packman.molecule.annotations module

The various annotation objects 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.

Citation:

Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics, Bioinformatics Advances, 2022;, vbac007, https://doi.org/10.1093/bioadv/vbac007

Example:

from packman.molecule import Hinge
help( Hinge )

Authors:

• Pranav Khade(https://github.com/Pranavkhade)

class packman.molecule.annotations.Hinge(hid, alpha_value, elements, stats, p)

Bases: object

This class contains the information about the ‘Hinge’ object (packman.molecule.Hinge).

This class contains all the information available about the Hinge. The Hinge class is the not in the hierarchy of the ‘molecule’ API classes. However, it resides in the packman.molecule.Chain object because there are unique hinges per chain. the order of hierarchy of Chain being being: Protein> Model> Chain> Residue> Atom. This class is also the component of the ‘molecule’ module API. Please read the Tutorials and Documentation for more details.

Parameters:

• hid (int) – Unique Hinge ID
• alpha_value (float) – The hinge prediction algorithm parameter (Alpha Value) of the Hinge.
• elements (packman.molecule.Residue) – The elements defining the current hinge (Currently residue objects)
• stats ([float]) – Everything about the statistics (mean/median/mode of B-factors)
• p (float) – p-value obtained from the permutation test (Please read the paper for more details)

get_alpha_value()

Get the hinge prediction algorithm parameter (Alpha Value) of the ‘Hinge’.

Returns:float if successful, None otherwise

get_elements()

Get the elements (Currently residue objects) of the ‘Hinge’

Returns:list of elements (Currently residue objects) if successful, None otherwise.

get_id()

Get the ID of the ‘Hinge’

Returns:int if successful, None otherwise.

get_pvalue()

Get the statistics of the ‘Hinge’

Returns:p-value obtained from the permutation test (Please read the paper for more details) Return type:p-value (float)

get_stats()

Get the statistics of the ‘Hinge’

Returns:Statistics of the Hinge such as mean/median/mode of B-factors if successful, None otherwise.