e8e9dc2a13
The previous `set(CMAKE_EXE_LINKER_FLAGS ...)` replaced the variable
wholesale, which clobbers any toolchain-supplied linker flags. In
particular, conda-forge's clang_osx-64 / clangxx_osx-64 packages set
`-stdlib=libc++ -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib` via
`CMAKE_EXE_LINKER_FLAGS`. Losing those flags causes the postgres
extension link to pick up the wrong libc++ and fail to resolve
ABI-tagged symbols on libc++ 19+:
[ 94%] Linking CXX executable rdkit.dylib
Undefined symbols for architecture x86_64:
"VTT for std::__1::basic_stringstream<...>"
"vtable for std::__1::basic_stringbuf<...>"
"vtable for std::__1::basic_stringstream<...>"
"vtable for std::__1::basic_istringstream<...>"
ld: symbol(s) not found for architecture x86_64
The missing symbols carry the `[abi:ne190107]` ABI tag introduced by
libc++ 19+ — references that only resolve against the conda-forge
libc++, not the system one the link was falling back to.
Append to `CMAKE_EXE_LINKER_FLAGS` instead so the toolchain flags
survive. The other rdkit `.dylib`s in the same build are linked via
the standard cmake toolchain path and were never affected.
Verified by building rdkit-postgresql on osx-64 + osx-arm64 via the
conda-forge feedstock (https://github.com/conda-forge/rdkit-feedstock)
with this fix applied as a downstream patch.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
RDKit
What is it?
The RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
- BSD license - a business friendly license for open source
- Core data structures and algorithms in C++
- Python 3.x wrapper generated using Boost.Python
- Java and C# wrappers generated with SWIG
- JavaScript (generated with emscripten) and CFFI wrappers around important functionality
- 2D and 3D molecular operations
- Descriptor and Fingerprint generation for machine learning
- Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
- Cheminformatics nodes for KNIME
- Contrib folder with useful community-contributed software harnessing the power of the RDKit
Installation and getting started
If you are working in Python and using conda (our recommendation), installation is super easy:
$ conda install -c conda-forge rdkit
You can then take a look at our Getting Started in Python guide.
More detailed installation instructions are available in Docs/Book/Install.md.
Documentation
Available on the RDKit page and in the Docs folder on GitHub
The RDKit blog often has useful tips and tricks.
Support and Community
If you have questions, comments, or suggestions, the best places for those are:
If you've found a bug or would like to request a feature, please create an issue
We also have a LinkedIn group
We have a yearly user group meeting (the UGM) where members of the community do presentations and lightning talks on things they've done with the RDKit. Materials from past UGMs, which can quite useful, are also online:
- 2012 UGM, London
- 2013 UGM, Hinxton
- 2014 UGM, Darmstadt
- 2015 UGM, Zurich
- 2016 UGM, Basel
- 2017 UGM, Berlin
- 2018 UGM, Cambridge
- 2019 UGM, Hamburg
- 2020 UGM, virtual
- 2021 UGM, virtual
- 2022 UGM, Berlin
- 2023 UGM, Mainz
- 2024 UGM, Zurich
License
Code released under the BSD license.