pycav install

PyCav is a Python package that allows users to easily perform cavity calculations on molecular structures. In order to use PyCav, you must first install the package using pip.

Installation

To install PyCav, simply enter the following command in your terminal:

pip install pycav

If you are using a virtual environment, make sure that it is activated before installing PyCav.

Requirements

PyCav requires the following dependencies:

• NumPy
• SciPy
• matplotlib
• ASE

These dependencies will be automatically installed when you install PyCav using pip.

Basic usage

Once you have installed PyCav, you can import the package in your Python scripts using the following line of code:

import pycav

You can then use the pycav.Cavity class to calculate the cavity of a molecule:

from ase import Atoms
import pycav

# Define a molecule
molecule = Atoms('H2O', positions=[[0,0,0],[0,0,1],[0,1,0]])

# Calculate the cavity
cavity = pycav.Cavity(molecule)

This will calculate the cavity of a water molecule and store the result in the cavity variable. You can then access the cavity properties using the following attributes:

• cavity.volume: the volume of the cavity in ų
• cavity.surface: the surface area of the cavity in Ų
• cavity.radius: the radius of the sphere that has the same volume as the cavity in Å

Advanced usage

PyCav also supports more advanced features, such as multiple cavity calculations and custom probe radii. You can find more information on these features in the PyCav documentation.

Conclusion

PyCav is a powerful Python package that allows users to easily perform cavity calculations on molecular structures. With its simple installation and easy-to-use interface, PyCav is a must-have tool for any computational chemist.