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---
date: 2020-07-01 14:23
description: Install RDKit on Google Colab with one code snippet.
tags: Tutorial, Code-Snippet, Colab
---
# Installing RDKit on Google Colab
**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 👍
```python
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()
```
|
