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The Benchmark for Structure Generators

While writing my Chemical Graph Generators review article, I classified all the structure generators with respect to their methods. There are also two types of structure generators: open source and commercial ones. In the field of chemical graph generation, MOLGEN is the commercial but the most efficient structure generator regarding the speed and its functionalities. On the other hand, although OMG is the first open source structure generator; the field still needs a faster structure generator. In the article, different structure generators are compared with respect to their speed, mathematical basis and a lot more. This post is for the benchmark carried out for MOLGEN and OMG.

Preliminaries

These generators were tested  20 different molecular formulas. These formulas were randomly selected from MASSBANK and  consist carbons, nitrogens, oxygens, sulfurs and halogens. The benchmarks were run in ARA cluster. The OMG jar file can be downloaded from here.  

MOLGEN vs OMG Benchmark


Molecular Formula
# Structures
OMG (ms)
MOLGEN (ms)
CHNO3P
165
1172 
12
C2H6O3S2
3298
18128 
18
C2H8NO3P
1089
20095 
37
C5H5N
987
1819 
92
P4O6
2292
438517 
101
C7F16
9
48086510 
103
C3H7NO2S
15978
82000 
156
C14H30
1858
1120054 
705
C4H4ClNOS
275462
978103 
945
C6H5Cl2N
70656
293869 
1108
C3HF3N2OS
1209535
33881068 
1153
C5H9NO3
160028
1201234
2491
C8H15NO
296397
36911352 
5190
C4H4ClN3O
2351322
17584015 
8979
C3H4N4O2
4706030
49655270
9533
C3H8NO6P
1658919
54984593 
15578
C5H5N3O
7174282
55204290
26071
C4H5NO4S
13320075
84478894 
29875

In this table, the number of generated structures and the run time (in milliseconds) of OMG and MOLGEN are given. The line chart of the table is built in log scale and given below:



As expected, MOLGEN is faster than OMG structure generator. Also, the duration time linearly grew for MOLGEN; on the other hand, the duration time differed for OMG based on the atom types not the size of molecular formula.

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