packman.molecule package

The ‘packman.molecule’ module is used to read, write, manipulate and analyze the molecule.

This module is the base of the tool packman. It is used as a base module for all the packman utilities such as HingePrediction, Compliance and Right Domain ANM. The molecule module can also be an API to utilize the objects such as Atom, Residue, Chain, Model and Protein. Please read the documentation and tutorials for more 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

Notes

• Tutorial link: https://py-packman.readthedocs.io/en/latest/tutorials/molecule.html#tutorials-molecule

Example

To Load the molecule::

from packman import molecule molecule.download_structure(‘1prw’,’1prw.pdb’) mol = molecule.load_structure(‘1prw.pdb’)

Submodules

• packman.molecule.annotations module
• packman.molecule.atom module
• packman.molecule.bond module
• packman.molecule.chain module
• packman.molecule.hetmol module
• packman.molecule.model module
• packman.molecule.molecule module
• packman.molecule.protein module
• packman.molecule.residue module