DEPRECATED. Please use https://pypi.org/project/rdkit-pypi/

rdkit_installer.py

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()

is it possible to import rdkit without installing every time

Hi, i tried to do it this way, however rdkit.Chem is not recognized

in smiles_to_onehot_mat(self, smiles)
245 onehot_mat = []
246 for smile in smiles:
--> 247 m = rdkit.Chem.MolFromSmiles(smile, sanitize=False)
248 if m is None:
249 onehot_mat.append(np.nan)

AttributeError: module 'rdkit' has no attribute 'Chem'

Any suggestions?

Hi,
I was trying to install rdkit using above code. But, got this error. Any help please !!!!

CalledProcessError Traceback (most recent call last)
in ()
84
85 if name == "main":
---> 86 install()

1 frames
in install(chunk_size, file_name, url_base, conda_path, rdkit_version, add_python_path, force)
76 "-c", "rdkit",
77 "python=={}".format(python_version),
---> 78 "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)])
79 logger.info("done")
80

/usr/lib/python3.7/subprocess.py in check_call(*popenargs, **kwargs)
361 if cmd is None:
362 cmd = popenargs[0]
--> 363 raise CalledProcessError(retcode, cmd)
364 return 0
365

CalledProcessError: Command '['/root/miniconda/bin/conda', 'install', '--yes', '-c', 'rdkit', 'python==3.7.10', 'rdkit']' returned non-zero exit status 1.

Well, the installation was complete. But why am I not able to access 'Chem' subpackage from rdkit? The only modules available from the installation are ['RDConfig',
'RDPaths',
'kernel_name',
'logger',
'logging',
'rdBase']
According to the rdkit documentation, there are so many subpackages but I am unable to access them!

Is this up to date? This does not work for me. I am getting below error:
CalledProcessError: Command '['/root/miniconda/bin/conda', 'install', '--yes', '-c', 'rdkit', 'python==3.7.12', 'rdkit']' returned non-zero exit status 1.

This script is DEPRECATED.
Please use rdkit-pypi package.