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February 3, 2022 18:41
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DEPRECATED. Please use https://pypi.org/project/rdkit-pypi/
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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 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.
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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!