
===========================================================================================================================
SMSD vs RDKit FindMCS -- Benchmark Results
Date: 2026-03-27 02:19:56
Platform: Darwin x86_64
Python: 3.13.7
RDKit: 2025.09.3
Runs per pair: 5  (best time reported)
Timeout: 10s (RDKit), 10000ms (SMSD)
===========================================================================================================================

 #  Pair                          Category              RDKit ms  R.MCS     SMSD ms  S.MCS  Winner    Speed  Quality       
---------------------------------------------------------------------------------------------------------------------------
 1  methane-ethane                Trivial                  0.021      1         587      1  RDKit   28019.5x  equal         
 2  benzene-toluene               Small aromatic           0.172      6         616      6  RDKit   3582.6x  equal         
 3  benzene-phenol                Heteroatom               0.168      6         628      6  RDKit   3732.3x  equal         
 4  aspirin-acetaminophen         Drug pair                0.251      7         600     10  RDKit   2392.6x  SMSD +3       
 5  caffeine-theophylline         N-methyl diff            0.367     13         661     13  RDKit   1798.4x  equal         
 6  morphine-codeine              Alkaloid                   598     20         632     20  tie         ~1x  equal         
 7  ibuprofen-naproxen            NSAID                      3.8     15         624     15  RDKit    165.4x  equal         
 8  ATP-ADP                       Nucleotide               0.958     27         659     27  RDKit    687.4x  equal         
 9  NAD-NADH                      Cofactor                10437*     33        1353     35  SMSD       7.7x  SMSD +2       
10  atorvastatin-rosuvastatin     Statin                    11.6     15        1199     23  RDKit    103.3x  SMSD +8       
11  paclitaxel-docetaxel          Taxane                  10026*     53        1561     51  SMSD       6.4x  RDKit +2      
12  erythromycin-azithromycin     Macrolide                 7353     50        1320     50  SMSD       5.6x  equal         
13  strychnine-quinine            Alkaloid scaffold          438     21        1204     19  RDKit      2.7x  RDKit +2      
14  vancomycin-self               Self-match large           N/A    ERR         430    ERR  SMSD             both failed   
15  adamantane-self               Symmetric                0.263     10         601     10  RDKit   2287.5x  equal         
16  cubane-self                   Cage                     0.265      8         604      8  RDKit   2278.2x  equal         
17  PEG12-PEG16                   Polymer                    2.2     40        1226     40  RDKit    554.0x  equal         
18  coronene-self                 PAH                      0.739     24         647     24  RDKit    875.9x  equal         
19  guanine-keto-enol             Tautomer                 0.295     10         673     11  RDKit   2283.3x  SMSD +1       
20  rdkit-1585-pair               Known failure           10106*     24        1115     29  SMSD       9.1x  SMSD +5       
---------------------------------------------------------------------------------------------------------------------------

SUMMARY
  Total RDKit time:     38980.0 ms
  Total SMSD  time:     16938.3 ms
  Overall speedup:   2.30x (SMSD vs RDKit)

  Speed wins:   SMSD=5  RDKit=14  tie=1
  MCS quality:  equal=12  SMSD better=5  RDKit better=2

