packman.entropy.entropy module

The Entropy method(s) host file.

This is file information, not the class information. This information is only for the API developers. Please read the corrosponding object documentation for details.

Example:

Authors:
class packman.entropy.entropy.PackingEntropy(atoms, chains=None, probe_size=1.4, onspherepoints=30)

Bases: object

This class contains all the methods required to obtain a protein complex’s entropy. Given a group of atoms in the :mod:’packman.molecule.Atom’ objects, the entropy for the each amino acid will be returned. The ‘chains’ argument should be used when the user wants to restrict the analysis to a chain or group of chains rather than the whole structure. :param atoms: The group of atoms user wisher to calculate Packing Entropy with. :type atoms: [packman.molecule.Atom] :param chains: Chain IDs for the Entropy calculation (None means all the chains are included; single string means only one chain ID; multiple chains should be an array of strings). :type chains: [str]/str :param probe_size: Radius of the probe to generate the surface points (This value should not be less than 1;Read the Publication for more details) :type probe_size: float :param onspherepoints: Number of points to be generated around each point for the surface (Read the Publication for more details) :type onspherepoints: int

calculate_entropy()

Calculate the Packing Entropy with the current setup.

calculate_spherepoints(atom)

Given a single point, this function generates point cloud around the given points. :param atom: Atom object around which the sphere of point cloud to be generated. :type atom: [packman.molecule.Atom]

calculate_surafacepoints()

Calculate the surface points with the current setup.

get_surafacepoints()

Get the surface points around the given set of atoms in the protein. :returns: Array of 3D points around the given set of atoms in the protein. :rtype: [[float]]

get_total_chain_entropy(chain)

The sum of Packing Entropies for the Residues in the provided atoms and chain.

Please note that the entropy for the chain you are selecting might not exist if you have not calculated it properly. Please make sure to run calculate_entropy() function properly. :param chain: chain ID of for the chain you wish to get the entropy. :type chain: str

get_total_entropy()

The sum of Packing Entropies for the Residues in the provided atoms. :returns: The sum of Residue Entropies (float)

get_total_packing_fraction()

The sum of Packing Fraction for the Residues in the provided atoms.

Returns:The sum of the Residue Packing Fraction (float)