Skip to main content

Table 4 Number of chemical structures generated by OMG and MOLGEN using as input an elemental composition and one or more prescribed and non-overlapping fragments

From: OMG: Open Molecule Generator

Structure Name HMDB ID elemental composition Prescribed substructure(s) MOLGEN OMG
# Candidate structures Time (s) Time per molecule (ms) # Candidate structures Time (s) Time per molecule (ms)
Glycine 6 0.167 27.833 6 0.539 89.833
HMDB00123
C2H5NO2
D-Cysteine 100 0.193 1.930 210 3.177 15.129
HMDB03417
C3H7NO2S
Phenylalanine 76,247 52.774 0.692 107,155 19386.019 180.916
  HMDB00159        
  C9H11NO2        
   * not possible * not possible * not possible 595 271.809 456.822
   * not possible * not possible * not possible 289 172.655 597.422
   * not possible * not possible * not possible 26 25.147 967.192
Cholic acid ** not possible ** not possible * not possible 334 120.519 360.835
  HMDB00619        
  C24H40O5        
   * not possible * not possible * not possible 2,505 119.418 47.672
Malic acid 1,436 0.229 0.159 1,436 4.688 3.265
  HMDB00156        
  C4H6O5        
Uric acid 150,114 962.016 6.409 6,069,863 155828.437 25.672
  HMDB00289        
  C5H4N4O3        
Phenyllactic acid 21,040 15.674 0.745 26,164 163.904 6.264
  HMDB00779        
  C9H10O3        
   * not possible * not possible * not possible 525 3.973 7.568
p-Cresol sulfate S_6 13,177 65.667 4.983 13,177 63.047 4.785
  HMDB11635        
  C7H8O4S        
  S_6 70,330 94.898 1.349 17,232 1204.357 69.891
  1. *MOLGEN can only accept one prescribed substructure, while OMG accepts multiple substructures, provided that these do not overlap, this is, they do not share any atom.
  2. **MOLGEN is not able to generate molecules using this large substructure as input. The reason could not be found.