ijpulidos

# Script to check order matters when generating conformers

from openff.toolkit.topology import Molecule
from openff.toolkit.utils.toolkits import ToolkitRegistry, OpenEyeToolkitWrapper, RDKitToolkitWrapper
import copy
from openeye import oeomega

openff_mol_1 = Molecule.from_smiles('CC(C)(C)c1sc(c2ccnc(N)n2)c(n1)c3cccc(N[S](=O)(=O)c4c(F)cccc4F)c3F')

# Pass it to OE to change order

ijpulidos

...
Starting contact map-based cluster analysis...

Building distance matrix...
Done.

There are more than 1000 frames, we will limit the interframe plots to approx. 1000x1000.
hierarchical...
Traceback (most recent call last):
  File "/home/user/CONAN/conan-software/conan.py", line 2090, in <module>

ijpulidos

[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true

[dev-packages]

[packages]
jupyterlab = "*"
pandas = "*"

ijpulidos

Using /usr/bin/python3 (3.7.6) to create virtualenv…
⠋ Creating virtual environment...Already using interpreter /usr/bin/python3
Using base prefix '/usr'
New python executable in /home/mefisto/.local/share/virtualenvs/covid19-support-backend-nAprNWA1/bin/python3
Also creating executable in /home/mefisto/.local/share/virtualenvs/covid19-support-backend-nAprNWA1/bin/python
Installing setuptools, pip, wheel...
done.

✔ Successfully created virtual environment! 
Virtualenv location: /home/mefisto/.local/share/virtualenvs/covid19-support-backend-nAprNWA1

ijpulidos

from sklearn import datasets
from sklearn.metrics import accuracy_score 
from sklearn.cluster import KMeans
import matplotlib.pyplot as plt
import numpy as np 

# Use iris dataset included in sklearn
iris = datasets.load_iris 
k = 3  # Number of clusters
km = KMeans(k, random_state=0) # make the randomness deterministic for centroid (reproducibility)

ijpulidos

Glue: 0.14.1
Python: 3.7.2
PyQt5: PyQt: 5.11.3 - Qt: 5.12.0
PySide2: Not installed
qtpy: 1.5.1
setuptools: 40.6.3
numpy: 1.16.0
bottleneck: 1.2.1
matplotlib: 3.0.2
pandas: 0.23.4

ijpulidos

➜ glue -v
INFO:glue:Input arguments: ['/home/user/anaconda3/envs/glueviz/bin/glue', '-v']
INFO:glue:Loading external plugins using setuptools==40.6.3
INFO:glue:Loading plugin vispy_volume succeeded
INFO:glue:Loading plugin vispy_scatter succeeded
INFO:glue:Loading plugin export_d3po succeeded
INFO:glue:Loading plugin export_plotly succeeded
INFO:glue:Loading plugin pv_slicer succeeded
INFO:glue:Loading plugin coordinate_helpers succeeded
INFO:glue:Loading plugin spectral_cube failed (Exception: No module named 'spectral_cube')

ijpulidos

Glue: 0.14.1
Python: 3.7.2
PyQt5: PyQt: 5.9.2 - Qt: 5.9.6
PySide2: Not installed
qtpy: 1.5.2
setuptools: 40.6.3
numpy: 1.15.4
bottleneck: 1.2.1
matplotlib: 3.0.2
pandas: 0.23.4

ijpulidos

# dpkg -l 
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                     Version           Architecture      Description
+++-========================-=================-=================-=====================================================
ii  adduser                  3.115             all               add and remove users and groups
ii  apt                      1.4.8             amd64             commandline package manager
ii  apt-transport-https      1.4.8             amd64             https download transport for APT
ii  base-files               9.9+deb9u4        amd64             Debian base system miscellaneous files

ijpulidos

Cygwin Package Information
Package                                 Version                      Status
_autorebase                             001006-1                     OK
adwaita-icon-theme                      3.24.0-1                     OK
algol68g                                2.7-0                        OK
alternatives                            1.3.30c-10                   OK
at-spi2-core                            2.24.1-1                     OK
autoconf                                13-1                         OK
autoconf2.1                             2.13-12                      OK
autoconf2.5                             2.69-3                       OK