chemistry model [UPDATED for release 2020.09.2]

We’ve added additional allowed valences for 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.”