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@philopon
Last active February 3, 2022 18:41
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DEPRECATED. Please use https://pypi.org/project/rdkit-pypi/
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()
@bikashd200
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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.

@Prajwalnazre
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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!

@saharctech
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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.

@philopon
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Author

philopon commented Feb 3, 2022

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

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