info about the new cut rgroup support

CHANGELOG.md

@@ -1,5 +1,31 @@
 # CHANGELOG
 
+## mmpdb (in development)
+
+The `fragment` and `smifrag` commands now support options for
+supervised fragmentation based on a specified set of R-group SMILES to
+use for the fragmentation. Multiple SMILES can be specified on the
+command-line using the `--cut-rgroup` argument, with one SMILES per
+argument, or using the `--cut-rgroup-file` argument with the name of
+an R-group file. The file must be formatted with one R-group SMILES
+per line.
+
+All SMILES strings must contain a single wildcard atom ("*"), which
+indicates the attachment point. The wildcard atom must contain only
+one single bond to the rest of the R-group, and cannot contain charge,
+hydrogens, isotope, or other properties.
+
+The SMILES strings are converted into a SMARTS pattern which matchs
+the SMILES exactly (each atom must have the same valence and hydrogen
+count, and the bond types must match). These SMARTS patterns are then
+merged into a single recusive SMARTS with two terms: the wildcard
+atom, single bonded to a recursive SMARTS term for each of the SMILES
+strings.
+
+The new `rgroup2smarts` command can be used to process the R-group
+SMILES into SMARTS, as a way to examine the conversion process and
+verify that it works.
+
 ## mmpdb 2.2 - 2019-01-11
 
   This minor release contains improvements that help reducing the