Unique SMARTS matches against a SMILES string

A number of molecular descriptors are based on how many times a given SMARTS pattern is uniquely found in a structure. For example, the CACTVS substructure key 122 is set if there are ">= 2 any ring size 3". That query can be written in SMARTS as "*1**1", but of course each ring of size 3 will match 6 times because of symmetry.

Most toolkits have have a way to find all matches for a given SMARTS and a way to find all unique matches for a given SMARTS. "Unique" here means that no two different matches will have the same set of matched atoms. The point of this task is to show how that's done.

Implementation

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OpenBabel/Pybel

import pybel
mol = pybel.readstring("smi", "C1CC12C3(C24CC4)CC3")
smarts = pybel.Smarts("*1**1")

# pybel doesn't have a direct way to get the non-unique matches, so
# use the lower-level OpenBabel API directly
smarts.obsmarts.Match(mol.OBMol)
num_matches = sum(1 for indicies in smarts.obsmarts.GetMapList())

num_unique_matches = len(smarts.findall(mol))

print "number of matches:", num_matches
print "number of unique matches:", num_unique_matches

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OpenEye/Python

from openeye.oechem import *

mol = OEGraphMol()
OEParseSmiles(mol, "C1CC12C3(C24CC4)CC3")
pat = OESubSearch("*1**1")

num_matches = sum(1 for match in pat.Match(mol))
num_unique_matches = sum(1 for match in pat.Match(mol, True))

print "number of matches:", num_matches
print "number of unique matches:", num_unique_matches

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RDKit/Python

from rdkit import Chem
mol = Chem.MolFromSmiles('C1CC12C3(C24CC4)CC3')
patt = Chem.MolFromSmarts('*1**1')

print "number of matches:", len(mol.GetSubstructMatches(patt,uniquify=False))
print "number of unique matches:", len(mol.GetSubstructMatches(patt))

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Cactvs/Tcl

set eh [ens create C1CC12C3(C24CC4)CC3]
puts "Number of matches: [match ss -mode all *1**1 $eh]"
puts "Number of atom set unique matches: [match ss -mode distinct *1**1 $eh]"
puts "Number of topologically unique matches: [match ss -mode unique *1**1 $eh]"

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