Introduction¶

GitHub: https://www.github.com/marcinmiklitz/pywindow

Overview¶

pywindow is a Python 3 library for the structural analysis of molecular pores.

For quick start head to Module Index and see pywindow.MolecularSystem.

Installation¶

pywindow can be installed with pip:

pip install pywindowx

Developer Setup¶

To develop with pywindow, you can clone the repo and use just and uv to setup the dev environment:

just setup

Examples¶

For the specific examples of pywindow usage see Examples/ directory in the pywindow Github repository.

Loading input¶

Using file as an input:

import pywindow as pw

molsys = pw.MolecularSystem.load_file("data/input/PUDXES.xyz")

Using RDKit molecule object as an input:

import pywindow as pw
from rdkit import Chem

rdkit_mol = Chem.MolFromMol2File("data/input/PUDXES.mol2")

molsys = pw.MolecularSystem.load_rdkit_mol(rdkit_mol)

Using a dictionary (or another MoleculeSystem.system) as input:

import pywindow as pw

molsys = pw.MolecularSystem.load_file("data/input/PUDXES.xyz")

molsys2 = pw.MolecularSystem.load_system(molsys.system)

Pre-processing¶

If our input requires pre-processing (rebuilding molecules through periodic boundary and/or force field atom ids deciphering) the following methods allow that:

Rebuilding a periodic system

rebuild_molsys = molsys.rebuild_system()

Deciphering force field atom ids

molsys.decipher_atom_keys('OPLS')

If the force field is not supported by pywindow we can use pywindow.MolecularSystem.decipher_atom_keys() to generate a custom force field deciphering tool.

some_forcefield = {
    'ca': 'C',
    'ni': 'N',
    'hc': 'H',
    'ha': 'H'
}

molsys.swap_atom_keys(some_forcefield)