I'm not sure if this is a good candidate for the cookbook. As Ivan said, it's a pretty dangerous function (exponentially complex) to run on molecules of arbitrary size/complexity. You may want a path-based approach with a cutoff for ring-size. (e.g. using https://networkx.github.io/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path )
*dan nealschneider* | lead developer [image: Schrodinger Logo] <https://www.schrodinger.com/> On Tue, Mar 17, 2020 at 6:50 AM Scalfani, Vincent <vfscalf...@ua.edu> wrote: > Hello Ivan and all, > > > I found this old thread about counting rings in bicyclics and I would like > to add it to the RDKit Cookbook, however, I'm not able to get the fuse > function to work. I get a 'Mol object is not iterable' error. > > > Any help appreciated. Thanks. > > > Vin > > > ------------------------------ > *From:* Ivan Tubert-Brohman <ivan.tubert-broh...@schrodinger.com> > *Sent:* Wednesday, December 5, 2018 9:06 AM > *To:* baptiste.cana...@gmail.com > *Cc:* RDKit Discuss > *Subject:* Re: [Rdkit-discuss] Count rings in bicyclic compounds > > Hi Baptiste, > > RDKit focuses on "simple rings". As far as I know, it has no builtin > function to return all possible cycles in a molecule. > > For a molecule with a "basis set" of N rings, there can be up to 2^N-1 > ring systems, which can be obtained by taking all possible subsets (aka the > powerset) of rings and fusing them. Below is an implementation based on > fusing simple rings. Another possibility would be to write an exhaustive > ring search (DFS or BFS) of the molecular graph and report all cycles that > are found, instead of only the simple ones. > > *Warning*: do not run this code on fullerenes or similar molecules unless > you are prepared to wait for a long, long time! > > def all_bond_rings(mol): > """ > Generate all ring systems for a molecule. A Ring is a set of bond > indexes. > > :type mol: rdkit.Chem.Mol > :rtype: set of int > """ > ring_info = mol.GetRingInfo() > rings = [set(r) for r in ring_info.BondRings()] > > # Truncate nrings to the basis set size because RDKit returns redundant > # rings (e.g., 6 instead of 5 for cubane). > nfrags = len(Chem.GetMolFrags(mol)) > nrings = mol.GetNumBonds() - mol.GetNumAtoms() + nfrags > del rings[nrings:] > > for i in range(1, len(rings)+1): > for comb in itertools.combinations(rings, i): > fused = fuse(comb) > if fused: > yield fused > > def fuse(rings): > """ > Return the ring system that results from fusing the given rings, if the > rings are fusable into a single ring system; otherwise None. > > :type rings: list of set of int > :rtype: set of in > """ > pending = list(rings) > fused = set(pending.pop()) > while pending: > for i in range(len(pending)): > ring = pending[i] > if fused & ring: # rings are fused > fused ^= ring > del pending[i] > break > else: > # None of the pending rings were fusable! > return None > return fused > > Hope this helps, > Ivan > > > > On Wed, Dec 5, 2018 at 5:54 AM Baptiste CANAULT < > baptiste.cana...@gmail.com> wrote: > >> Hi RDKiters, >> >> I would like to identify all cycles present in a molecular >> structure. However, when the molecules correspond to bicyclic compounds, >> the ring count does not correspond to the number actually observed in the >> structure. Simple example: >> >> >>> m = Chem.MolFromSmiles('C1CC2CCC1O2') >> >>> r = m.GetRingInfo() >> >>> r.NumRings() >> 2 >> >> In reality, this molecular structure has 3 cycles with the cyclohexan. Am >> I completely wrong and is there a trick to identify all the cycles present >> in a structure? >> >> Thanks in advance, >> >> Best regards, >> >> Baptiste >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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