search

openphacts / GLOBAL

Global project issues [private for now. owner lee harland]
3 stars 0 forks source link

Methyl group removed to get uncharged molecule? #109

Open danidi opened 10 years ago

danidi commented 10 years ago

Why is http://ops.rsc.org/Compounds/Get/56927 a charge unsensitive parent of http://ops.rsc.org/Compounds/Get/56926? As OPS56926 has a quarternary Nitrogen, it needs the removal of a methyl group to get the uncharged molecule. Should this really happen?

Christian-B commented 10 years ago

This comes from Chebi via http://openphacts.cs.man.ac.uk/ims/originals/RSC_2013-11-11/CHEBI/LINKSET_CLOSE_PARENT_CHILD_CHARGE_UNSENSITIVE_PARENT_CHEBI20131111.ttl

danidi commented 10 years ago

Yes, I think thats more a question whether this specific link should be generated by the chemistry registry at the first place.

karapetk commented 10 years ago

Dealing with such cases is tricky. For simple cases where quarternary nitrogen has a proton,Me, or Et the substituent will be removed in same order to neutralize the compound to get charge unsensitive parent.

About the value of this for the users.. Wouldn't it be beneficial for users to get other flavors of quarternary nitrogen when they provide a quarternary query molecule?

@valt @ChemConnector

danidi commented 10 years ago

Removing protons is fine to generate an uncharged molecule, but I don't think removing a Me or Et would be beneficial for the user, rather confusing as this is then a completely different molecule! I would say in this case there is simply no possibility to generate a charge insensitive parent. But maybe this would be something for the Chemistry Working Group to decide?