Installing RDKit on Google Colab

• Installing RDKit on Google Colab
  • Old Method (Still Works)

Update: March 2024

rdkit-pypi has been deprecated in favour of rdkit

You can simply run:

!pip install rdkit

EDIT: Try installing RDKit using pip

!pip install rdkit-pypi

Old Method (Still Works)

RDKit is one of the most integral part of any Cheminfomatic specialist's toolkit but it is notoriously difficult to install unless you already have conda installed. I originally found this in a GitHub Gist but I have not been able to find that gist again :/

Just copy and paste this in a Colab cell and it will install it 👍

import sys
import os
import requests
import subprocess
import shutil
from logging import getLogger, StreamHandler, INFO


logger = getLogger(__name__)
logger.addHandler(StreamHandler())
logger.setLevel(INFO)


def install(
        chunk_size=4096,
        file_name="Miniconda3-latest-Linux-x86_64.sh",
        url_base="https://repo.continuum.io/miniconda/",
        conda_path=os.path.expanduser(os.path.join("~", "miniconda")),
        rdkit_version=None,
        add_python_path=True,
        force=False):
    """install rdkit from miniconda
   

import rdkit_installer
rdkit_installer.install()
```
"""

python_path = os.path.join(
    conda_path,
    "lib",
    "python{0}.{1}".format(*sys.version_info),
    "site-packages",
)

if add_python_path and python_path not in sys.path:
    logger.info("add {} to PYTHONPATH".format(python_path))
    sys.path.append(python_path)

if os.path.isdir(os.path.join(python_path, "rdkit")):
    logger.info("rdkit is already installed")
    if not force:
        return

    logger.info("force re-install")

url = url_base + file_name
python_version = "{0}.{1}.{2}".format(*sys.version_info)

logger.info("python version: {}".format(python_version))

if os.path.isdir(conda_path):
    logger.warning("remove current miniconda")
    shutil.rmtree(conda_path)
elif os.path.isfile(conda_path):
    logger.warning("remove {}".format(conda_path))
    os.remove(conda_path)

logger.info('fetching installer from {}'.format(url))
res = requests.get(url, stream=True)
res.raise_for_status()
with open(file_name, 'wb') as f:
    for chunk in res.iter_content(chunk_size):
        f.write(chunk)
logger.info('done')

logger.info('installing miniconda to {}'.format(conda_path))
subprocess.check_call(["bash", file_name, "-b", "-p", conda_path])
logger.info('done')

logger.info("installing rdkit")
subprocess.check_call([
    os.path.join(conda_path, "bin", "conda"),
    "install",
    "--yes",
    "-c", "rdkit",
    "python=={}".format(python_version),
    "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)])
logger.info("done")

import rdkit
logger.info("rdkit-{} installation finished!".format(rdkit.__version__))

if name == "main": install() ```