Monomers Go Missing When Exported

[jvermaas]

I've been playing with LigninGraphs, and I think there is a problem with how the internal representation is converted to SMILES, and the beta-1 linkage seems to be the origin of the problem. Take the example script below:

import os
import numpy as np
import time
import matplotlib.pyplot as plt

import ligning.monomer as mono
import ligning.characterization as ch
import ligning.polymer as poly
import ligning.utils as ut
P0 = mono.Monomer("G")
polymer = poly.Polymer(P0)
polymer.add_specific_linkage('beta-beta', monomer_type = 'S')
polymer.add_specific_linkage('beta-O-4', monomer_type = 'H')
polymer.add_specific_linkage('beta-1', monomer_type = 'G')
polymer.add_specific_linkage('4-O-5', monomer_type = 'G')
polymer.add_specific_linkage('alpha-O-4', monomer_type = 'S')
polymer.add_specific_linkage('5-5', monomer_type = 'H')
polymer.add_specific_linkage('beta-5', monomer_type = 'G')
ut.draw_atomic_graph(polymer.G)
plt.savefig("test2.png")
fout = open("test.smi", "w")
fout.write("Title\n")
fout.write(ut.graph_to_smile(polymer.G)+"\n")
fout.close()
ut.draw_big_graph(polymer.bigG)
plt.savefig("test.png")

I have gotten all kinds of output, but the one I'm most concerned by is the SMILES string. This is the SMILES string I get with this input:

OCCCc1cc(OC)c(OC(CO)Cc2ccc(OC(CCO)c3cc(OC)c(O)c(OC)c3)cc2)c(c2c(O)ccc(C3C(c4c(O3)c(OC)cc(C=CCO)c4)CO)c2)c1

This only has 5 rings, whereas we would expect 8 based on the polymers I added. The png files for the graphs look fine (see attached), but the SMILES is a problem.