Strange metabolizer output when used as command line tool

User 25aae95547

14-01-2015 08:51:01

Dear all,

i am using the metabolizer command line tool within KNIME to predict transformation products (TPs) for several hundred input molecules over night. However, this morning i realized that an error occured during the execution, because one of the generated output files containing the smiles of the TPs differed from the usual structure.

#SMILES	name	Synthesis Code	Generation	Phase	Formation	Degradation	Production	Accumulation	Route	Exact Mass
OC1CC2=CC(OCCCCC3=NN=NN3C3CCCCC3)=CC=C2NC1=O		1	0	0	0	63270	100.00%	< 0.001%		385.2113897
O=C1NC2=CC=C(OCCCCC3=NN=NN3C3CCCCC3)C=C2C=C1		Dehydration(1):1	1	0	16807	190121	26.56%	< 0.001%	Dehydration	367.2008251
O=C1CCCCC1		Aromatic N-Dealkylation(1):1/2	1	0	2401	134458	3.80%	< 0.001%	Aromatic N-Dealkylation	98.07316494
OC(CCCOC1=CC=C2NC(=O)C(O)CC2=C1)C1=NN=NN1C1CCCCC1		BenzylicHydroxylation(1):1	1	0	2401	176508	3.80%	< 0.001%	$BenzylicHydroxylation	401.2063044	TRUE
OC1C(O)C2=CC(OCCCCC3=NN=NN3C3CCCCC3)=CC=C2NC1=O		BenzylicHydroxylation(1):2	1	0	2401	293472	3.80%	< 0.001%	$BenzylicHydroxylation	401.2063044	TRUE
O=C1CC2=CC(OCCCCC3=NN=NN3C3CCCCC3)=CC=C2NC1=O		SecondaryAlcoholOxidation(1):1	1	0	2401	173414	3.80%	< 0.001%	SecondaryAlcoholOxidation	383.1957397

As you can see the 4th and 5th prediction contain an additional column without header at the end which contains TRUE as value. Furthermore the transformation route is given as $BenzylicHydroxylation, while benzylic hydroxylations of other input molecules did not contain the additional $-sign in the route description and also not the additional column. Unfortunately, this is messing up my workflow as i cannot define a fixed number of input cells when using the R command read.table to read in the generated output files. I think i could come up with a work-around but i would prefer to understand why this happens for certain molecules and not for all and what the TRUE value in the last column actually represents.

You should be able to reproduce the output when typing this command into the command line: metabolize OC1CC2=CC(OCCCCC3=NN=NN3C3CCCCC3)=CC=C2NC1=O and in case it matters i have the version 15.1.5 of Metabolizer installed on my computer.

Best regards,

ChemAxon d76e6e95eb

15-01-2015 13:59:58

Regarding the dollar sign in front of a transformation name:
Some molecules have multiple sites for a certain transformation type, such as benzylic hydroxylation. In this case, some of the sites may be preferred to others. This is indicated by the dollar sign. So in your case, the transformations marked with the $ sign are unpreferred sites, the benzylic hydroxlation is more likely on another position.

The trailing true is a printout issue, please ignore it.