FPSim2: Simple package for fast molecular similarity searches
FPSim2 is a small NumPy centric Python/C++ RDKit based package to run fast compound similarity searches. FPSim2 performs better with high search thresholds (>=0.7). Currently used in the ChEMBL and SureChEMBL interfaces.
Highlights:
- Uses CPU POPCNT instruction for fast bit counting
- Bounds for sublinear speedups from 10.1021/ci600358f
- A compressed file format with optimised read speed based in PyTables and BLOSC2
- Fast multicore CPU and GPU similarity searches
- In memory and on disk search modes
- Distance matrix calculation
Installation
With pip:
pip install fpsim2
With conda:
conda install conda-forge::fpsim2
With SBGrid:
sbgrid-cli install fpsim2
Documentation
Documentation is available at https://chembl.github.io/FPSim2/
Trying it online
To try out FPSim2 interactively in your web browser, check out this Google Colab notebook
2 maintainers
Release files for FPSim2 0.7.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| fpsim2-0.7.4.tar.gz | 28.0 kB | Details |
Built distributions (wheels)
Total release size: 13.6 MB
Release files / fpsim2-0.7.4.tar.gz
| Download URL | fpsim2-0.7.4.tar.gz |
|---|---|
| Size | 28.0 kB |
| Tags | Source |
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Release files / fpsim2-0.7.4-cp314-cp314-win_amd64.whl
| Download URL | fpsim2-0.7.4-cp314-cp314-win_amd64.whl |
|---|---|
| Size | 132.6 kB |
| Tags | CPython 3.14 Windows x86-64 |
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Release files / fpsim2-0.7.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | fpsim2-0.7.4-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.14 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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twine/6.1.0 CPython/3.13.7
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Release files / fpsim2-0.7.4-cp314-cp314-macosx_11_0_arm64.whl
| Download URL | fpsim2-0.7.4-cp314-cp314-macosx_11_0_arm64.whl |
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| Size | 150.6 kB |
| Tags | CPython 3.14 macOS 11.0+ ARM64 |
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Release files / fpsim2-0.7.4-cp314-cp314-macosx_10_15_x86_64.whl
| Download URL | fpsim2-0.7.4-cp314-cp314-macosx_10_15_x86_64.whl |
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| Size | 157.8 kB |
| Tags | CPython 3.14 macOS 10.15+ x86-64 |
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Release files / fpsim2-0.7.4-cp313-cp313-win_amd64.whl
| Download URL | fpsim2-0.7.4-cp313-cp313-win_amd64.whl |
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| Size | 129.7 kB |
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Release files / fpsim2-0.7.4-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / fpsim2-0.7.4-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | fpsim2-0.7.4-cp313-cp313-macosx_11_0_arm64.whl |
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Release files / fpsim2-0.7.4-cp313-cp313-macosx_10_13_x86_64.whl
| Download URL | fpsim2-0.7.4-cp313-cp313-macosx_10_13_x86_64.whl |
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| Size | 157.7 kB |
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Release files / fpsim2-0.7.4-cp312-cp312-win_amd64.whl
| Download URL | fpsim2-0.7.4-cp312-cp312-win_amd64.whl |
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| Size | 129.6 kB |
| Tags | CPython 3.12 Windows x86-64 |
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Release files / fpsim2-0.7.4-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / fpsim2-0.7.4-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | fpsim2-0.7.4-cp312-cp312-macosx_11_0_arm64.whl |
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Release files / fpsim2-0.7.4-cp312-cp312-macosx_10_13_x86_64.whl
| Download URL | fpsim2-0.7.4-cp312-cp312-macosx_10_13_x86_64.whl |
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| Size | 157.6 kB |
| Tags | CPython 3.12 macOS 10.13+ x86-64 |
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Release files / fpsim2-0.7.4-cp311-cp311-win_amd64.whl
| Download URL | fpsim2-0.7.4-cp311-cp311-win_amd64.whl |
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| Size | 127.4 kB |
| Tags | CPython 3.11 Windows x86-64 |
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Release files / fpsim2-0.7.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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| Tags | CPython 3.11 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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| Download URL | fpsim2-0.7.4-cp311-cp311-macosx_11_0_arm64.whl |
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