Welcome to `pywindow`’s documentation!¶

GitHub:

https://github.com/JelfsMaterialsGroup/pywindow - stable release

https://github.com/marcinmiklitz/pywindow - most up-to-date release

Overview¶

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

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

Installation¶

Git clone the pywindow repository or download a zipped version.

cd pywindow/

python setup.py install

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)

Welcome to pywindow’s documentation!¶