Can I standardize my molecules before loading them into ClassPharmer?
Yes, by using the Standardize Molecules option on the Batch menu. The default operations are (a) remove all molecule connected components (fragments) except the largest one; (b) convert certain functional groups (such as nitros and azides) to a conventional representation; and (c) neutralize acidic and basic groups. The dialog box also allows you to modify these rules or customize your own.
