packman.apps.predict_hinge module

The ‘predict_hinge’ object host file.

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

Example:

from packman.apps import predict_hinge
help( predict_hinge )

Authors:

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

packman.apps.predict_hinge.hinge_cli(args, mol)

Command-line Interface for the ‘hinge’ command. Please check the packman.bin.PACKMAN file for more details.

This function is for the CLI and not an integral function for the API.

Parameters:

• args (parser.parse_args()) – The arguments that were passed by the user to the PACKMAN-hinge app.
• mol (packman.molecule.Protein) – The ‘Protein’ object for the anaylsis.

packman.apps.predict_hinge.predict_hinge(atoms, outputfile, Alpha=inf, method='alpha_shape', filename='Output.pdb', MinimumHingeLength=5, nclusters=4)

This function is used to carry out hinge prediction given the parameters.

Notes

• The packman.bin.PACKMAN uses this function
• Ideally, the alpha values should be scanned from 0 to 10 to obtain conclusively repetative hinges (Use ‘’ for this purpose)

• Please refer to the following paper for the details on the algorithm and citation:

  Pranav M. Khade, Ambuj Kumar, Robert L. Jernigan, Characterizing and Predicting Protein Hinges for Mechanistic Insight, Journal of Molecular Biology, Volume 432, Issue 2, 2020, Pages 508-522, ISSN 0022-2836, https://doi.org/10.1016/j.jmb.2019.11.018. (http://www.sciencedirect.com/science/article/pii/S0022283619306837)

• Tutorial Link: https://py-packman.readthedocs.io/en/latest/tutorials/hinge_predict.html#tutorials-predict-hinge
• The predicted hinges are stored in packman.molecule.Chain object as an packman.molecule.Hinge object.

Parameters:

• atoms ([packman.molecule.Atom]) – PACKMAN uses backbone atoms of the protein. However, any number and type of atoms can be used (Alpha value range will change)
• outputfile (file) – Output File.
• Alpha (float, optional) – Please refer to the paper for this parameter. Defaults to float(‘Inf’).
• method (str, optional) – Please refer to the paper for this parameter. Defaults to ‘alpha_shape’.
• filename (str, optional) – Please refer to the paper for this parameter. Defaults to ‘Output.pdb’.
• MinimumHingeLength (int, optional) – Please refer to the paper for this parameter. Defaults to 5.
• nclusters (int, optional) – Please refer to the paper for this parameter. Defaults to 4.

Returns:

The Alpha Shape (Subset of Delaunay Tesselations)

Return type:

alpha_shape