05_random_linkages¶

Random structure generation

Install the package from pip (skip this step if the package is already installed)

[ ]:

! pip install ligning

[1]:

# set ligning path (optional if installed via pip)
import sys, os
project_path = os.path.abspath(os.path.join(os.getcwd(), '..\..\..'))
print(project_path)
sys.path.insert(0, project_path)

import numpy as np
import time

import ligning.monomer as mono
import ligning.polymer as poly
import ligning.utils as ut

c:\Users\yifan\Documents\GitHub\LigninGraphs

RDKit WARNING: [17:54:19] Enabling RDKit 2019.09.3 jupyter extensions

[2]:

# Set the random seed
np.random.seed(1)

# Starting from a random monomer
P0 = mono.Monomer('S')
polymer = poly.Polymer(P0)

start = time.time()

# Set the number of polymerization iteration
n_iter = 12

# list for graphs
P_Gs = []

# list for mols
P_mols = []

# Polymerization loop
for i in range(n_iter):
    polymer.add_random_monomer()
    Px = polymer.G.copy()
    P_Gs.append(Px)
    Px_mol = ut.graph_to_mol(Px)
    P_mols.append(Px_mol)

end = time.time()

n_monomer = n_iter + 2
run_time = end - start

print("Lignin polymerization: %2d monomers takes %5.5f s" %(n_monomer, run_time))

Connect a S to a H unit (in polymer) via a 4-O-5 bond
Connect a S to a G unit (in polymer) via a alpha-O-4 bond
Connect a S to a H unit (in polymer) via a beta-1 bond
Connect a H to a G unit (in polymer) via a 4-O-5 bond
Connect a G to a S unit (in polymer) via a beta-1 bond
Connect a H to a H unit (in polymer) via a beta-5 bond
Connect a G to a S unit (in polymer) via a alpha-O-4 bond
Connect a G to a S unit (in polymer) via a 4-O-5 bond
Connect a S to a H unit (in polymer) via a beta-5 bond
Connect a H to a G unit (in polymer) via a beta-1 bond
Connect a H to a S unit (in polymer) via a beta-1 bond
Connect a H to a G unit (in polymer) via a alpha-O-4 bond
Lignin polymerization: 14 monomers takes 0.18176 s