Cheminformatics Tutorials - Herong's Tutorial Examples - v2.03, by Herong Yang
Install RDKit in an Anaconda Environment
This section provides a tutorial example on how to install RDKit Python library in an Anaconda environment. It's easy and fast.
The easiest and fastest way to install RDKit is to use the Anaconda package manager. Here is what I did to install RDKit with Anaconda on my Linux computer.
1. Make sure that Anaconda is installed.
herong$ conda --version conda 4.10.3
2. Creating a new Conda environment with the RDKit installed with one single command. This will take several minutes.
$ conda create -c conda-forge -n my-rdkit-env rdkit
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local/anaconda3/envs/my-rdkit-env
added / updated specs:
- rdkit
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB
_openmp_mutex-4.5 | 1_gnu 22 KB
boost-1.74.0 | py39h5472131_3 368 KB
boost-cpp-1.74.0 | h312852a_4 16.3 MB
bzip2-1.0.8 | h7f98852_4 484 KB
cairo-1.16.0 | h6cf1ce9_1008 1.5 MB
certifi-2021.5.30 | py39hf3d152e_0 141 KB
cycler-0.10.0 | py_2 9 KB
fontconfig-2.13.1 | hba837de_1005 357 KB
freetype-2.10.4 | h0708190_1 890 KB
gettext-0.19.8.1 | h0b5b191_1005 3.6 MB
greenlet-1.1.1 | py39he80948d_0 83 KB
jbig-2.1 | h7f98852_2003 43 KB
jpeg-9d | h36c2ea0_0 264 KB
kiwisolver-1.3.1 | py39h1a9c180_1 80 KB
lcms2-2.12 | hddcbb42_0 443 KB
ld_impl_linux-64-2.36.1 | hea4e1c9_2 667 KB
lerc-2.2.1 | h9c3ff4c_0 213 KB
libblas-3.9.0 |11_linux64_openblas 12 KB
libcblas-3.9.0 |11_linux64_openblas 11 KB
libdeflate-1.7 | h7f98852_5 67 KB
libffi-3.3 | h58526e2_2 51 KB
libgcc-ng-11.1.0 | hc902ee8_8 908 KB
libgfortran-ng-11.1.0 | h69a702a_8 19 KB
libgfortran5-11.1.0 | h6c583b3_8 1.7 MB
libglib-2.68.4 | h3e27bee_0 3.0 MB
libgomp-11.1.0 | hc902ee8_8 427 KB
libiconv-1.16 | h516909a_0 1.4 MB
liblapack-3.9.0 |11_linux64_openblas 11 KB
libopenblas-0.3.17 |pthreads_h8fe5266_1 9.2 MB
libpng-1.6.37 | h21135ba_2 306 KB
libstdcxx-ng-11.1.0 | h56837e0_8 4.2 MB
libtiff-4.3.0 | hf544144_1 668 KB
libuuid-2.32.1 | h7f98852_1000 28 KB
libwebp-base-1.2.1 | h7f98852_0 845 KB
libxcb-1.13 | h7f98852_1003 395 KB
libxml2-2.9.12 | h72842e0_0 772 KB
lz4-c-1.9.3 | h9c3ff4c_1 179 KB
matplotlib-base-3.4.3 | py39h2fa2bec_0 7.3 MB
ncurses-6.2 | h58526e2_4 985 KB
numpy-1.21.2 | py39hdbf815f_0 6.2 MB
olefile-0.46 | pyh9f0ad1d_1 32 KB
openjpeg-2.4.0 | hb52868f_1 444 KB
openssl-1.1.1k | h7f98852_1 2.1 MB
pandas-1.3.2 | py39hde0f152_0 13.0 MB
pcre-8.45 | h9c3ff4c_0 253 KB
pillow-8.3.1 | py39ha612740_0 687 KB
pip-21.2.4 | pyhd8ed1ab_0 1.1 MB
pixman-0.40.0 | h36c2ea0_0 627 KB
pthread-stubs-0.4 | h36c2ea0_1001 5 KB
pycairo-1.20.1 | py39hedcb9fc_0 77 KB
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB
python-3.9.6 |h49503c6_1_cpython 27.5 MB
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB
python_abi-3.9 | 2_cp39 4 KB
pytz-2021.1 | pyhd8ed1ab_0 239 KB
rdkit-2021.03.5 | py39hccf6a74_0 38.3 MB
readline-8.1 | h46c0cb4_0 295 KB
reportlab-3.5.68 | py39he59360d_0 2.4 MB
setuptools-57.4.0 | py39hf3d152e_0 934 KB
six-1.16.0 | pyh6c4a22f_0 14 KB
sqlalchemy-1.4.23 | py39h3811e60_0 2.3 MB
sqlite-3.36.0 | h9cd32fc_0 1.4 MB
tk-8.6.11 | h21135ba_0 3.3 MB
tornado-6.1 | py39h3811e60_1 646 KB
tzdata-2021a | he74cb21_1 121 KB
wheel-0.37.0 | pyhd8ed1ab_1 31 KB
xorg-kbproto-1.0.7 | h7f98852_1002 27 KB
xorg-libice-1.0.10 | h7f98852_0 58 KB
xorg-libsm-1.2.3 | hd9c2040_1000 26 KB
xorg-libx11-1.7.2 | h7f98852_0 941 KB
xorg-libxau-1.0.9 | h7f98852_0 13 KB
xorg-libxdmcp-1.1.3 | h7f98852_0 19 KB
xorg-libxext-1.3.4 | h7f98852_1 54 KB
xorg-libxrender-0.9.10 | h7f98852_1003 32 KB
xorg-renderproto-0.11.1 | h7f98852_1002 9 KB
xorg-xextproto-7.3.0 | h7f98852_1002 28 KB
xorg-xproto-7.0.31 | h7f98852_1007 73 KB
xz-5.2.5 | h516909a_1 343 KB
zlib-1.2.11 | h516909a_1010 106 KB
zstd-1.5.0 | ha95c52a_0 490 KB
------------------------------------------------------------
Total: 162.2 MB
...
3. Activate the new Conda environment, my-rdkit-env.
herong$ conda activate my-rdkit-env (my-rdkit-env) herong$
4. Verify RDKit installation.
(my-rdkit-env) herong$ python -c "import rdkit; print(rdkit.__version__);" 2021.03.5
Cool. I can use RDKit through its Python API now.
Note that installing RDKit with Anaconda will not give you the C++ API. If you need it, you can follow next tutorials to build it from source code or find a binary package for your computer system.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
►RDKit: Open-Source Cheminformatics Software
►Install RDKit in an Anaconda Environment
Install RDKit Binary Package for CentOS
Build RDKit from Source Code on CentOS System
Compile, Link and Run RDKit C++ API Examples
Try Python API with RDKit Native Code
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction