Path Length
The first pair illustrates that features which only differ beyond the maximum path length in the fingerprint (default: 7) don't affect the generated fingerprint. This can be addressed by changing the maximum length at the expense of CPU time and much higher fingerprint density.
$ fingerprint -s 0/7 $SMI<CC(=O)OCCCCCCCC> FP<50dxACUP.7FZY.IE1w6MK...1;2048;51;128;46;1> | $ fingerprint -s 0/11 $SMI<CC(=O)OCCCCCCCC> FP<50fxACUv.NNZa.IE1wMML...1;2048;59;128;53;1> |
$ fingerprint -s 0/7 $SMI<CC(=O)OCCCCCCCC> FP<50dxACUP.7FZY.IE1w6MK...1;2048;51;128;46;1> | $ fingerprint -s 0/11 $SMI<CC(=O)OCCCCCCCC> FP<50fxACcv.NRZa.IEXwMMT...1;2048;67;128;57;1> |
Repeating Structural Units
$ fingerprint $SMI<Cl.Clc1ccncc1> FP<IDk1Bq.07sB+S6P5Z4kXCE..1;2048;60;128;53;1> |
$ fingerprint $SMI<Clc1ccncc1> FP<IDk1Bq.07sB+S6P5Z4kXCE..1;2048;60;128;53;1> |