Open In Colab

In [1]:
# install conda
!wget https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh
!chmod ./Miniconda3-4.4.10-Linux-x86_64.sh
!time bash ./Miniconda3-4.4.10-Linux-x86_64.sh -b -f -p /usr/local
# install rdkit via conda command
!time conda install -c conda-forge rdkit -y
--2019-04-09 12:04:42--  https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 58304693 (56M) [application/x-sh]
Saving to: ‘Miniconda3-4.4.10-Linux-x86_64.sh’

Miniconda3-4.4.10-L 100%[===================>]  55.60M   143MB/s    in 0.4s    

2019-04-09 12:04:43 (143 MB/s) - ‘Miniconda3-4.4.10-Linux-x86_64.sh’ saved [58304693/58304693]

chmod: missing operand after ‘./Miniconda3-4.4.10-Linux-x86_64.sh’
Try 'chmod --help' for more information.
PREFIX=/usr/local
installing: python-3.6.4-hc3d631a_1 ...
Python 3.6.4 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 ...
installing: conda-env-2.6.0-h36134e3_1 ...
installing: libgcc-ng-7.2.0-h7cc24e2_2 ...
installing: libstdcxx-ng-7.2.0-h7a57d05_2 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.0-h9df7e31_2 ...
installing: openssl-1.0.2n-hb7f436b_0 ...
installing: tk-8.6.7-hc745277_3 ...
installing: xz-5.2.3-h55aa19d_2 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-ha838bed_2 ...
installing: libedit-3.1-heed3624_0 ...
installing: readline-7.0-ha6073c6_4 ...
installing: sqlite-3.22.0-h1bed415_0 ...
installing: asn1crypto-0.24.0-py36_0 ...
installing: certifi-2018.1.18-py36_0 ...
installing: chardet-3.0.4-py36h0f667ec_1 ...
installing: idna-2.6-py36h82fb2a8_1 ...
installing: pycosat-0.6.3-py36h0a5515d_0 ...
installing: pycparser-2.18-py36hf9f622e_1 ...
installing: pysocks-1.6.7-py36hd97a5b1_1 ...
installing: ruamel_yaml-0.15.35-py36h14c3975_1 ...
installing: six-1.11.0-py36h372c433_1 ...
installing: cffi-1.11.4-py36h9745a5d_0 ...
installing: setuptools-38.4.0-py36_0 ...
installing: cryptography-2.1.4-py36hd09be54_0 ...
installing: wheel-0.30.0-py36hfd4bba0_1 ...
installing: pip-9.0.1-py36h6c6f9ce_4 ...
installing: pyopenssl-17.5.0-py36h20ba746_0 ...
installing: urllib3-1.22-py36hbe7ace6_0 ...
installing: requests-2.18.4-py36he2e5f8d_1 ...
installing: conda-4.4.10-py36_0 ...
installation finished.
WARNING:
    You currently have a PYTHONPATH environment variable set. This may cause
    unexpected behavior when running the Python interpreter in Miniconda3.
    For best results, please verify that your PYTHONPATH only points to
    directories of packages that are compatible with the Python interpreter
    in Miniconda3: /usr/local

real	0m13.053s
user	0m11.407s
sys	0m2.925s
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\ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.6.11

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /usr/local

  added / updated specs: 
    - rdkit


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    freetype-2.9.1             |       h6debe1e_4         800 KB  conda-forge
    cairo-1.16.0               |       h761e891_0         1.4 MB  conda-forge
    libxml2-2.9.8              |       h422b904_5         1.8 MB  conda-forge
    mkl_random-1.0.2           |           py36_0         1.3 MB  conda-forge
    xorg-xextproto-7.3.0       |       h470a237_2          26 KB  conda-forge
    ca-certificates-2019.3.9   |       hecc5488_0         146 KB  conda-forge
    xz-5.2.4                   |       h470a237_1         328 KB  conda-forge
    libgfortran-ng-7.3.0       |       hdf63c60_0         1.3 MB
    xorg-libxext-1.3.3         |       h470a237_4          45 KB  conda-forge
    pixman-0.34.0              |       h470a237_3         1.2 MB  conda-forge
    libuuid-2.32.1             |       h470a237_2          24 KB  conda-forge
    boost-cpp-1.68.0           |       h3a22d5f_0        20.1 MB  conda-forge
    numpy-base-1.15.0          |   py36h3dfced4_0         4.2 MB
    python-dateutil-2.8.0      |             py_0         219 KB  conda-forge
    openssl-1.0.2p             |       h470a237_2         3.1 MB  conda-forge
    libiconv-1.15              |       h470a237_4         2.0 MB  conda-forge
    glib-2.58.2                |       h2dc5807_1         3.4 MB  conda-forge
    libpng-1.6.36              |       ha92aebf_0         276 KB  conda-forge
    xorg-kbproto-1.0.7         |       h470a237_2          25 KB  conda-forge
    xorg-xproto-7.0.31         |       h470a237_7          72 KB  conda-forge
    icu-58.2                   |       hfc679d8_0        22.8 MB  conda-forge
    mkl-2018.0.3               |                1       198.7 MB
    boost-1.68.0               |   py36h3e44d54_1         328 KB  conda-forge
    libxcb-1.12                |                0         1.6 MB  conda-forge
    jpeg-9c                    |       h470a237_1         229 KB  conda-forge
    bzip2-1.0.6                |       h470a237_2         310 KB  conda-forge
    xorg-libice-1.0.9          |       h470a237_4          55 KB  conda-forge
    pandas-0.23.4              |   py36hf8a1672_0        27.8 MB  conda-forge
    pytz-2018.9                |             py_0         229 KB  conda-forge
    numpy-1.15.0               |   py36h1b885b7_0          35 KB
    rdkit-2018.09.1            |   py36h548bfbe_1        19.6 MB  conda-forge
    xorg-libxrender-0.9.10     |       h470a237_2          28 KB  conda-forge
    fontconfig-2.13.1          |       h65d0f4c_0         320 KB  conda-forge
    olefile-0.46               |             py_0          31 KB  conda-forge
    mkl_fft-1.0.10             |           py36_0         650 KB  conda-forge
    pycairo-1.15.4             |   py36h1b9232e_1          67 KB
    intel-openmp-2019.3        |              199         886 KB
    pcre-8.41                  |       hfc679d8_3         243 KB  conda-forge
    certifi-2019.3.9           |           py36_0         149 KB  conda-forge
    gettext-0.19.8.1           |       h5e8e0c9_1         3.5 MB  conda-forge
    xorg-libsm-1.2.3           |       h8c8a85c_0          24 KB  conda-forge
    xorg-libx11-1.6.6          |       h470a237_0         890 KB  conda-forge
    libtiff-4.0.10             |       he6b73bb_1         517 KB  conda-forge
    xorg-renderproto-0.11.1    |       h470a237_2           8 KB  conda-forge
    blas-1.0                   |              mkl           6 KB
    pillow-5.2.0               |   py36heded4f4_0         586 KB
    ------------------------------------------------------------
                                           Total:       321.2 MB

The following NEW packages will be INSTALLED:

    blas:             1.0-mkl                             
    boost:            1.68.0-py36h3e44d54_1    conda-forge
    boost-cpp:        1.68.0-h3a22d5f_0        conda-forge
    bzip2:            1.0.6-h470a237_2         conda-forge
    cairo:            1.16.0-h761e891_0        conda-forge
    fontconfig:       2.13.1-h65d0f4c_0        conda-forge
    freetype:         2.9.1-h6debe1e_4         conda-forge
    gettext:          0.19.8.1-h5e8e0c9_1      conda-forge
    glib:             2.58.2-h2dc5807_1        conda-forge
    icu:              58.2-hfc679d8_0          conda-forge
    intel-openmp:     2019.3-199                          
    jpeg:             9c-h470a237_1            conda-forge
    libgfortran-ng:   7.3.0-hdf63c60_0                    
    libiconv:         1.15-h470a237_4          conda-forge
    libpng:           1.6.36-ha92aebf_0        conda-forge
    libtiff:          4.0.10-he6b73bb_1        conda-forge
    libuuid:          2.32.1-h470a237_2        conda-forge
    libxcb:           1.12-0                   conda-forge
    libxml2:          2.9.8-h422b904_5         conda-forge
    mkl:              2018.0.3-1                          
    mkl_fft:          1.0.10-py36_0            conda-forge
    mkl_random:       1.0.2-py36_0             conda-forge
    numpy:            1.15.0-py36h1b885b7_0               
    numpy-base:       1.15.0-py36h3dfced4_0               
    olefile:          0.46-py_0                conda-forge
    pandas:           0.23.4-py36hf8a1672_0    conda-forge
    pcre:             8.41-hfc679d8_3          conda-forge
    pillow:           5.2.0-py36heded4f4_0                
    pixman:           0.34.0-h470a237_3        conda-forge
    pycairo:          1.15.4-py36h1b9232e_1               
    python-dateutil:  2.8.0-py_0               conda-forge
    pytz:             2018.9-py_0              conda-forge
    rdkit:            2018.09.1-py36h548bfbe_1 conda-forge
    xorg-kbproto:     1.0.7-h470a237_2         conda-forge
    xorg-libice:      1.0.9-h470a237_4         conda-forge
    xorg-libsm:       1.2.3-h8c8a85c_0         conda-forge
    xorg-libx11:      1.6.6-h470a237_0         conda-forge
    xorg-libxext:     1.3.3-h470a237_4         conda-forge
    xorg-libxrender:  0.9.10-h470a237_2        conda-forge
    xorg-renderproto: 0.11.1-h470a237_2        conda-forge
    xorg-xextproto:   7.3.0-h470a237_2         conda-forge
    xorg-xproto:      7.0.31-h470a237_7        conda-forge

The following packages will be UPDATED:

    ca-certificates:  2017.08.26-h1d4fec5_0                --> 2019.3.9-hecc5488_0 conda-forge
    certifi:          2018.1.18-py36_0                     --> 2019.3.9-py36_0     conda-forge
    openssl:          1.0.2n-hb7f436b_0                    --> 1.0.2p-h470a237_2   conda-forge
    xz:               5.2.3-h55aa19d_2                     --> 5.2.4-h470a237_1    conda-forge


Downloading and Extracting Packages
freetype 2.9.1: 100% 1.0/1 [00:00<00:00,  2.01it/s]               
cairo 1.16.0: 100% 1.0/1 [00:00<00:00,  1.23it/s]               
libxml2 2.9.8: 100% 1.0/1 [00:01<00:00,  1.15s/it]               
mkl_random 1.0.2: 100% 1.0/1 [00:00<00:00,  1.80it/s]               
xorg-xextproto 7.3.0: 100% 1.0/1 [00:00<00:00, 15.47it/s]
ca-certificates 2019.3.9: 100% 1.0/1 [00:00<00:00, 10.87it/s]
xz 5.2.4: 100% 1.0/1 [00:00<00:00,  4.40it/s] 
libgfortran-ng 7.3.0: 100% 1.0/1 [00:00<00:00,  1.37it/s]               
xorg-libxext 1.3.3: 100% 1.0/1 [00:00<00:00, 16.49it/s]
pixman 0.34.0: 100% 1.0/1 [00:00<00:00,  1.24it/s]              
libuuid 2.32.1: 100% 1.0/1 [00:00<00:00, 12.86it/s]
boost-cpp 1.68.0: 100% 1.0/1 [00:18<00:00, 18.61s/it]               
numpy-base 1.15.0: 100% 1.0/1 [00:02<00:00,  2.27s/it]              
python-dateutil 2.8.0: 100% 1.0/1 [00:00<00:00,  8.12it/s]               
openssl 1.0.2p: 100% 1.0/1 [00:01<00:00,  1.46s/it]               
libiconv 1.15: 100% 1.0/1 [00:00<00:00,  1.44it/s]               
glib 2.58.2: 100% 1.0/1 [00:01<00:00,  1.88s/it]               
libpng 1.6.36: 100% 1.0/1 [00:00<00:00,  5.57it/s] 
xorg-kbproto 1.0.7: 100% 1.0/1 [00:00<00:00, 20.67it/s]
xorg-xproto 7.0.31: 100% 1.0/1 [00:00<00:00, 11.06it/s]
icu 58.2: 100% 1.0/1 [00:09<00:00,  9.44s/it]               
mkl 2018.0.3: 100% 1.0/1 [01:28<00:00, 764.29s/it]               
boost 1.68.0: 100% 1.0/1 [00:00<00:00,  2.76it/s]              
libxcb 1.12: 100% 1.0/1 [00:01<00:00,  1.52s/it]               
jpeg 9c: 100% 1.0/1 [00:00<00:00,  5.40it/s] 
bzip2 1.0.6: 100% 1.0/1 [00:00<00:00,  5.19it/s] 
xorg-libice 1.0.9: 100% 1.0/1 [00:00<00:00, 17.69it/s]
pandas 0.23.4: 100% 1.0/1 [00:11<00:00, 11.95s/it]               
pytz 2018.9: 100% 1.0/1 [00:00<00:00,  2.67it/s]               
numpy 1.15.0: 100% 1.0/1 [00:00<00:00, 18.53it/s]
rdkit 2018.09.1: 100% 1.0/1 [00:08<00:00,  8.47s/it]               
xorg-libxrender 0.9.10: 100% 1.0/1 [00:00<00:00, 16.08it/s]
fontconfig 2.13.1: 100% 1.0/1 [00:00<00:00,  5.10it/s]               
olefile 0.46: 100% 1.0/1 [00:00<00:00, 19.29it/s]
mkl_fft 1.0.10: 100% 1.0/1 [00:00<00:00,  2.99it/s]               
pycairo 1.15.4: 100% 1.0/1 [00:00<00:00, 14.07it/s]
intel-openmp 2019.3: 100% 1.0/1 [00:00<00:00,  2.11it/s]               
pcre 8.41: 100% 1.0/1 [00:00<00:00,  6.42it/s]               
certifi 2019.3.9: 100% 1.0/1 [00:00<00:00,  8.99it/s]               
gettext 0.19.8.1: 100% 1.0/1 [00:02<00:00,  2.42s/it]               
xorg-libsm 1.2.3: 100% 1.0/1 [00:00<00:00, 16.46it/s]
xorg-libx11 1.6.6: 100% 1.0/1 [00:00<00:00,  2.06it/s]               
libtiff 4.0.10: 100% 1.0/1 [00:00<00:00,  3.16it/s]               
xorg-renderproto 0.11.1: 100% 1.0/1 [00:00<00:00, 19.58it/s]
blas 1.0: 100% 1.0/1 [00:00<00:00, 38.74it/s]
pillow 5.2.0: 100% 1.0/1 [00:00<00:00,  2.98it/s]               
Preparing transaction: / - \ | / - done
Verifying transaction: | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
Executing transaction: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done

real	16m11.023s
user	15m41.363s
sys	0m13.059s
In [2]:
import sys
import os
sys.path.append('/usr/local/lib/python3.6/site-packages/')
from rdkit import Chem
from rdkit import rdBase
print(rdBase.rdkitVersion)
2018.09.1
In [3]:
!nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2018 NVIDIA Corporation
Built on Sat_Aug_25_21:08:01_CDT_2018
Cuda compilation tools, release 10.0, V10.0.130
In [6]:
! conda config --add channels omnia --add channels conda-forge
Warning: 'omnia' already in 'channels' list, moving to the top
Warning: 'conda-forge' already in 'channels' list, moving to the top
In [7]:
! conda install -y openforcefield
Solving environment: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.6.11

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /usr/local

  added / updated specs: 
    - openforcefield


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    openmm-7.3.1               | py36_cuda92_rc_2        11.4 MB  omnia
    networkx-2.2               |             py_1         1.1 MB  conda-forge
    pyparsing-2.4.0            |             py_0          55 KB  conda-forge
    decorator-4.4.0            |             py_0          11 KB  conda-forge
    pyyaml-3.13                |   py36h470a237_1         460 KB  conda-forge
    msgpack-python-0.6.0       |   py36h2d50403_0         257 KB  conda-forge
    libgcc-7.2.0               |       h69d50b8_2         304 KB  conda-forge
    parmed-3.1.0               |           py36_0         1.1 MB  omnia
    openforcefield-0.2.0       |           py36_0        28.0 MB  omnia
    bson-0.5.8                 |             py_0          13 KB  conda-forge
    xmltodict-0.12.0           |             py_0          11 KB  conda-forge
    fftw3f-3.3.4               |                2         1.2 MB  omnia
    ambermini-16.16.0          |                7        21.7 MB  omnia
    toml-0.10.0                |             py_0          16 KB  conda-forge
    packaging-19.0             |             py_0          23 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        65.6 MB

The following NEW packages will be INSTALLED:

    ambermini:      16.16.0-7              omnia      
    bson:           0.5.8-py_0             conda-forge
    decorator:      4.4.0-py_0             conda-forge
    fftw3f:         3.3.4-2                omnia      
    libgcc:         7.2.0-h69d50b8_2       conda-forge
    msgpack-python: 0.6.0-py36h2d50403_0   conda-forge
    networkx:       2.2-py_1               conda-forge
    openforcefield: 0.2.0-py36_0           omnia      
    openmm:         7.3.1-py36_cuda92_rc_2 omnia      
    packaging:      19.0-py_0              conda-forge
    parmed:         3.1.0-py36_0           omnia      
    pyparsing:      2.4.0-py_0             conda-forge
    pyyaml:         3.13-py36h470a237_1    conda-forge
    toml:           0.10.0-py_0            conda-forge
    xmltodict:      0.12.0-py_0            conda-forge


Downloading and Extracting Packages
openmm 7.3.1: 100% 1.0/1 [00:07<00:00,  7.02s/it]               
networkx 2.2: 100% 1.0/1 [00:00<00:00,  1.06it/s]               
pyparsing 2.4.0: 100% 1.0/1 [00:00<00:00, 13.30it/s]
decorator 4.4.0: 100% 1.0/1 [00:00<00:00, 18.86it/s]
pyyaml 3.13: 100% 1.0/1 [00:00<00:00,  3.98it/s] 
msgpack-python 0.6.0: 100% 1.0/1 [00:00<00:00,  4.00it/s]               
libgcc 7.2.0: 100% 1.0/1 [00:00<00:00,  5.73it/s]               
parmed 3.1.0: 100% 1.0/1 [00:01<00:00,  1.36s/it]               
openforcefield 0.2.0: 100% 1.0/1 [00:13<00:00, 13.60s/it]                
bson 0.5.8: 100% 1.0/1 [00:00<00:00, 12.94it/s]
xmltodict 0.12.0: 100% 1.0/1 [00:00<00:00, 21.25it/s]
fftw3f 3.3.4: 100% 1.0/1 [00:01<00:00,  1.16s/it]               
ambermini 16.16.0: 100% 1.0/1 [00:12<00:00, 12.74s/it]               
toml 0.10.0: 100% 1.0/1 [00:00<00:00, 19.26it/s]
packaging 19.0: 100% 1.0/1 [00:00<00:00, 16.36it/s]
Preparing transaction: \ | done
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In [0]:
from openforcefield.topology import Molecule
from openforcefield.topology import Topology
from openforcefield.utils import RDKitToolkitWrapper
from openforcefield.typing.engines.smirnoff import ForceField
from simtk import openmm
from simtk import unit
In [0]:
def get_energy(system, positions):
    """
    Return the potential energy.

    Parameters
    ----------
    system : simtk.openmm.System
        The system to check
    positions : simtk.unit.Quantity of dimension (natoms,3) with units of length
        The positions to use
    Returns
    ---------
    energy
    """

    integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds)
    context = openmm.Context(system, integrator)
    context.setPositions(positions)
    state = context.getState(getEnergy=True)
    energy = state.getPotentialEnergy().in_units_of(unit.kilocalories_per_mole)
    return energy
In [0]:
mol = Molecule.from_smiles('CCO')
In [17]:
mol
Out[17]:
Molecule with name '' and SMILES '[H][O][C]([H])([H])[C]([H])([H])[H]'
In [0]:
mol.generate_conformers()
positions = mol.conformers[0]
In [0]:
#load Force Field
ff = ForceField('smirnoff99Frosst.offxml')
In [0]:
topology = mol.to_topology()
In [26]:
orginal_system = ff.create_openmm_system(topology)
In AmberToolsToolkitwrapper.computer_partial_charges_am1bcc: Molecule '' has more than one conformer, but this function will only generate charges for the first one.
In [0]:
orig_energy = get_energy(orginal_system, positions)
In [29]:
print(orig_energy)
2.3399880921635527 kcal/mol
In [0]:
mol = Chem.MolFromSmiles('c1ccccc1')
In [0]:
rdw = RDKitToolkitWrapper()
In [0]:
ofmol = rdw.from_rdkit(mol)
In [0]:
ofmol.generate_conformers()
In [38]:
positions = ofmol.conformers[0]
topology = ofmol.to_topology()
orginal_system = ff.create_openmm_system(topology)
orig_energy = get_energy(orginal_system, positions)
print(orig_energy)
7.987402593200566 kcal/mol
In [0]: