afrc

afrc is a Python package that implements an analytical version of the Flory Random Coil (i.e. the AFRC) for polypeptides.

This analytical solution is based on the rotational isomeric state approximation of Flory and Volkenstein and parameterized using numerical simulations of residue-specific Flory Random Coil. It provides an interface into sequence-specific polymeric properties (i.e. intra-molecular distances) expected for a given sequence and behaves like a polymer in a true theta solvent. In this way it provides a convenient reference state though which real simulations or experiments can be normalized against.

Installation

To install afrc:

pip install afrc 

Quickstart

There is a single user-facing object that is built from the afrc package which is the AnalyticalFRC object. This object gives access to a bunch of additional object functions. As an example

from afrc import AnalyticalFRC

A = AnalyticalFRC('APPAPAPAPPAPAPAPPAPPAPPAPAPPA')

# prints the expected radius of gyration if the associated sequence 
# behaved like a bona fide Flory Random Coil
print(A.get_mean_radius_of_gyration())  

# prints the expected end-to-end distance if the associated sequence 
# behaved like a bona fide Flory Random Coil
print(A.get_mean_end_to_end_distance())

Documentation

For full documentation, see here

Help

If you find a bug or have any feature requests please submit an issue here on GitHub. Also feel free to shoot Alex an email

License

The afrc package is distributed by the Holehouse Lab under the GNU LESSER GENERAL PUBLIC LICENSE.