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Tutorial: Install ReacNetGenerator on Google Colaboratory

In this series of tutorials, we will try to install and run ReacNetGenerator on Google Colaboratory. You can click the above button to repeat it.

In this tutorial, we will use pip to install ReacNetGenerator. This is the eastiest way without compiling the package.

Install ReacNetGenerator

We use pip to install the ReacNetGenerator. It's very simple as follows!

In [1]:
!pip install reacnetgenerator
Collecting reacnetgenerator
  Downloading https://files.pythonhosted.org/packages/1f/e9/56819faadf4d9c253b4110fb0e1304a2a80094e03c4e9e9a8a67fb6c1751/reacnetgenerator-1.4.164-cp37-cp37m-manylinux2010_x86_64.whl (4.3MB)
     |████████████████████████████████| 4.3MB 6.3MB/s 
Collecting lz4
  Downloading https://files.pythonhosted.org/packages/e3/52/151c815a486290608e4dc6699a0cfd74141dc5191f8fe928e7d1b28b569e/lz4-3.1.3-cp37-cp37m-manylinux2010_x86_64.whl (1.8MB)
     |████████████████████████████████| 1.8MB 37.9MB/s 
Collecting coloredlogs
  Downloading https://files.pythonhosted.org/packages/84/a6/837dbf6eac344cb74f0ba86b79e8180855570af3e26bcb1ea5f650cf944c/coloredlogs-15.0-py2.py3-none-any.whl (45kB)
     |████████████████████████████████| 51kB 4.6MB/s 
Collecting scour
  Downloading https://files.pythonhosted.org/packages/75/19/f519ef8aa2f379935a44212c5744e2b3a46173bf04e0110fb7f4af4028c9/scour-0.38.2.tar.gz (52kB)
     |████████████████████████████████| 61kB 5.7MB/s 
Requirement already satisfied: networkx in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (2.5)
Collecting ase
  Downloading https://files.pythonhosted.org/packages/a5/36/de17e79f29e06d9a92746d0dd9ec4636487ab03f6af10e78586aae533f7a/ase-3.21.1-py3-none-any.whl (2.2MB)
     |████████████████████████████████| 2.2MB 33.9MB/s 
Requirement already satisfied: requests in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (2.23.0)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (3.2.2)
Collecting openbabel-wheel
  Downloading https://files.pythonhosted.org/packages/f3/e8/74018a601ec40dd76b9ba6d0ddfa22a67bb5802fd6ffa46a344915d46ff4/openbabel_wheel-3.1.1.5-cp37-cp37m-manylinux2014_x86_64.whl (13.6MB)
     |████████████████████████████████| 13.6MB 258kB/s 
Requirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.19.5)
Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.1.5)
Collecting pybase64
  Downloading https://files.pythonhosted.org/packages/71/9c/fc5a2734645f9cdc7c0a549a4ee063cf25c05e728d287508fd14c437ac4e/pybase64-1.1.4-cp37-cp37m-manylinux2014_x86_64.whl (170kB)
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Requirement already satisfied: scipy>=0.20.1 in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.4.1)
Collecting rdkit-pypi
  Downloading https://files.pythonhosted.org/packages/6f/1b/053bddf14b39000ff95c59d012934fcbe96fef681ece0f8315c126c0bb5b/rdkit_pypi-2021.3.1.2-cp37-cp37m-manylinux2014_x86_64.whl (31.4MB)
     |████████████████████████████████| 31.4MB 111kB/s 
Collecting hmmlearn>=0.2.1
  Downloading https://files.pythonhosted.org/packages/4b/98/a2829aeb942b7146034d497afb3fc738a78a4fbd4797a039c19a94bb31f7/hmmlearn-0.2.5-cp37-cp37m-manylinux1_x86_64.whl (369kB)
     |████████████████████████████████| 378kB 34.7MB/s 
Requirement already satisfied: tqdm in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (4.41.1)
Collecting humanfriendly>=9.1
  Downloading https://files.pythonhosted.org/packages/93/66/363d01a81da2108a5cf446daf619779f06d49a0c4426dd02b40734f10e2f/humanfriendly-9.1-py2.py3-none-any.whl (86kB)
     |████████████████████████████████| 92kB 7.4MB/s 
Requirement already satisfied: six>=1.9.0 in /usr/local/lib/python3.7/dist-packages (from scour->reacnetgenerator) (1.15.0)
Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.7/dist-packages (from networkx->reacnetgenerator) (4.4.2)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (1.24.3)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (2020.12.5)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (2.10)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (1.3.1)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (0.10.0)
Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->reacnetgenerator) (2018.9)
Requirement already satisfied: scikit-learn>=0.16 in /usr/local/lib/python3.7/dist-packages (from hmmlearn>=0.2.1->reacnetgenerator) (0.22.2.post1)
Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.7/dist-packages (from scikit-learn>=0.16->hmmlearn>=0.2.1->reacnetgenerator) (1.0.1)
Building wheels for collected packages: scour
  Building wheel for scour (setup.py) ... done
  Created wheel for scour: filename=scour-0.38.2-cp37-none-any.whl size=54253 sha256=5c236125ed4b03b44f5f87c711b62d82acf7d183e110bee4250ae7cfbd78aa33
  Stored in directory: /root/.cache/pip/wheels/0e/85/c0/989d78aef861a7859c2ec1e56157abc1255498e49dcbfa23f4
Successfully built scour
Installing collected packages: lz4, humanfriendly, coloredlogs, scour, ase, openbabel-wheel, pybase64, rdkit-pypi, hmmlearn, reacnetgenerator
Successfully installed ase-3.21.1 coloredlogs-15.0 hmmlearn-0.2.5 humanfriendly-9.1 lz4-3.1.3 openbabel-wheel-3.1.1.5 pybase64-1.1.4 rdkit-pypi-2021.3.1.2 reacnetgenerator-1.4.164 scour-0.38.2

Now, ReacNetGenerator has been already installed in the environment. Try it now!

In [2]:
!reacnetgenerator -h
usage: reacnetgenerator [-h] -i [INPUTFILENAME [INPUTFILENAME ...]] -a
                        [ATOMNAME [ATOMNAME ...]] [--nohmm] [--dump]
                        [--type TYPE] [--nopbc] [--cell CELL CELL CELL]
                        [-n NPROC] [-s [SELECTATOMS [SELECTATOMS ...]]]
                        [--stepinterval STEPINTERVAL] [--split SPLIT]
                        [--maxspecies MAXSPECIES]
                        [--matrixa MATRIXA MATRIXA MATRIXA MATRIXA]
                        [--matrixb MATRIXB MATRIXB MATRIXB MATRIXB]
                        [--urls URLS URLS]

ReacNetGenerator 1.4.164

optional arguments:
  -h, --help            show this help message and exit
  -i [INPUTFILENAME [INPUTFILENAME ...]], --inputfilename [INPUTFILENAME [INPUTFILENAME ...]]
                        Input trajectory file, e.g. bonds.reaxc
  -a [ATOMNAME [ATOMNAME ...]], --atomname [ATOMNAME [ATOMNAME ...]]
                        Atomic names in the trajectory, e.g. C H O
  --nohmm               Process trajectory without Hidden Markov Model (HMM)
  --dump                Process the LAMMPS dump file
  --type TYPE, -t TYPE  Input file type
  --nopbc               Disable PBC.
  --cell CELL CELL CELL, -c CELL CELL CELL
                        Cell
  -n NPROC, -np NPROC, --nproc NPROC
                        Number of processes
  -s [SELECTATOMS [SELECTATOMS ...]], --selectatoms [SELECTATOMS [SELECTATOMS ...]]
                        Select atoms in the reaction network, e.g. C
  --stepinterval STEPINTERVAL
                        Step interval
  --split SPLIT         Split number for the time axis
  --maxspecies MAXSPECIES
                        Max number of nodes (species) in the network
  --matrixa MATRIXA MATRIXA MATRIXA MATRIXA
                        Matrix A of HMM parameters
  --matrixb MATRIXB MATRIXB MATRIXB MATRIXB
                        Matrix B of HMM parameters
  --urls URLS URLS      Download files