I have installed the Debian Stretch distribution of Spyder3 and the RDKit.
Neither installation resulted in either warning or error messages.
However, when I attempt running a cookbook Python3 script utilizing RDKit I
get the following:
Python 3.5.3 (default, Jan 19 2017, 14:11:04)
Type "copyright", "credits" or "license" for more information.
IPython 6.1.0 -- An enhanced Interactive Python.
runfile('/home/comp/Apps/Python/untitled0.py',
wdir='/home/comp/Apps/Python')
Traceback (most recent call last):
File "<ipython-input-1-3842c59475d8>", line 1, in <module>
runfile('/home/comp/Apps/Python/untitled0.py',
wdir='/home/comp/Apps/Python')
File
"/usr/local/lib/python3.5/dist-packages/spyder/utils/site/sitecustomize.py",
line 688, in runfile
execfile(filename, namespace)
File
"/usr/local/lib/python3.5/dist-packages/spyder/utils/site/sitecustomize.py",
line 101, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "/home/comp/Apps/Python/untitled0.py", line 11, in <module>
from rdkit import Chem
ImportError: No module named 'rdkit'
The Pyhon script is attached.
I have no idea as to what the problem might be. Any assistance will be
appreciated.
Thanks in advance,
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 17 11:06:00 2017
@author: comp
"""
""" contribution from Andrew Dalke """
import sys
from rdkit import Chem
from rdkit.Chem import AllChem
# Download this from http://pypi.python.org/pypi/futures
from concurrent import futures
# Download this from http://pypi.python.org/pypi/progressbar
import progressbar
## On my machine, it takes 39 seconds with 1 worker and 10 seconds with 4.
## 29.055u 0.102s 0:28.68 101.6% 0+0k 0+3io 0pf+0w
#max_workers=1
## With 4 threads it takes 11 seconds.
## 34.933u 0.188s 0:10.89 322.4% 0+0k 125+1io 0pf+0w
max_workers=4
# (The "u"ser time includes time spend in the children processes.
# The wall-clock time is 28.68 and 10.89 seconds, respectively.)
# This function is called in the subprocess.
# The parameters (molecule and number of conformers) are passed via a Python
def generateconformations(m, n):
m = Chem.AddHs(m)
ids=AllChem.EmbedMultipleConfs(m, numConfs=n)
for id in ids:
AllChem.UFFOptimizeMolecule(m, confId=id)
# EmbedMultipleConfs returns a Boost-wrapped type which
# cannot be pickled. Convert it to a Python list, which can.
return m, list(ids)
smi_input_file, sdf_output_file = sys.argv[1:3]
n = int(sys.argv[3])
writer = Chem.SDWriter(sdf_output_file)
suppl = Chem.SmilesMolSupplier(smi_input_file, titleLine=False)
with futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
# Submit a set of asynchronous jobs
jobs = []
for mol in suppl:
if mol:
job = executor.submit(generateconformations, mol, n)
jobs.append(job)
widgets = ["Generating conformations; ", progressbar.Percentage(), " ",
progressbar.ETA(), " ", progressbar.Bar()]
pbar = progressbar.ProgressBar(widgets=widgets, maxval=len(jobs))
for job in pbar(futures.as_completed(jobs)):
mol,ids=job.result()
for id in ids:
writer.write(mol, confId=id)
writer.close()
