science/rdkit 2026.03.6
Collection of cheminformatics and machine-learning software
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
bba96c42a2- License
- BSD3CLAUSE
- Categories
- science
- Package size
- 34404.8 KiB, 155117.3 KiB installed
Description
Open source toolkit for cheminformatics.
Features: * Input/Output: SMILES/SMARTS, SDF, TDT, SLN 1, Corina mol2 1, PDB, sequence notation, FASTA (peptides only), HELM (peptides only) * Substructure searching * Canonical SMILES * Chirality support (i.e. R/S or E/Z labeling) * Chemical transformations (e.g. remove matching substructures) * Chemical reactions * Molecular serialization (e.g. mol <-> text) * 2D depiction, including constrained depiction * Fingerprinting: Daylight-like, atom pairs, topological torsions, Morgan algorithm, "MACCS keys", extended reduced graphs, etc. * Similarity/diversity picking * Gasteiger-Marsili charges * Bemis and Murcko scaffold determination * Salt stripping * Functional-group filters
Install
As a binary package — by origin, or by package name:
pkg install science/rdkit
pkg install rdkitFrom the ports tree:
cd /usr/ports/science/rdkit/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= rdkit>0:science/rdkit
LIB_DEPENDS= libRDKitAbbreviations.so:science/rdkitPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2026.03.6 | 2026.03.6 | - | 2025.03.1_1 | 2026.03.6 |
| FreeBSD:14:quarterly | 2026.03.6 | 2026.03.6 | n/a | 2025.03.1_1 | 2026.03.6 |
| FreeBSD:15:latest | 2026.03.6 | 2026.03.6 | n/a | - | - |
| FreeBSD:15:quarterly | 2026.03.6 | 2026.03.6 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2026.03.6 | 2026.03.6 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 2
catch>0: devel/catchflex: textproc/flex
Library 3
libboost_thread.so: devel/boost-libslibexpat.so: textproc/expat2libfreetype.so: print/freetype2
The full lists below include those, and their dependencies in turn.
All build dependencies 57
- archivers/brotli
- archivers/liblz4
- archivers/lzo2
- archivers/zstd
- converters/libiconv
- devel/binutils
- devel/bison
- devel/boost-libs
- devel/boost-python-libs
- devel/catch
- devel/cmake-core
- devel/gettext-runtime
- devel/glib20
- devel/icu
- devel/jsoncpp
- devel/libffi
- devel/libinotify
- devel/libtextstyle
- devel/libunistring
- devel/libuv
- devel/llvm23
- devel/m4
- devel/ninja
- devel/pcre2
- devel/pkgconf
- devel/py-packaging
- devel/readline
- dns/libidn2
- graphics/cairo
- graphics/png
- lang/gcc14
- lang/python312
- lang/python315
- math/blas
- math/eigen3
- math/gmp
- math/lapack
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-numpy
- ports-mgmt/pkg
- print/freetype2
- print/indexinfo
- security/rhash
- textproc/expat2
- textproc/flex
- x11-fonts/fontconfig
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXrender
- x11/libxcb
- x11/pixman
- x11/xorgproto
All run dependencies 89
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/lzo2
- archivers/py-brotli
- archivers/py-zopfli
- archivers/zopfli
- archivers/zstd
- converters/fribidi
- converters/libiconv
- devel/binutils
- devel/boost-libs
- devel/boost-python-libs
- devel/gettext-runtime
- devel/glib20
- devel/icu
- devel/libffi
- devel/libinotify
- devel/pcre2
- devel/py-cycler
- devel/py-lxml
- devel/py-olefile
- devel/py-packaging
- devel/py-pyparsing
- devel/py-python-dateutil
- devel/py-six
- devel/py-unicodedata2
- devel/readline
- graphics/cairo
- graphics/gdk-pixbuf2
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/libavif
- graphics/libimagequant
- graphics/libyuv
- graphics/openjpeg
- graphics/png
- graphics/py-pillow
- graphics/tiff
- graphics/webp
- lang/gcc14
- lang/python312
- lang/python315
- lang/tcl86
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-contourpy
- math/py-kiwisolver
- math/py-matplotlib
- math/py-numpy
- math/qhull
- misc/shared-mime-info
- multimedia/aom
- multimedia/dav1d
- multimedia/vmaf
- print/adobe-cmaps
- print/freetype2
- print/harfbuzz
- print/indexinfo
- print/libraqm
- print/py-fonttools
- print/py-reportlab
- security/libgcrypt
- security/libgpg-error
- textproc/expat2
- textproc/libxml2
- textproc/libxslt
- x11-fonts/fontconfig
- x11-fonts/libXft
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-toolkits/py-tkinter
- x11-toolkits/tk86
- x11/libX11
- x11/libXScrnSaver
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXrender
- x11/libxcb
- x11/pixman
- x11/xorgproto
Configuration
Options name: science_rdkit
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| PGSQL | off | Build the PostgreSQL cartridge |
| PYTHON | on | Python bindings or support |
- USES
- bison:build cmake:testing compiler:c++11-lang eigen:3 gnome llvm:23 pkgconfig python
- Service scripts
- none
Files
pkg-plist 1234
- include/rdkit/Catalogs/Catalog.h
- include/rdkit/Catalogs/CatalogEntry.h
- include/rdkit/Catalogs/CatalogParams.h
- include/rdkit/ChemicalFeatures/ChemicalFeature.h
- include/rdkit/ChemicalFeatures/FreeChemicalFeature.h
- include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h
- include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h
- include/rdkit/DataStructs/BitOps.h
- include/rdkit/DataStructs/BitVect.h
- include/rdkit/DataStructs/BitVectUtils.h
- include/rdkit/DataStructs/BitVects.h
- include/rdkit/DataStructs/DatastructsException.h
- include/rdkit/DataStructs/DatastructsStreamOps.h
- include/rdkit/DataStructs/DiscreteDistMat.h
- include/rdkit/DataStructs/DiscreteValueVect.h
- include/rdkit/DataStructs/ExplicitBitVect.h
- include/rdkit/DataStructs/FPBReader.h
- include/rdkit/DataStructs/MultiFPBReader.h
- include/rdkit/DataStructs/RealValueVect.h
- include/rdkit/DataStructs/SparseBitVect.h
- include/rdkit/DataStructs/SparseIntVect.h
- include/rdkit/DataStructs/base64.h
- include/rdkit/DistGeom/BoundsMatrix.h
- include/rdkit/DistGeom/ChiralSet.h
- include/rdkit/DistGeom/ChiralViolationContribs.h
- include/rdkit/DistGeom/DistGeomUtils.h
- include/rdkit/DistGeom/DistViolationContribs.h
- include/rdkit/DistGeom/FourthDimContribs.h
- include/rdkit/DistGeom/TriangleSmooth.h
- include/rdkit/Features/Feature.h
- include/rdkit/ForceField/AngleConstraint.h
- include/rdkit/ForceField/AngleConstraints.h
- include/rdkit/ForceField/Contrib.h
- include/rdkit/ForceField/DistanceConstraint.h
- include/rdkit/ForceField/DistanceConstraints.h
- include/rdkit/ForceField/ForceField.h
- include/rdkit/ForceField/MMFF/AngleBend.h
- include/rdkit/ForceField/MMFF/AngleConstraint.h
- include/rdkit/ForceField/MMFF/BondStretch.h
- include/rdkit/ForceField/MMFF/Contribs.h
- include/rdkit/ForceField/MMFF/DistanceConstraint.h
- include/rdkit/ForceField/MMFF/Nonbonded.h
- include/rdkit/ForceField/MMFF/OopBend.h
- include/rdkit/ForceField/MMFF/Params.h
- include/rdkit/ForceField/MMFF/PositionConstraint.h
- include/rdkit/ForceField/MMFF/StretchBend.h
- include/rdkit/ForceField/MMFF/TorsionAngle.h
- include/rdkit/ForceField/MMFF/TorsionConstraint.h
- include/rdkit/ForceField/PositionConstraint.h
- include/rdkit/ForceField/TorsionConstraint.h
- include/rdkit/ForceField/UFF/AngleBend.h
- include/rdkit/ForceField/UFF/AngleConstraint.h
- include/rdkit/ForceField/UFF/BondStretch.h
- include/rdkit/ForceField/UFF/Contribs.h
- include/rdkit/ForceField/UFF/DistanceConstraint.h
- include/rdkit/ForceField/UFF/Inversion.h
- include/rdkit/ForceField/UFF/Inversions.h
- include/rdkit/ForceField/UFF/Nonbonded.h
- include/rdkit/ForceField/UFF/Params.h
- include/rdkit/ForceField/UFF/PositionConstraint.h
- include/rdkit/ForceField/UFF/TorsionAngle.h
- include/rdkit/ForceField/UFF/TorsionConstraint.h
- include/rdkit/ForceField/UFF/Utils.h
- include/rdkit/GaussianShape.h
- include/rdkit/Geometry/Grid3D.h
- include/rdkit/Geometry/GridUtils.h
- include/rdkit/Geometry/Transform.h
- include/rdkit/Geometry/Transform2D.h
- include/rdkit/Geometry/Transform3D.h
- include/rdkit/Geometry/UniformGrid3D.h
- include/rdkit/Geometry/UniformRealValueGrid3D.h
- include/rdkit/Geometry/Utils.h
- include/rdkit/Geometry/point.h
- include/rdkit/GraphMol/Abbreviations/Abbreviations.h
- include/rdkit/GraphMol/Atom.h
- include/rdkit/GraphMol/AtomIterators.h
- include/rdkit/GraphMol/Atropisomers.h
- include/rdkit/GraphMol/Bond.h
- include/rdkit/GraphMol/BondIterators.h
- include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h
- include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h
- include/rdkit/GraphMol/Canon.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h
- include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h
- include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h
- include/rdkit/GraphMol/ChemReactions/Reaction.h
- include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h
- include/rdkit/GraphMol/ChemReactions/ReactionParser.h
- include/rdkit/GraphMol/ChemReactions/ReactionPickler.h
- include/rdkit/GraphMol/ChemReactions/ReactionRunner.h
- include/rdkit/GraphMol/ChemReactions/ReactionUtils.h
- include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h
- include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h
- include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h
The first 100 are listed.
distinfo 8
| File | Size | SHA256 |
|---|---|---|
| rdkit-2026.03.6/v1.3.3.tar.gz | 39896 | 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 |
| rdkit-2026.03.6/v3.0.2.tar.gz | 166817 | f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 |
| rdkit-2026.03.6/v1.0.14 | 530904 | bedd75643b9bfaee1663fc41814370ac9329c8d0934e970179929cb355a82aff |
| rdkit-2026.03.6/ComicNeue-Regular.ttf | 21915 | 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 |
| rdkit-2026.03.6/rdkit-rdkit-Release_2026_03_6_GH0.tar.gz | 8.4044449e+07 | d4d20b3b140237084694518aab34fdba6929d44bd7f720bce69329516abef663 |
| rdkit-2026.03.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz | 137931 | 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 |
| rdkit-2026.03.6/ncbi-pubchem-align3d-daefab3_GH0.tar.gz | 112376 | d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 |
| rdkit-2026.03.6/aantron-better-enums-520d8ee_GH0.tar.gz | 136592 | 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 |
Master sites 4
- https://github.com/schrodinger/maeparser/archive/:maeparser
- https://github.com/schrodinger/coordgenlibs/archive/:coordgen
- https://codeload.github.com/Glysade/chemdraw/tar.gz/refs/tags/:chemdraw
- LOCAL/yuri/:font