packman.molecule.molecule module

The ‘Molecule’ object host file.

This is file information, not the class information. This information is only for the API developers. Please read the ‘Model’ 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 Model
help( Model )
Authors:
packman.molecule.molecule.download_structure(pdbid, save_name=None, ftype='cif')

This class helps user to download the 3D structure of the protein and save it on a disk.

Example:

from packman import molecule
molecule.download_structure('1prw')
Parameters:
  • pdbid (str) – A Unique 4 Letter PDB ID (eg.. 1PRW)
  • save_name (str) – Save name of the downloaded file (extension will be added automatically depending on the ftype argument).
  • ftype (str) – Format name (‘.cif’ or ‘.pdb’)
packman.molecule.molecule.load_cif(filename)

Load the CIF (.cif) file into the ‘Protein’ Object.

Links::
  1. https://www.rcsb.org/docs/general-help/identifiers-in-pdb
packman.molecule.molecule.load_pdb(filename)

Load the PDB (.pdb) file into the ‘Protein’ Object.

packman.molecule.molecule.load_structure(filename, ftype='cif')

Load a Molecule from a file.

This class helps user to load the 3D structure of the protein onto a packman.molecule.Protein object.

Example:

from packman import molecule
molecule.download_structure('1prw')
molecule.load_structure('1prw.cif')
Parameters:
  • filename (str) – Name of the input file
  • ftype (str) – Format name (‘cif’ or ‘pdb’); Default: cif
Returns:

Protein object containing all the information about the Protein
Return type:

packman.molecule.Protein