Install

cgbind is built in Python 3 and has been tested with v. 3.7. An anaconda or miniconda installation is highly recommended to easily install the dependencies.

Note

The autode package is an optional dependency to perform semi-emprical, DFT and ab initio calculations.

pip

If the requirements (autode, rdkit, numpy, scipy, networkx, Cython) are already available cgbind can be install with pip:

$ pip install cgbind

Mac OSX / Linux

To install cgbind inside a conda environment first clone the repository and cd there:

$ git clone https://github.com/duartegroup/cgbind.git
$ cd cgbind

then install the appropriate dependencies (you may want to create a new virtual environment) and install:

$ conda install --file requirements.txt -c conda-forge
$ python setup.py install

The whole process including installing miniconda is shown here.

Windows

On Windows without a git installation cgbind can be installed with anaconda by, on the GitHub page using Clone or download → Download ZIP then extracting it. Then, open an anaconda command prompt and cd to the directory and proceed as above e.g.:

$ cd Downloads/cgbind-master/
$ conda config --append channels conda-forge
$ conda install --file requirements.txt
$ python setup.py install

The above commands assume you have extracted the zip to C:\Users\yourusername\Downloads.

Note

By default Windows doesn’t have a C++ compiler required to build the extension to generate electrostatic potentials, as such this feature is not enabled by default. If a C++ compiler is available install with python setup.py install --esp_gen to build the ESP extension.

Common Problems

Conda is not found:

$ conda config --append channels conda-forge
conda command not found

First, make sure either miniconda or anaconda installed then ensure you’ve closed and reopened your terminal after installation.

A required module is not found (setuptools, rdkit, Cython):

$ python setup.py install
Traceback (most recent call last):
  File "setup.py", line 2, in <module>
    from Cython.Build import cythonize
ImportError: No module named Cython.Build

Check that you’ve run conda install --file requirements.txt and that you’re using the conda version of python (i.e. running which python returns /some/path/(ana/mini)conda/bin/python). If which python returns /usr/bin/python or another non-conda version of python then you may need to activate the base conda environment with conda activate base.