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 >
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