Computing Graph Edit Distance between two molecules using RDKit and Networkx

During a Twitter discussion Noel O'Boyle introduced me to Graph Edit Distance (GDE) as a useful measure of molecular similarity. The advantages over other approaches such as Tanimoto similarity is discussed in these slides by Roger Sayle.

It turns out Networkx can compute this, so it's relatively easy to interface with RDKit and the implementation is shown below.

Unfortunately, the time required for computing GDE increases exponentially with molecule size, so this implementation is not really of practical use.

Sayle's slides discusses one solution to this, but it's far from trivial to implement. If you know of other open source implementations, please let me know.

Update: GitHub page

	'''
	Written by Jan H. Jensen, 2020
	'''
	from rdkit import Chem
	import networkx as nx
	def get_graph(mol):
	Chem.Kekulize(mol)
	atoms = [atom.GetAtomicNum() for atom in mol.GetAtoms()]
	am = Chem.GetAdjacencyMatrix(mol,useBO=True)
	for i,atom in enumerate(atoms):
	am[i,i] = atom
	G = nx.from_numpy_matrix(am)
	return G
	mol1 = Chem.MolFromSmiles('c1ccccc1')
	#mol2 = Chem.MolFromSmiles('c1cnccc1')
	mol2 = Chem.MolFromSmiles('C=CC=CC=C')
	G1 = get_graph(mol1)
	G2 = get_graph(mol2)
	GDE = nx.graph_edit_distance(G1, G2, edge_match=lambda a,b: a['weight'] == b['weight'])
	print(GDE)

view raw graph_edit_distance.py hosted with ❤ by GitHub

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Open access chemistry publishing options in 2020

Here is an updated list of affordable impact neutral and other select OA publishing options for chemistry

Impact neutral journals
$0 (in 2020) PeerJ chemistry journals. Open peer review. (Disclaimer I am an editor for PeerJ Physical Chemistry)

$638 (normally $850) Results in Chemistry. Closed peer review

$1000 F1000Research. Open peer review. Bio-related

$1095 PeerJ - Life and Environment. Open peer review. Bio-related. PeerJ also has a membership model, which may be cheaper than the APC.

$1250 ACS Omega. Closed peer review. WARNING: not real OA. You still sign away your copyright to the ACS.

$1260. Royal Society Open Science.  Open peer review. 

(The RSC manages "the journal’s chemistry section by commissioning articles and overseeing the peer-review process")

$1350 Cogent Chemistry. Has a "pay what you can" policy. Closed peer review.

$1595 PLoS ONE. Closed peer review.

$1790 Scientific Reports. Closed peer review

Free or reasonably priced journals that judge perceived impact

$0 Chemical Science Closed peer review

$0 CSS Chemistry Closed peer review

$0 Beilstein Journal of Organic Chemistry. Closed peer review.

$0 Beilstein Journal of Nanotechnology. Closed peer review.

$0 ACS Central Science. Closed peer review. ($500-1000 for CC-BY, WARNING: not real OA. You still sign away your copyright to the ACS as far as I know) 

$100 Living Journal of Computational Molecular Science. Closed peer review

€500 Chemistry². Closed peer review.

£750 RSC Advances. Closed peer review.


Let me know if I have missed anything.




This work is licensed under a Creative Commons Attribution 4.0